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(Wikimedia Commons)\" width=\"800\" height=\"532\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We can now begin to piece back together the DNA of individuals from the past using the DNA of their modern relatives. (\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Denslow's_Humpty_Dumpty_pg_5.jpg\">Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Have you ever wondered about one of your relatives from long ago? Maybe he was famous or you want to know where your family’s blue eyes came from or you’re just plain curious.\u003c/p>\n\u003cp>Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.\u003c/p>\n\u003cp>This is exactly what the good folks at the San Francisco-based company AncestryDNA \u003ca href=\"http://www.foxnews.com/science/2014/12/16/ancestrydna-reconstructs-partial-genome-1th-century-father/\">just did with David Speegle\u003c/a>, a man born sometime around 1806. They were able to use the DNA of Speegle’s living descendants to piece together around 12% of the length of his genome. From this work, they were able to figure out that either he or one of his two wives probably had blue eyes and had the genes for early baldness.\u003c/p>\n\u003cp>This is just a start. As we learn more about human DNA, we will be able to learn a whole lot more about this long dead man from his recreated genome.\u003c/p>\n\u003cp>And now that AncestryDNA has worked out how to do this, they may be able to apply it to other deceased individuals as well. We may soon have a whole new way to learn about our past.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cstrong>A Little Bit of Luck\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_26093\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26093\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\" alt=\"This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black-and-white photo. (restorationmovement.com)\" width=\"200\" height=\"374\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black and white photo. (\u003ca href=\"http://www.therestorationmovement.com/alabama/speegle.htm\">restorationmovement.com\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Most everyone knows that they get half their DNA from their mom and half from their dad. What they might not have thought about is what happens to their DNA if they have just one child. Basically, at its simplest, half their DNA is lost forever!\u003c/p>\n\u003cp>Now of course it isn’t as simple as that. If you have brothers or sisters, they share right around half of their DNA with you and so their kids will share some of your DNA too. And if your parents had brothers and sisters they will share some of your DNA too. And so on.\u003c/p>\n\u003cp>Still, it becomes very tricky to track down DNA from people with few descendants. Which is why David Speegle made such an ideal test case.\u003c/p>\n\u003cp>He had 26(!) kids with two different wives and over 150 grandkids. His full set of DNA was pretty much passed on to the next generation multiple times.\u003c/p>\n\u003cp>This is where the luck comes in. For now, if you wanted something similar done for one of your relatives, you’d need to focus on someone that had lots of kids. That long-lost relative with two kids and four grandkids will probably remain a mystery for the foreseeable future.\u003c/p>\n\u003cp>So the first step is picking a relative with lots of kids and grandkids. But this is by no means the whole story. You also need to know the DNA of lots of your relatives and have lots of accurate, overlapping family trees.\u003c/p>\n\u003cp>\u003cstrong>A Lot of Science and Genealogy\u003c/strong>\u003c/p>\n\u003cp>David Speegle, his kids and his grandkids have all been dead for a very long time. What this means is that anyone alive today has, at most, tiny splinters of his DNA in theirs. These wisps of DNA need to be recognized and then combined to recreate David Speegle’s DNA.\u003c/p>\n\u003cfigure id=\"attachment_26095\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26095\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\" alt=\"We are getting closer to being able to recreate the genomes of long dead people. (Flickr)\" width=\"250\" height=\"375\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We are getting closer to being able to recreate the genomes of long dead people. (\u003ca href=\"https://www.flickr.com/photos/greyloch/9121238998/\">Flickr\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Remember, you can’t compare the DNA of a relative with David’s DNA. His DNA is not available.\u003c/p>\n\u003cp>So, basically you are looking at as many of the people as you can at the bottom level of an enormous family tree that starts with David and his two wives. Fortunately, AncestryDNA has a good number of David Speegle’s descendants in the over 500,000 genomes in their database.\u003c/p>\n\u003cp>The researchers at AncestryDNA compared the DNA of all of the pairs of people for whom Speegle was the most recent common ancestor, one pair at a time, and looked for common DNA. They found a whole lot of it.\u003c/p>\n\u003cp>The next step was to find the DNA that is actually David’s and not some other shared relative’s DNA. This is trickier than it sounds because DNA doesn’t get passed down in predictable chunks from generation to generation. It gets all mixed, matched, and diluted in each generation.\u003c/p>\n\u003cp>This is where those family trees come in handy. You can subtract out DNA that is shared because of other relatives.\u003c/p>\n\u003cp>In fact, this is where the David’s two wives really helped. They made it easier to separate out the DNA that came from these two women compared to the DNA that came from David.\u003c/p>\n\u003cp>\u003cstrong>Not Just a Parlor Trick\u003c/strong>\u003c/p>\n\u003cp>Recreating David’s genome is more than just some heroic academic exercise. It also points to what we can learn about ourselves from testing the DNA of many relatives.\u003c/p>\n\u003cp>For example, people are using their DNA to trace their family’s ancestry. In fact, whole companies (including AncestryDNA) are based on just that premise.\u003c/p>\n\u003cp>Unfortunately, you can lose a lot of information if you test only yourself. Remember, you have only half of your mom and dad’s DNA. What this means is that you may miss more distant ancestry information.\u003c/p>\n\u003cp>Imagine that you had an Asian ancestor 5 or 6 generations back. This might mean that your parent has less than 5% of that Asian ancestor’s DNA in his or her DNA. If you happened to not inherit that part of your parent’s DNA, then the history of your Asian ancestry would be lost. (Click \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist/uneven-passing-dna\">here \u003c/a>for more information on these scenarios.)\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>One way to recover that information would be through something similar to what was done here for David Speegle. By comparing the DNA of lots of relatives you might be able to piece together that lost Asian history and learn a bit about yourself or confirm a family story.\u003c/p>\n\n","blocks":[],"excerpt":"Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.","status":"publish","parent":0,"modified":1704932415,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":28,"wordCount":1073},"headData":{"title":"Scientists Used Modern DNA to Reconstruct Part of a 19th-Century Man’s Genome | KQED","description":"Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Scientists Used Modern DNA to Reconstruct Part of a 19th-Century Man’s Genome","datePublished":"2015-01-12T14:00:49.000Z","dateModified":"2024-01-11T00:20:15.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"sticky":false,"path":"/science/26088/scientists-use-modern-dna-to-reconstruct-part-of-a-19th-century-mans-genome","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_26091\" class=\"wp-caption aligncenter\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/HumptyDumpty.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26091\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/HumptyDumpty.jpg\" alt=\"We can now begin to piece back together the DNA of long dead people using the DNA of their modern relatives. (Wikimedia Commons)\" width=\"800\" height=\"532\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We can now begin to piece back together the DNA of individuals from the past using the DNA of their modern relatives. (\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Denslow's_Humpty_Dumpty_pg_5.jpg\">Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Have you ever wondered about one of your relatives from long ago? Maybe he was famous or you want to know where your family’s blue eyes came from or you’re just plain curious.\u003c/p>\n\u003cp>Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.\u003c/p>\n\u003cp>This is exactly what the good folks at the San Francisco-based company AncestryDNA \u003ca href=\"http://www.foxnews.com/science/2014/12/16/ancestrydna-reconstructs-partial-genome-1th-century-father/\">just did with David Speegle\u003c/a>, a man born sometime around 1806. They were able to use the DNA of Speegle’s living descendants to piece together around 12% of the length of his genome. From this work, they were able to figure out that either he or one of his two wives probably had blue eyes and had the genes for early baldness.\u003c/p>\n\u003cp>This is just a start. As we learn more about human DNA, we will be able to learn a whole lot more about this long dead man from his recreated genome.\u003c/p>\n\u003cp>And now that AncestryDNA has worked out how to do this, they may be able to apply it to other deceased individuals as well. We may soon have a whole new way to learn about our past.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>A Little Bit of Luck\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_26093\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26093\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\" alt=\"This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black-and-white photo. (restorationmovement.com)\" width=\"200\" height=\"374\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black and white photo. (\u003ca href=\"http://www.therestorationmovement.com/alabama/speegle.htm\">restorationmovement.com\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Most everyone knows that they get half their DNA from their mom and half from their dad. What they might not have thought about is what happens to their DNA if they have just one child. Basically, at its simplest, half their DNA is lost forever!\u003c/p>\n\u003cp>Now of course it isn’t as simple as that. If you have brothers or sisters, they share right around half of their DNA with you and so their kids will share some of your DNA too. And if your parents had brothers and sisters they will share some of your DNA too. And so on.\u003c/p>\n\u003cp>Still, it becomes very tricky to track down DNA from people with few descendants. Which is why David Speegle made such an ideal test case.\u003c/p>\n\u003cp>He had 26(!) kids with two different wives and over 150 grandkids. His full set of DNA was pretty much passed on to the next generation multiple times.\u003c/p>\n\u003cp>This is where the luck comes in. For now, if you wanted something similar done for one of your relatives, you’d need to focus on someone that had lots of kids. That long-lost relative with two kids and four grandkids will probably remain a mystery for the foreseeable future.\u003c/p>\n\u003cp>So the first step is picking a relative with lots of kids and grandkids. But this is by no means the whole story. You also need to know the DNA of lots of your relatives and have lots of accurate, overlapping family trees.\u003c/p>\n\u003cp>\u003cstrong>A Lot of Science and Genealogy\u003c/strong>\u003c/p>\n\u003cp>David Speegle, his kids and his grandkids have all been dead for a very long time. What this means is that anyone alive today has, at most, tiny splinters of his DNA in theirs. These wisps of DNA need to be recognized and then combined to recreate David Speegle’s DNA.\u003c/p>\n\u003cfigure id=\"attachment_26095\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26095\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\" alt=\"We are getting closer to being able to recreate the genomes of long dead people. (Flickr)\" width=\"250\" height=\"375\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We are getting closer to being able to recreate the genomes of long dead people. (\u003ca href=\"https://www.flickr.com/photos/greyloch/9121238998/\">Flickr\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Remember, you can’t compare the DNA of a relative with David’s DNA. His DNA is not available.\u003c/p>\n\u003cp>So, basically you are looking at as many of the people as you can at the bottom level of an enormous family tree that starts with David and his two wives. Fortunately, AncestryDNA has a good number of David Speegle’s descendants in the over 500,000 genomes in their database.\u003c/p>\n\u003cp>The researchers at AncestryDNA compared the DNA of all of the pairs of people for whom Speegle was the most recent common ancestor, one pair at a time, and looked for common DNA. They found a whole lot of it.\u003c/p>\n\u003cp>The next step was to find the DNA that is actually David’s and not some other shared relative’s DNA. This is trickier than it sounds because DNA doesn’t get passed down in predictable chunks from generation to generation. It gets all mixed, matched, and diluted in each generation.\u003c/p>\n\u003cp>This is where those family trees come in handy. You can subtract out DNA that is shared because of other relatives.\u003c/p>\n\u003cp>In fact, this is where the David’s two wives really helped. They made it easier to separate out the DNA that came from these two women compared to the DNA that came from David.\u003c/p>\n\u003cp>\u003cstrong>Not Just a Parlor Trick\u003c/strong>\u003c/p>\n\u003cp>Recreating David’s genome is more than just some heroic academic exercise. It also points to what we can learn about ourselves from testing the DNA of many relatives.\u003c/p>\n\u003cp>For example, people are using their DNA to trace their family’s ancestry. In fact, whole companies (including AncestryDNA) are based on just that premise.\u003c/p>\n\u003cp>Unfortunately, you can lose a lot of information if you test only yourself. Remember, you have only half of your mom and dad’s DNA. What this means is that you may miss more distant ancestry information.\u003c/p>\n\u003cp>Imagine that you had an Asian ancestor 5 or 6 generations back. This might mean that your parent has less than 5% of that Asian ancestor’s DNA in his or her DNA. If you happened to not inherit that part of your parent’s DNA, then the history of your Asian ancestry would be lost. (Click \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist/uneven-passing-dna\">here \u003c/a>for more information on these scenarios.)\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>One way to recover that information would be through something similar to what was done here for David Speegle. By comparing the DNA of lots of relatives you might be able to piece together that lost Asian history and learn a bit about yourself or confirm a family story.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/26088/scientists-use-modern-dna-to-reconstruct-part-of-a-19th-century-mans-genome","authors":["6177"],"categories":["science_30"],"tags":["science_305","science_326"],"featImg":"science_26091","label":"science"},"science_17133":{"type":"posts","id":"science_17133","meta":{"index":"posts_1591205157","site":"science","id":"17133","score":null,"sort":[1399296641000]},"guestAuthors":[],"slug":"consumer-gene-tests-whats-the-future","title":"Consumer Gene Tests Face Uncertain Future","publishDate":1399296641,"format":"aside","headTitle":"Consumer Gene Tests Face Uncertain Future | KQED","labelTerm":{"site":"science"},"content":"\u003cdiv class=\"audio-wrap\">\n\u003ch2>Listen:\u003c/h2>\n\u003cp>http://www.kqed.org/.stream/anon/radio/science/2014/05/20140505science.mp3\u003c/p>\n\u003c/div>\n\u003cfigure id=\"attachment_17201\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17201\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/DNA-2.jpg\" alt=\"A magnified strand of DNA. (Credit: Tomasz Wyszomirski)\" width=\"640\" height=\"360\">\u003cfigcaption class=\"wp-caption-text\">A magnified strand of DNA. (Tomasz Wyszomirski)\u003c/figcaption>\u003c/figure>\n\u003cp>Consumers who want to find out about their genetic health risks without going to the doctor and paying a hefty price may have to wait. For a while, personal genetic tests were becoming more affordable and informative. But the industry took a blow last year when the government cracked down on Mountain View company \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a>.\u003c/p>\n\u003cp>That was the last consumer gene testing company still offering health information after two years of federal efforts to regulate the industry. Unlike other companies, many of which folded or sold, 23andMe is working with regulators to come back to the consumer genetic health market.\u003c/p>\n\u003cp>\u003cstrong>A Passion for Consumer Genetics\u003c/strong>\u003c/p>\n\u003cp>On a recent Thursday evening at the \u003ca href=\"http://www.calacademy.org/\">California Academy of Sciences\u003c/a> in San Francisco, the star of the show was not the giant T-Rex skeleton in the lobby but a small-framed, energetic Silicon Valley entrepreneur speaking about personal genetics.\u003c/p>\n\u003caside class=\"pullquote alignleft\">‘One of the main things people think about when they think of their genetic information, is that they want the health interpretation.’\u003c/aside>\n\u003cp>“I want to ask this audience, how many people have ever had a genetic test?” said \u003ca href=\"https://www.23andme.com/about/board/\">Anne Wojcicki\u003c/a>, CEO of 23andMe.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Of about 150 people in the audience, some 30 people raised their hands.\u003c/p>\n\u003cp>“So my goal is in the next ten years that every single one of you would raise your hand,” Wojcicki said.\u003c/p>\n\u003cp>Wojcicki said since 2007, more than half a million customers have sent in a saliva sample and gotten information that included their risks for developing cardiac disease and breast cancer, as well genetic traits such as how fast they metabolize caffeine. But last November the FDA ordered 23andMe to stop sales of its $99 tests.\u003c/p>\n\u003cp>\u003cstrong>FDA to 23andMe: Stop Selling Gene Tests\u003c/strong>\u003c/p>\n\u003cp>\u003ca href=\"http://www.fda.gov/newsevents/testimony/ucm219925.htm\">The FDA said\u003c/a>, in a very public letter, that the company’s test kit was a medical device that needed to be regulated and that 23andMe failed to prove it was interpreting health results accurately.\u003c/p>\n\u003cfigure id=\"attachment_17192\" class=\"wp-caption alignleft\" style=\"max-width: 252px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"wp-image-17192\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/Wojcicki-216x162.jpg\" alt=\"23andMe CEO Anne Wojcicki, speaking at the annual SXSW festival in Austin, Texas in March 2014. (Jenny Oh/KQED)\" width=\"252\" height=\"189\">\u003cfigcaption class=\"wp-caption-text\">23andMe CEO Anne Wojcicki, speaking at the annual SXSW festival in Austin, Texas in March 2014. (Jenny Oh/KQED)\u003c/figcaption>\u003c/figure>\n\u003cp>Wojcicki said the ruling has hit her company hard. “As a result, we have had to stop offering our healthcare service, and it’s had a significant impact because it’s one of the main things people think about when they think of their genetic information, is that they want the health interpretation.”\u003c/p>\n\u003cp>So now, 23andMe is working with the FDA in an effort to once again be able to offer health information. Meanwhile, the company can still provide ancestry information, which is already a crowded field.\u003c/p>\n\u003cp>Hank Greely directs the \u003ca href=\"https://www.law.stanford.edu/organizations/programs-and-centers/center-for-law-and-the-biosciences\">Center for Law and the Biosciences\u003c/a> at Stanford. He said dwindling sales will impact the company’s efforts to build a sizable research database—and that’s important to its business strategy.\u003c/p>\n\u003cp>“For those customers who agree to it by signing a somewhat opaque consent form,” Greely said, “they can sell that information to pharma and bio, but without lots of new customers coming in that service becomes less attractive to pharma and biotech.”\u003c/p>\n\u003cp>Some have criticized 23andme for considering selling anonymized data. But Wojcicki is unapologetic.\u003c/p>\n\u003cp>“23andMe partners with those companies because those are the people who are making therapies,” she said. “And if we want to get better therapies for breast cancer, and you want to get better therapies for asthma and migraines and all kinds of the other conditions that impact our lives, we have to work with pharma companies.”\u003cbr>\n\u003cstrong>\u003cbr>\nBig Data May Lead to Medical Breakthroughs\u003c/strong>\u003c/p>\n\u003cp>And here’s where consumer genetics isn’t just about the consumer. All that genetic information, or big data, can be used to run studies in search of medical breakthroughs. That means any company that wants to stay at the forefront has to keep up with the changing science.\u003c/p>\n\u003caside class=\"pullquote alignleft\">‘We know that the world has been quite focused on getting the so-called thousand-dollar genome.’\u003c/aside>\n\u003cp>In your human genome you have an entire set of 23 human chromosomes, made up of, among other things, DNA building blocks called base pairs. The human genome is composed of 3 billion base pairs.\u003c/p>\n\u003cp>Right now consumer gene tests take tiny snips of less than a million base pairs to look at one person’s unique genetic blueprint. Each of these unique variations is called a snp (yep, pronounced “snip”), for “single nucleotide polymorphism.”\u003c/p>\n\u003cp>\u003cstrong>The Future Lies in Sequencing the Whole Genome\u003c/strong>\u003c/p>\n\u003cp>But a snp is just a fraction of the entire genome. Scientists say the key to the future of genetics lies in sequencing the whole genome.\u003c/p>\n\u003cp>“We know that the world has been quite focused on getting the so-called thousand-dollar genome,” said Vance Vanier, vice president of reproductive and genetic health at San Diego-based \u003ca href=\"http://www.illumina.com/\">Illumina\u003c/a>. The company has just unveiled a system it claims can sequence a human genome for $1,000. That’s a big drop from the nearly $3 billion dollar price tag to sequence the first genome in 2003.\u003c/p>\n\u003cp>“I think the story of the next five years is to see that affordability spread more and more to broader segments of society and to clinical laboratories specifically,” said Vanier, who was CEO of an early consumer gene testing company called Navigenics.\u003c/p>\n\u003cp>And while he believes genetic testing will continue to be done primarily through medical professionals, he said he still sees a place for consumer gene tests. After all, Vanier said, there was a time home pregnancy tests had to be done in a doctor’s office. Now people can even buy over-the-counter HIV tests.\u003c/p>\n\u003cp>“I think the pattern you see,” Vanier said, “is as information gets better understood and as there are more social safeguards around it to protect from a misuse of it, then there is increasing comfort of how it can evolve into the consumer market.”\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>And so the debate continues between those that believe accessing your DNA has become a basic right and those who believe gene tests are better left to a doctor.\u003cbr>\n\u003cem>\u003cbr>\nSince this story published, 23andMe officials confirm they \u003ca href=\"http://www.reuters.com/article/2014/05/06/23andme-genetictesting-idUSL2N0NS0Y820140506?feedType=RSS\">are considering selling their gene tests in markets outside the U.S.\u003c/a> after facing hurdles with the FDA.\u003c/em>\u003c/p>\n\n","blocks":[],"excerpt":"Personal genetics companies that offer health insights are working to satisfy federal regulators and keep up with changing science.","status":"publish","parent":0,"modified":1704933731,"stats":{"hasAudio":true,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":28,"wordCount":1086},"headData":{"title":"Consumer Gene Tests Face Uncertain Future | KQED","description":"Personal genetics companies that offer health insights are working to satisfy federal regulators and keep up with changing science.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Consumer Gene Tests Face Uncertain Future","datePublished":"2014-05-05T13:30:41.000Z","dateModified":"2024-01-11T00:42:11.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"audioUrl":"http://www.kqed.org/.stream/anon/radio/science/2014/05/20140505science.mp3","sticky":false,"path":"/science/17133/consumer-gene-tests-whats-the-future","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cdiv class=\"audio-wrap\">\n\u003ch2>Listen:\u003c/h2>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"audioLink","attributes":{"named":{"src":"http://www.kqed.org/.stream/anon/radio/science/2014/05/20140505science.mp3"},"numeric":[]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/div>\n\u003cfigure id=\"attachment_17201\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17201\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/DNA-2.jpg\" alt=\"A magnified strand of DNA. (Credit: Tomasz Wyszomirski)\" width=\"640\" height=\"360\">\u003cfigcaption class=\"wp-caption-text\">A magnified strand of DNA. (Tomasz Wyszomirski)\u003c/figcaption>\u003c/figure>\n\u003cp>Consumers who want to find out about their genetic health risks without going to the doctor and paying a hefty price may have to wait. For a while, personal genetic tests were becoming more affordable and informative. But the industry took a blow last year when the government cracked down on Mountain View company \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a>.\u003c/p>\n\u003cp>That was the last consumer gene testing company still offering health information after two years of federal efforts to regulate the industry. Unlike other companies, many of which folded or sold, 23andMe is working with regulators to come back to the consumer genetic health market.\u003c/p>\n\u003cp>\u003cstrong>A Passion for Consumer Genetics\u003c/strong>\u003c/p>\n\u003cp>On a recent Thursday evening at the \u003ca href=\"http://www.calacademy.org/\">California Academy of Sciences\u003c/a> in San Francisco, the star of the show was not the giant T-Rex skeleton in the lobby but a small-framed, energetic Silicon Valley entrepreneur speaking about personal genetics.\u003c/p>\n\u003caside class=\"pullquote alignleft\">‘One of the main things people think about when they think of their genetic information, is that they want the health interpretation.’\u003c/aside>\n\u003cp>“I want to ask this audience, how many people have ever had a genetic test?” said \u003ca href=\"https://www.23andme.com/about/board/\">Anne Wojcicki\u003c/a>, CEO of 23andMe.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Of about 150 people in the audience, some 30 people raised their hands.\u003c/p>\n\u003cp>“So my goal is in the next ten years that every single one of you would raise your hand,” Wojcicki said.\u003c/p>\n\u003cp>Wojcicki said since 2007, more than half a million customers have sent in a saliva sample and gotten information that included their risks for developing cardiac disease and breast cancer, as well genetic traits such as how fast they metabolize caffeine. But last November the FDA ordered 23andMe to stop sales of its $99 tests.\u003c/p>\n\u003cp>\u003cstrong>FDA to 23andMe: Stop Selling Gene Tests\u003c/strong>\u003c/p>\n\u003cp>\u003ca href=\"http://www.fda.gov/newsevents/testimony/ucm219925.htm\">The FDA said\u003c/a>, in a very public letter, that the company’s test kit was a medical device that needed to be regulated and that 23andMe failed to prove it was interpreting health results accurately.\u003c/p>\n\u003cfigure id=\"attachment_17192\" class=\"wp-caption alignleft\" style=\"max-width: 252px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"wp-image-17192\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/Wojcicki-216x162.jpg\" alt=\"23andMe CEO Anne Wojcicki, speaking at the annual SXSW festival in Austin, Texas in March 2014. (Jenny Oh/KQED)\" width=\"252\" height=\"189\">\u003cfigcaption class=\"wp-caption-text\">23andMe CEO Anne Wojcicki, speaking at the annual SXSW festival in Austin, Texas in March 2014. (Jenny Oh/KQED)\u003c/figcaption>\u003c/figure>\n\u003cp>Wojcicki said the ruling has hit her company hard. “As a result, we have had to stop offering our healthcare service, and it’s had a significant impact because it’s one of the main things people think about when they think of their genetic information, is that they want the health interpretation.”\u003c/p>\n\u003cp>So now, 23andMe is working with the FDA in an effort to once again be able to offer health information. Meanwhile, the company can still provide ancestry information, which is already a crowded field.\u003c/p>\n\u003cp>Hank Greely directs the \u003ca href=\"https://www.law.stanford.edu/organizations/programs-and-centers/center-for-law-and-the-biosciences\">Center for Law and the Biosciences\u003c/a> at Stanford. He said dwindling sales will impact the company’s efforts to build a sizable research database—and that’s important to its business strategy.\u003c/p>\n\u003cp>“For those customers who agree to it by signing a somewhat opaque consent form,” Greely said, “they can sell that information to pharma and bio, but without lots of new customers coming in that service becomes less attractive to pharma and biotech.”\u003c/p>\n\u003cp>Some have criticized 23andme for considering selling anonymized data. But Wojcicki is unapologetic.\u003c/p>\n\u003cp>“23andMe partners with those companies because those are the people who are making therapies,” she said. “And if we want to get better therapies for breast cancer, and you want to get better therapies for asthma and migraines and all kinds of the other conditions that impact our lives, we have to work with pharma companies.”\u003cbr>\n\u003cstrong>\u003cbr>\nBig Data May Lead to Medical Breakthroughs\u003c/strong>\u003c/p>\n\u003cp>And here’s where consumer genetics isn’t just about the consumer. All that genetic information, or big data, can be used to run studies in search of medical breakthroughs. That means any company that wants to stay at the forefront has to keep up with the changing science.\u003c/p>\n\u003caside class=\"pullquote alignleft\">‘We know that the world has been quite focused on getting the so-called thousand-dollar genome.’\u003c/aside>\n\u003cp>In your human genome you have an entire set of 23 human chromosomes, made up of, among other things, DNA building blocks called base pairs. The human genome is composed of 3 billion base pairs.\u003c/p>\n\u003cp>Right now consumer gene tests take tiny snips of less than a million base pairs to look at one person’s unique genetic blueprint. Each of these unique variations is called a snp (yep, pronounced “snip”), for “single nucleotide polymorphism.”\u003c/p>\n\u003cp>\u003cstrong>The Future Lies in Sequencing the Whole Genome\u003c/strong>\u003c/p>\n\u003cp>But a snp is just a fraction of the entire genome. Scientists say the key to the future of genetics lies in sequencing the whole genome.\u003c/p>\n\u003cp>“We know that the world has been quite focused on getting the so-called thousand-dollar genome,” said Vance Vanier, vice president of reproductive and genetic health at San Diego-based \u003ca href=\"http://www.illumina.com/\">Illumina\u003c/a>. The company has just unveiled a system it claims can sequence a human genome for $1,000. That’s a big drop from the nearly $3 billion dollar price tag to sequence the first genome in 2003.\u003c/p>\n\u003cp>“I think the story of the next five years is to see that affordability spread more and more to broader segments of society and to clinical laboratories specifically,” said Vanier, who was CEO of an early consumer gene testing company called Navigenics.\u003c/p>\n\u003cp>And while he believes genetic testing will continue to be done primarily through medical professionals, he said he still sees a place for consumer gene tests. After all, Vanier said, there was a time home pregnancy tests had to be done in a doctor’s office. Now people can even buy over-the-counter HIV tests.\u003c/p>\n\u003cp>“I think the pattern you see,” Vanier said, “is as information gets better understood and as there are more social safeguards around it to protect from a misuse of it, then there is increasing comfort of how it can evolve into the consumer market.”\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>And so the debate continues between those that believe accessing your DNA has become a basic right and those who believe gene tests are better left to a doctor.\u003cbr>\n\u003cem>\u003cbr>\nSince this story published, 23andMe officials confirm they \u003ca href=\"http://www.reuters.com/article/2014/05/06/23andme-genetictesting-idUSL2N0NS0Y820140506?feedType=RSS\">are considering selling their gene tests in markets outside the U.S.\u003c/a> after facing hurdles with the FDA.\u003c/em>\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/17133/consumer-gene-tests-whats-the-future","authors":["212"],"categories":["science_46","science_30","science_29","science_39","science_40","science_43"],"tags":["science_304","science_1050","science_64","science_326"],"featImg":"science_17201","label":"science"},"science_15545":{"type":"posts","id":"science_15545","meta":{"index":"posts_1591205157","site":"science","id":"15545","score":null,"sort":[1395669618000]},"guestAuthors":[],"slug":"scanning-dna-for-health-risks-in-the-clinic-gets-an-incomplete-but-still-might-save-your-life","title":"Testing Complete DNA Sequences Yields Only Partial Info but Could Still Save Your Life","publishDate":1395669618,"format":"aside","headTitle":"Testing Complete DNA Sequences Yields Only Partial Info but Could Still Save Your Life | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_15547\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/GenomePerson.jpg\" rel=\"attachment wp-att-15547\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-15547\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/GenomePerson.jpg\" alt=\"Reading all of your DNA at once can’t yet find all of your future health risks. But if you get lucky, it just might save your life. (Richard Ricciardi/Flickr)\" width=\"640\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Reading all of your DNA at once can’t find all of your future health risks yet. But if you get lucky, it just might save your life. (Richard Ricciardi/\u003ca href=\"http://www.flickr.com/photos/ricricciardi/11622986115/\">Flickr\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>For a while now, we have been told that soon we will be able to learn a whole lot about our health risks from studying our complete DNA sequence. Our future health will be read by scientists in the tea leaves that are DNA.\u003c/p>\n\u003cp>A \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24618965\">new study\u003c/a> out of Stanford University in the Journal of the American Medical Association (JAMA) shows just how far we are from that brave new world. For around $15,000 or so per patient, these researchers managed to only get a partial read of key health genes and to only catch around half of a certain class of DNA differences in twelve patients. Not only that, but they also struggled to understand what many parts of these DNA reads meant. We are not yet at a point where we can cheaply and easily get and interpret the complete set of instructions for a single person.\u003c/p>\n\u003cp>Still, it isn’t all doom and gloom. You may not be able to learn everything from your DNA but as one patient in the study found, you can still find things that just might save your life. This kind of thing may make even an imperfect test worth the cost; it certainly was for this one patient.\u003c/p>\n\u003cp>\u003cstrong>Found Gene\u003c/strong>\u003c/p>\n\u003cp>In the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24618965\">study\u003c/a>, 12 people had their whole genome sequenced. This means that the scientists tried to get a read on all six billion or so of each person’s A, G, C and T nucleobases in their DNA. For one of the 12 patients, things went as everyone thinks these sorts of things eventually will.\u003c/p>\n\u003caside class=\"pullquote alignleft\">Only an unbiased test could find her broken BRCA1 gene.\u003c/aside>\n\u003cp>The researchers discovered that this woman had a difference in one copy of her BRCA1 gene; that meant she almost certainly had a very high chance of getting breast and/or ovarian cancer later in life. With this knowledge, she took steps to lessen her risk. She had her ovaries removed and will undergo much more frequent mammograms to catch any breast cancer early. This testing may have saved her from an early death from cancer.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>But out in the real world, she may never have found out that she had a broken BRCA1 gene. Breast cancer doesn’t run in her family, which means no one would recommend her for one of these tests. She could only find her cancer risk in a test that looked at lots of different genes. Only an unbiased test could find her broken BRCA1 gene.\u003c/p>\n\u003cp>Of course, this is just one of the many genes the researchers looked at in one of 12 patients. The results for the other genes and the other patients were not so clear-cut. A surprising number of important genes were not read and an equally surprising number of DNA differences missed.\u003c/p>\n\u003cp>\u003cstrong>Missed DNA\u003c/strong>\u003c/p>\n\u003cp>The researchers first used a company called \u003ca href=\"http://www.illumina.com/\">Illumina Inc.\u003c/a> to do the sequencing. Depending on the patient, anywhere from 5%-34% (median was 10%) of genes known to be involved in disease didn’t get read well enough to draw any conclusions. Doing the same on nine of the patients with a second company, \u003ca href=\"http://www.completegenomics.com/\">Complete Genomics Inc.\u003c/a>, gave similar results. This time 18%-21% (median was 19%) of disease-related genes remained a mystery.\u003c/p>\n\u003cfigure id=\"attachment_15562\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/ReadTeaLeaves.jpg\" rel=\"attachment wp-att-15562\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-15562\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/ReadTeaLeaves.jpg\" alt=\"Reading DNA is still better than reading tea leaves to predict your future health. But we still have a long way to go. (MochaSwirl/Wikimedia Commons)\" width=\"300\" height=\"225\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Reading DNA is still better than reading tea leaves to predict your future health. But we still have a long way to go.\u003c/figcaption>\u003c/figure>\n\u003cp>This is a big deal because the test might miss an important DNA difference that could cause problems for the patient. Imagine that a second patient has a broken BRCA1 gene and the test missed it, or the BRCA1 patient had a different broken gene that caused some other problem. These types of false negative results might give the patients a false sense of security about their health.\u003c/p>\n\u003cp>Using two companies also gave the researchers the chance to compare the two results. The two did not line up as well as you might think.\u003c/p>\n\u003cp>The two tests did very well for known, common, disease-causing variants (like those \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a> could see for a lot less money). These would be like the variant of the hemoglobin gene that can cause sickle cell anemia. The companies agreed on 99% of these. Where they had more trouble was with small insertions or deletions.\u003c/p>\n\u003cp>An insertion is when one or a few letters are put into the DNA and a deletion is when one or a few are removed. This is the kind of thing that can, for example, cause some cases of cystic fibrosis or make people resistant to HIV infection. Here the two companies’ results only matched up between 53% and 59% of the time.\u003c/p>\n\u003cp>If anything, this is even more troubling than an unread gene. At least with an unread gene, you can tell a patient that you couldn’t read the gene or you could try to reread it. If you miss a disease causing DNA difference, you don’t have any way of knowing whether it was there or not. This leads to even more false negatives.\u003c/p>\n\u003cp>\u003cstrong>Interpreting DNA Is No Picnic\u003c/strong>\u003c/p>\n\u003cp>Up until now, I have focused on problems in reading the DNA. Figuring out what the DNA means is no easy task either! I don’t have the space to go into it here, but suffice it to say that interpreting DNA is at least as tricky and time consuming as reading it and a whole lot more subjective. We don’t yet have a good handle on what it all means and what to do with it (although we are learning).\u003c/p>\n\u003cp>\u003cstrong>Future Still Bright\u003c/strong>\u003c/p>\n\u003cp>The bottom line is that whole genome sequencing for health risks is not quite up to snuff yet. But that doesn’t mean it’s no better than reading tea leaves for predicting the future.\u003c/p>\n\u003caside class=\"pullquote alignleft\">Warning: Right now results will be incomplete\u003c/aside>\n\u003cp>Even in its current form, this sort of test can help patients live healthier lives; it just won’t catch everything. Maybe the results should come with a warning that many health risks will have been missed.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>While we wait for the inevitable march of technology to further perfect this sort of test, one way around the technical issues may be to narrow the DNA we choose to read. For now, we could focus on those genes known to be involved in inherited disease and add more genes as they become available. The less DNA to read, the more likely we are to catch every last letter.\u003c/p>\n\n","blocks":[],"excerpt":"Evaluating your whole genome sequence to determine your health risks is not yet up to snuff. But as imperfect as it is, you still might see something that could save your life.","status":"publish","parent":0,"modified":1704933960,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":23,"wordCount":1161},"headData":{"title":"Testing Complete DNA Sequences Yields Only Partial Info but Could Still Save Your Life | KQED","description":"Evaluating your whole genome sequence to determine your health risks is not yet up to snuff. But as imperfect as it is, you still might see something that could save your life.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Testing Complete DNA Sequences Yields Only Partial Info but Could Still Save Your Life","datePublished":"2014-03-24T14:00:18.000Z","dateModified":"2024-01-11T00:46:00.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"sticky":false,"path":"/science/15545/scanning-dna-for-health-risks-in-the-clinic-gets-an-incomplete-but-still-might-save-your-life","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_15547\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/GenomePerson.jpg\" rel=\"attachment wp-att-15547\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-15547\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/GenomePerson.jpg\" alt=\"Reading all of your DNA at once can’t yet find all of your future health risks. But if you get lucky, it just might save your life. (Richard Ricciardi/Flickr)\" width=\"640\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Reading all of your DNA at once can’t find all of your future health risks yet. But if you get lucky, it just might save your life. (Richard Ricciardi/\u003ca href=\"http://www.flickr.com/photos/ricricciardi/11622986115/\">Flickr\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>For a while now, we have been told that soon we will be able to learn a whole lot about our health risks from studying our complete DNA sequence. Our future health will be read by scientists in the tea leaves that are DNA.\u003c/p>\n\u003cp>A \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24618965\">new study\u003c/a> out of Stanford University in the Journal of the American Medical Association (JAMA) shows just how far we are from that brave new world. For around $15,000 or so per patient, these researchers managed to only get a partial read of key health genes and to only catch around half of a certain class of DNA differences in twelve patients. Not only that, but they also struggled to understand what many parts of these DNA reads meant. We are not yet at a point where we can cheaply and easily get and interpret the complete set of instructions for a single person.\u003c/p>\n\u003cp>Still, it isn’t all doom and gloom. You may not be able to learn everything from your DNA but as one patient in the study found, you can still find things that just might save your life. This kind of thing may make even an imperfect test worth the cost; it certainly was for this one patient.\u003c/p>\n\u003cp>\u003cstrong>Found Gene\u003c/strong>\u003c/p>\n\u003cp>In the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24618965\">study\u003c/a>, 12 people had their whole genome sequenced. This means that the scientists tried to get a read on all six billion or so of each person’s A, G, C and T nucleobases in their DNA. For one of the 12 patients, things went as everyone thinks these sorts of things eventually will.\u003c/p>\n\u003caside class=\"pullquote alignleft\">Only an unbiased test could find her broken BRCA1 gene.\u003c/aside>\n\u003cp>The researchers discovered that this woman had a difference in one copy of her BRCA1 gene; that meant she almost certainly had a very high chance of getting breast and/or ovarian cancer later in life. With this knowledge, she took steps to lessen her risk. She had her ovaries removed and will undergo much more frequent mammograms to catch any breast cancer early. This testing may have saved her from an early death from cancer.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>But out in the real world, she may never have found out that she had a broken BRCA1 gene. Breast cancer doesn’t run in her family, which means no one would recommend her for one of these tests. She could only find her cancer risk in a test that looked at lots of different genes. Only an unbiased test could find her broken BRCA1 gene.\u003c/p>\n\u003cp>Of course, this is just one of the many genes the researchers looked at in one of 12 patients. The results for the other genes and the other patients were not so clear-cut. A surprising number of important genes were not read and an equally surprising number of DNA differences missed.\u003c/p>\n\u003cp>\u003cstrong>Missed DNA\u003c/strong>\u003c/p>\n\u003cp>The researchers first used a company called \u003ca href=\"http://www.illumina.com/\">Illumina Inc.\u003c/a> to do the sequencing. Depending on the patient, anywhere from 5%-34% (median was 10%) of genes known to be involved in disease didn’t get read well enough to draw any conclusions. Doing the same on nine of the patients with a second company, \u003ca href=\"http://www.completegenomics.com/\">Complete Genomics Inc.\u003c/a>, gave similar results. This time 18%-21% (median was 19%) of disease-related genes remained a mystery.\u003c/p>\n\u003cfigure id=\"attachment_15562\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/ReadTeaLeaves.jpg\" rel=\"attachment wp-att-15562\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-15562\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/03/ReadTeaLeaves.jpg\" alt=\"Reading DNA is still better than reading tea leaves to predict your future health. But we still have a long way to go. (MochaSwirl/Wikimedia Commons)\" width=\"300\" height=\"225\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Reading DNA is still better than reading tea leaves to predict your future health. But we still have a long way to go.\u003c/figcaption>\u003c/figure>\n\u003cp>This is a big deal because the test might miss an important DNA difference that could cause problems for the patient. Imagine that a second patient has a broken BRCA1 gene and the test missed it, or the BRCA1 patient had a different broken gene that caused some other problem. These types of false negative results might give the patients a false sense of security about their health.\u003c/p>\n\u003cp>Using two companies also gave the researchers the chance to compare the two results. The two did not line up as well as you might think.\u003c/p>\n\u003cp>The two tests did very well for known, common, disease-causing variants (like those \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a> could see for a lot less money). These would be like the variant of the hemoglobin gene that can cause sickle cell anemia. The companies agreed on 99% of these. Where they had more trouble was with small insertions or deletions.\u003c/p>\n\u003cp>An insertion is when one or a few letters are put into the DNA and a deletion is when one or a few are removed. This is the kind of thing that can, for example, cause some cases of cystic fibrosis or make people resistant to HIV infection. Here the two companies’ results only matched up between 53% and 59% of the time.\u003c/p>\n\u003cp>If anything, this is even more troubling than an unread gene. At least with an unread gene, you can tell a patient that you couldn’t read the gene or you could try to reread it. If you miss a disease causing DNA difference, you don’t have any way of knowing whether it was there or not. This leads to even more false negatives.\u003c/p>\n\u003cp>\u003cstrong>Interpreting DNA Is No Picnic\u003c/strong>\u003c/p>\n\u003cp>Up until now, I have focused on problems in reading the DNA. Figuring out what the DNA means is no easy task either! I don’t have the space to go into it here, but suffice it to say that interpreting DNA is at least as tricky and time consuming as reading it and a whole lot more subjective. We don’t yet have a good handle on what it all means and what to do with it (although we are learning).\u003c/p>\n\u003cp>\u003cstrong>Future Still Bright\u003c/strong>\u003c/p>\n\u003cp>The bottom line is that whole genome sequencing for health risks is not quite up to snuff yet. But that doesn’t mean it’s no better than reading tea leaves for predicting the future.\u003c/p>\n\u003caside class=\"pullquote alignleft\">Warning: Right now results will be incomplete\u003c/aside>\n\u003cp>Even in its current form, this sort of test can help patients live healthier lives; it just won’t catch everything. Maybe the results should come with a warning that many health risks will have been missed.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>While we wait for the inevitable march of technology to further perfect this sort of test, one way around the technical issues may be to narrow the DNA we choose to read. For now, we could focus on those genes known to be involved in inherited disease and add more genes as they become available. The less DNA to read, the more likely we are to catch every last letter.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/15545/scanning-dna-for-health-risks-in-the-clinic-gets-an-incomplete-but-still-might-save-your-life","authors":["6177"],"categories":["science_30","science_39"],"tags":["science_64","science_326"],"featImg":"science_15547","label":"science"},"science_12153":{"type":"posts","id":"science_12153","meta":{"index":"posts_1591205157","site":"science","id":"12153","score":null,"sort":[1387333004000]},"guestAuthors":[],"slug":"click-to-like-my-genome-part-two","title":"Click to \"Like\" My Genome: Part Two","publishDate":1387333004,"format":"aside","headTitle":"Click to “Like” My Genome: Part Two | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_12154\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/12/healthrisks.jpeg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-12154\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/12/healthrisks.jpeg\" alt=\"Click image to enlarge. \" width=\"640\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Screenshot of my test results from the 23andme.com website. Click image to enlarge.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/2013/09/12/click-to-like-my-genome-home-genetic-testing-goes-social/\">In my last post,\u003c/a> I wrote about my decision to test my DNA by sending a saliva sample to the popular personal genomics company \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a>. I had just received my results and was eager to spend some private time with my DNA. There are two basic areas of 23andMe to explore: health and ancestry — at least there used to be. Last month, the \u003ca href=\"http://www.npr.org/templates/story/story.php?storyId=247220418\">FDA ordered the Silicon Valley company to shut down its genetics service\u003c/a>, declaring it was making marketing claims beyond what is legal. Now consumers buying the test will get their raw genetic data and ancestry information but — unlike my results — none of the meaty stuff, like disease risk, individual health traits or drug interaction possibilities.\u003c/p>\n\u003cp>If I had signed up for the new, paltrier 23andMe service, I would not have learned that I have a slightly elevated risk for 22 diseases, including immune disorders like Crohn’s and Lupus. I wouldn’t have found out that I am a fast metabolizer of caffeine, have a \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&term=19228618\">sensitivity to the anticoagulant Coumadin,\u003c/a> am resistant to the stomach flu, am likely lactose-intolerant, and that my \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&term=17984066\">IQ was likely raised 5-7 points because I was breast-fed.\u003c/a>\u003c/p>\n\u003cp>This genetics information was my entree into a community of 23andMe’ers who share some of my findings. For example, one click on the Crohn’s Community tab and I found several dozen members discussing their shared risk for the disease and raising questions such as:\u003c/p>\n\u003cp>\u003cem>…What if those of us with Crohn’s could sequence our gut bacterial colonies? …Would this be something others here might consider?\u003c/em>\u003c/p>\n\u003cp>And in response, another user got to the heart of the personalized testing philosophy:\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cem>I think between my 23 and me and \u003ca href=\"http://ubiome.com/\">uBiome testing\u003c/a> it will give me a lot more data to work with in actively managing my health care.\u003c/em>\u003cem> I may have to be pushy about it though. My old Doc was excited to have somebody that wasn’t a passive consumer of doctor services and instead researched and discussed data and courses of action in managing health care. \u003c/em>\u003c/p>\n\u003cp>There are hundreds of forums on 23andMe, each buzzing about shared traits, mutations and tendencies.\u003c/p>\n\u003cp>The kvetching was often quite sophisticated:\u003c/p>\n\u003cp>\u003cem>Is there an identifier for \u003c/em>\u003ca href=\"http://www.dysphonia.org/\">\u003cem>Spasmodic Dysphonia\u003c/em>\u003c/a>\u003cem> (vocal cords) or \u003c/em>\u003ca href=\"http://www.blepharospasm.org/\">\u003cem>Blepharospasms\u003c/em>\u003c/a>\u003cem> (eyelids)?\u003c/em>\u003cem> I have Spasmodic Dysphonia and my mother and older sister have blepharospasms…\u003c/em> \u003cem>How do I find out if my children have this gene?\u003c/em>\u003cem>\u003c/em>\u003c/p>\n\u003cp>There’s nothing new about people getting together to compare notes about their health. We all look to those around us to determine whether we’re OK — whether whatever symptom we might have is normal. I realized these forums were, at least in part, support groups. But many of these people – who spanned age, gender, race, and location — were connecting based on extremely specific health concerns for which they often had no symptoms. \u003cem>\u003c/em>\u003c/p>\n\u003cp>Clearly, people were striving to connect the dots of their health, and maybe to find some comfort from people whose genetic makeup was similar to their own. I wondered if these nests of speculation were where a genetic counselor might fit in, particularly for those who were sick. Would some of these people seek medical treatment based on some combination of 23andMe’s reports and their conversations in its forums? The U.S. government is asking the same questions.\u003c/p>\n\u003cp>The FDA challenge may hurt the personal genetics industry in the short run. No traits, no health risks — no fun. But the company is still allowed to show ancestry results. In fact, there was a message glowing green in my 23andMe Inbox.\u003c/p>\n\u003cp>\u003cem> \u003c/em>\u003cem>A relative would like to make contact with you.\u003c/em>\u003c/p>\n\u003cp>The message:\u003c/p>\n\u003cp>\u003cem>Through our shared DNA, 23andMe has identified us as relatives. Our predicted relationship is 5th Cousin, with a likely range of 3rd to Distant Cousin. \u003c/em>\u003c/p>\n\u003cp>\u003cem>Thank you for your time and I hope you’ll be interested in sharing genomes!\u003c/em>\u003c/p>\n\u003cfigure id=\"attachment_4466\" class=\"wp-caption aligncenter\" style=\"max-width: 1673px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/Arwen-working.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-4466 \" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/Arwen-working.jpg\" alt=\"Arwen working-scaled\" width=\"1673\" height=\"941\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">With a click, I decide whether to “share genomes” with distant cousins around the world. Photo: Joshua Cassidy / KQED Science\u003c/figcaption>\u003c/figure>\n\u003cp>So. If I were to “share genomes” with this relative, a heredity buff of Norwegian descent whose pedigree, he went on to say, was posted elsewhere online — what exactly would that mean? What exactly would I be sharing – my entire results or just select information? How would this be similar to friending a distant acquaintance on Facebook, and how would it be different?\u003c/p>\n\u003cp>I clicked on a tab that produced a shocking list of 972 distant cousins, ranked by their genetic proximity to me via maternal \u003ca href=\"http://en.wikipedia.org/wiki/Haplotype\">haplotype\u003c/a>. Depending on how much personal information these cousins of mine had submitted to the site, I could see their birthdates, places of origin and residence, names and sometimes photos. They were young women, old men and everyone in between. If I chose, I could expand my family by nearly a thousand with a few clicks.\u003c/p>\n\u003cp>Shown as colored dots on a map of the world, the multitude of my relations was even more impressive. I found familial hotspots in New England, old England and Ireland, Central and Eastern Europe, Sicily, Scandinavia, North Africa, even a few odd cousins scattered in the islands.\u003c/p>\n\u003cp>None of us are really that far apart, genetically, and the map offered a glimpse of the movement of people across the world. The more people who joined 23andMe and shared their genomes, the more comprehensive a picture we could form of a global family tree. A day might come when I would know precisely how related I was to, for example — you. As I explored 23andMe, I enjoyed reading what other people thought about their ancestry and health.\u003c/p>\n\u003cp>So it might sound selfish when I say I still didn’t want to become friends with them, much less relatives. Our kinship was about our fascination with and curiosity about our own bodies and roots, not really about each other. Here we all were, gathered to celebrate the miracle of this new kind of self-awareness we’d purchased for only $99. But increasingly, I’ve found that I share in \u003ca href=\"http://www.scientificamerican.com/article.cfm?id=23andme-is-terrifying-but-not-for-reasons-fda\">concerns about giving away my most personal information\u003c/a> to a private company based mostly on the assumption of its benevolence, a la Google, and that I didn’t want to share my genes with my new online brethren.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>This week, as the company continues to negotiate with the FDA behind the scenes over the rights to market its genetic health data, I realized that at least for a brief time, I’m one of a select group that can still log in and peruse my genetic health risks and traits online. But if I have access to the 23andMe’s studies and predictions, shouldn’t everyone? I suspect that snatching away access to this data has only fanned the flames of our curiosity. In this context, 23andMe’s results feel less like a diversion and more like something we have a right to explore.\u003c/p>\n\n","blocks":[],"excerpt":"The FDA challenge may hurt the personal genetics industry in the short run. No traits, no health risks -- no fun. But the company is still allowed to show ancestry results. 23andMe's map of my distant relations offered a glimpse of the movement of people across the world. The more people who joined and shared their genomes, the more comprehensive a picture we could form of a global family tree. A day might come when I would know precisely how related I was to, for example -- you. ","status":"publish","parent":0,"modified":1704934526,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":24,"wordCount":1206},"headData":{"title":"Click to \"Like\" My Genome: Part Two | KQED","description":"The FDA challenge may hurt the personal genetics industry in the short run. No traits, no health risks -- no fun. But the company is still allowed to show ancestry results. 23andMe's map of my distant relations offered a glimpse of the movement of people across the world. The more people who joined and shared their genomes, the more comprehensive a picture we could form of a global family tree. A day might come when I would know precisely how related I was to, for example -- you. ","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Click to \"Like\" My Genome: Part Two","datePublished":"2013-12-18T02:16:44.000Z","dateModified":"2024-01-11T00:55:26.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"sticky":false,"path":"/science/12153/click-to-like-my-genome-part-two","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_12154\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/12/healthrisks.jpeg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-12154\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/12/healthrisks.jpeg\" alt=\"Click image to enlarge. \" width=\"640\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Screenshot of my test results from the 23andme.com website. Click image to enlarge.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/2013/09/12/click-to-like-my-genome-home-genetic-testing-goes-social/\">In my last post,\u003c/a> I wrote about my decision to test my DNA by sending a saliva sample to the popular personal genomics company \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a>. I had just received my results and was eager to spend some private time with my DNA. There are two basic areas of 23andMe to explore: health and ancestry — at least there used to be. Last month, the \u003ca href=\"http://www.npr.org/templates/story/story.php?storyId=247220418\">FDA ordered the Silicon Valley company to shut down its genetics service\u003c/a>, declaring it was making marketing claims beyond what is legal. Now consumers buying the test will get their raw genetic data and ancestry information but — unlike my results — none of the meaty stuff, like disease risk, individual health traits or drug interaction possibilities.\u003c/p>\n\u003cp>If I had signed up for the new, paltrier 23andMe service, I would not have learned that I have a slightly elevated risk for 22 diseases, including immune disorders like Crohn’s and Lupus. I wouldn’t have found out that I am a fast metabolizer of caffeine, have a \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&term=19228618\">sensitivity to the anticoagulant Coumadin,\u003c/a> am resistant to the stomach flu, am likely lactose-intolerant, and that my \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&term=17984066\">IQ was likely raised 5-7 points because I was breast-fed.\u003c/a>\u003c/p>\n\u003cp>This genetics information was my entree into a community of 23andMe’ers who share some of my findings. For example, one click on the Crohn’s Community tab and I found several dozen members discussing their shared risk for the disease and raising questions such as:\u003c/p>\n\u003cp>\u003cem>…What if those of us with Crohn’s could sequence our gut bacterial colonies? …Would this be something others here might consider?\u003c/em>\u003c/p>\n\u003cp>And in response, another user got to the heart of the personalized testing philosophy:\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cem>I think between my 23 and me and \u003ca href=\"http://ubiome.com/\">uBiome testing\u003c/a> it will give me a lot more data to work with in actively managing my health care.\u003c/em>\u003cem> I may have to be pushy about it though. My old Doc was excited to have somebody that wasn’t a passive consumer of doctor services and instead researched and discussed data and courses of action in managing health care. \u003c/em>\u003c/p>\n\u003cp>There are hundreds of forums on 23andMe, each buzzing about shared traits, mutations and tendencies.\u003c/p>\n\u003cp>The kvetching was often quite sophisticated:\u003c/p>\n\u003cp>\u003cem>Is there an identifier for \u003c/em>\u003ca href=\"http://www.dysphonia.org/\">\u003cem>Spasmodic Dysphonia\u003c/em>\u003c/a>\u003cem> (vocal cords) or \u003c/em>\u003ca href=\"http://www.blepharospasm.org/\">\u003cem>Blepharospasms\u003c/em>\u003c/a>\u003cem> (eyelids)?\u003c/em>\u003cem> I have Spasmodic Dysphonia and my mother and older sister have blepharospasms…\u003c/em> \u003cem>How do I find out if my children have this gene?\u003c/em>\u003cem>\u003c/em>\u003c/p>\n\u003cp>There’s nothing new about people getting together to compare notes about their health. We all look to those around us to determine whether we’re OK — whether whatever symptom we might have is normal. I realized these forums were, at least in part, support groups. But many of these people – who spanned age, gender, race, and location — were connecting based on extremely specific health concerns for which they often had no symptoms. \u003cem>\u003c/em>\u003c/p>\n\u003cp>Clearly, people were striving to connect the dots of their health, and maybe to find some comfort from people whose genetic makeup was similar to their own. I wondered if these nests of speculation were where a genetic counselor might fit in, particularly for those who were sick. Would some of these people seek medical treatment based on some combination of 23andMe’s reports and their conversations in its forums? The U.S. government is asking the same questions.\u003c/p>\n\u003cp>The FDA challenge may hurt the personal genetics industry in the short run. No traits, no health risks — no fun. But the company is still allowed to show ancestry results. In fact, there was a message glowing green in my 23andMe Inbox.\u003c/p>\n\u003cp>\u003cem> \u003c/em>\u003cem>A relative would like to make contact with you.\u003c/em>\u003c/p>\n\u003cp>The message:\u003c/p>\n\u003cp>\u003cem>Through our shared DNA, 23andMe has identified us as relatives. Our predicted relationship is 5th Cousin, with a likely range of 3rd to Distant Cousin. \u003c/em>\u003c/p>\n\u003cp>\u003cem>Thank you for your time and I hope you’ll be interested in sharing genomes!\u003c/em>\u003c/p>\n\u003cfigure id=\"attachment_4466\" class=\"wp-caption aligncenter\" style=\"max-width: 1673px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/Arwen-working.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-4466 \" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/Arwen-working.jpg\" alt=\"Arwen working-scaled\" width=\"1673\" height=\"941\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">With a click, I decide whether to “share genomes” with distant cousins around the world. Photo: Joshua Cassidy / KQED Science\u003c/figcaption>\u003c/figure>\n\u003cp>So. If I were to “share genomes” with this relative, a heredity buff of Norwegian descent whose pedigree, he went on to say, was posted elsewhere online — what exactly would that mean? What exactly would I be sharing – my entire results or just select information? How would this be similar to friending a distant acquaintance on Facebook, and how would it be different?\u003c/p>\n\u003cp>I clicked on a tab that produced a shocking list of 972 distant cousins, ranked by their genetic proximity to me via maternal \u003ca href=\"http://en.wikipedia.org/wiki/Haplotype\">haplotype\u003c/a>. Depending on how much personal information these cousins of mine had submitted to the site, I could see their birthdates, places of origin and residence, names and sometimes photos. They were young women, old men and everyone in between. If I chose, I could expand my family by nearly a thousand with a few clicks.\u003c/p>\n\u003cp>Shown as colored dots on a map of the world, the multitude of my relations was even more impressive. I found familial hotspots in New England, old England and Ireland, Central and Eastern Europe, Sicily, Scandinavia, North Africa, even a few odd cousins scattered in the islands.\u003c/p>\n\u003cp>None of us are really that far apart, genetically, and the map offered a glimpse of the movement of people across the world. The more people who joined 23andMe and shared their genomes, the more comprehensive a picture we could form of a global family tree. A day might come when I would know precisely how related I was to, for example — you. As I explored 23andMe, I enjoyed reading what other people thought about their ancestry and health.\u003c/p>\n\u003cp>So it might sound selfish when I say I still didn’t want to become friends with them, much less relatives. Our kinship was about our fascination with and curiosity about our own bodies and roots, not really about each other. Here we all were, gathered to celebrate the miracle of this new kind of self-awareness we’d purchased for only $99. But increasingly, I’ve found that I share in \u003ca href=\"http://www.scientificamerican.com/article.cfm?id=23andme-is-terrifying-but-not-for-reasons-fda\">concerns about giving away my most personal information\u003c/a> to a private company based mostly on the assumption of its benevolence, a la Google, and that I didn’t want to share my genes with my new online brethren.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>This week, as the company continues to negotiate with the FDA behind the scenes over the rights to market its genetic health data, I realized that at least for a brief time, I’m one of a select group that can still log in and peruse my genetic health risks and traits online. But if I have access to the 23andMe’s studies and predictions, shouldn’t everyone? I suspect that snatching away access to this data has only fanned the flames of our curiosity. In this context, 23andMe’s results feel less like a diversion and more like something we have a right to explore.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/12153/click-to-like-my-genome-part-two","authors":["6444"],"categories":["science_30","science_39"],"tags":["science_304","science_1050","science_327","science_326","science_5181"],"featImg":"science_12154","label":"science"},"science_6821":{"type":"posts","id":"science_6821","meta":{"index":"posts_1591205157","site":"science","id":"6821","score":null,"sort":[1376320791000]},"guestAuthors":[],"slug":"virus-induced-type-2-diabetes","title":"Virus-Induced Type 2 Diabetes","publishDate":1376320791,"format":"aside","headTitle":"Virus-Induced Type 2 Diabetes | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_6845\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/RSV.jpg\" rel=\"attachment wp-att-6845\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-6845\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/RSV.jpg\" alt=\"For at least one man, it looks like this virus, RSV, might have set off his type 2 diabetes. Electron micrograph image courtesy of Wikimedia Commons.\" width=\"640\" height=\"365\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">For at least one man, it looks like this virus, RSV, might have set off his type 2 diabetes. Electron micrograph image courtesy of \u003ca href=\"http://en.wikipedia.org/wiki/File:Respiratory_syncytial_virus_01.jpg\">Wikimedia Commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>Some of the most interesting findings in science happen on fishing exhibitions. No, I don’t mean going out on a boat (although lots of cool things have been found that way); I mean just gathering lots of data and seeing what you can find.\u003c/p>\n\u003cp>Something really interesting came out of just such a project from the lab of Dr. Mike Snyder at Stanford University. He set out to study himself in every way possible over a period of a few years. His lab looked at his DNA, how his DNA was being used, what sorts of things were in his blood, what his immune system was doing and lots more. His lab also then determined how these things changed over the course of the experiment.\u003c/p>\n\u003cp>One of the most fascinating things to come out of this study so far was actually a bit of a lucky break (for science, not for Mike). Over the course of the experiment, Mike developed type 2 diabetes. And not only did we get to pretty much watch this happen in real time, but we also got to see that it might have been caused in a totally unexpected way—a respiratory syncytial virus (RSV) infection. To my knowledge, this is the first time the progression to type 2 diabetes has been seen to be caused by a virus and also seen in such detail.\u003c/p>\n\u003cp>Here is the data:\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/2013/08/12/virus-induced-type-2-diabetes/msglucose2/\" rel=\"attachment wp-att-6826\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-6826\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/MSglucose2.jpg\" alt=\"MSglucose2\" width=\"479\" height=\"265\">\u003c/a>\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>There is a lot going on here so let’s break it down. We are graphing Mike’s glucose levels over time and indicating when he developed viral infections and when he changed what he ate and how much he exercised (“lifestyle changes”). In addition, his HbA1c numbers are indicated at various times. This is a measure that gets at what his glucose levels were like over the previous three months (above 6 is trouble).\u003c/p>\n\u003cp>A person is diagnosed with type 2 diabetes when his or her fasting glucose levels get above 125 mg/dL (and a person is deemed prediabetic if his or her levels are between 100 and 125). As you can see, Mike’s glucose levels are a little high but he is not even prediabetic. He might be flirting with it around day 250 but then his glucose levels come back down.\u003c/p>\n\u003cp>Then, around day 325, his glucose levels suddenly shoot up. He is now officially diabetic. His glucose levels continue to be high for a long period thereafter.\u003c/p>\n\u003cp>This sudden spike is not how most cases of type 2 diabetes are thought to happen. The usual line is that a person’s cells slowly become more resistant to insulin which makes that person’s pancreas slowly increase its insulin production. The patient’s cells need more and more insulin to get the job done.\u003c/p>\n\u003cp>After a while, the pancreas tires out and can’t keep up with the ever increasing amounts of insulin the cells demand. The result is that the patient’s glucose levels are less and less under control until type 2 diabetes develops. This is thought to be a slow, steady process.\u003c/p>\n\u003cfigure id=\"attachment_6850\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/Glucometer.jpg\" rel=\"attachment wp-att-6850\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-6850\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/Glucometer.jpg\" alt=\"All cases of type 2 diabetes might not happen in the same way. Image courtesy of Wikimedia Commons.\" width=\"200\" height=\"353\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">All cases of type 2 diabetes might not happen in the same way. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Device_to_check_for_diabetes_3.jpg\">Wikimedia Commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>Mike’s diabetes did not follow this path. Instead of slow and steady it appeared pretty suddenly, right after a severe cold caused by an RSV infection. It certainly looks as if the viral infection did something to his body that caused his pancreas to no longer be able to make enough insulin.\u003c/p>\n\u003cp>His lab was also able to see some major changes in how his genes were being used and what was in his blood right after this infection, as his type 2 diabetes was developing. The major changes were in pathways responsible for regulating his insulin levels. Something happened that caused his insulin regulation to go completely out of whack which is probably behind his rising glucose levels.\u003c/p>\n\u003cp>At around day 380, Mike radically changed his diet and exercise to try to bring his glucose levels back under control. He cut out all sugars and began to bike regularly. As you can see, his glucose levels started dropping by day 430 or so and continued to drop until they returned to normal. His diabetes is now under control.\u003c/p>\n\u003cp>We don’t know why this worked so well in Mike’s case. It may have been so effective because he was able to catch his diabetes so early or maybe because of how his diabetes developed or for some other reason.\u003c/p>\n\u003cp>We also don’t know how common it is for a virus to cause Type 2 diabetes. Most people have doctor’s appointments every few years (and some of us even less often!) and so they might miss a sudden spike like this in their glucose levels.\u003c/p>\n\u003cp>It may also be that some people have a set of genes that makes them more likely to end up with type 2 diabetes from a viral infection. Or that some people have a set of genes that make them more likely to respond to lifestyle changes if their diabetes is caught early. Or…\u003c/p>\n\u003cp>The Snyder lab is trying to get at these and many other questions by expanding the study from one to fifty participants. The study will focus on diabetes and there are still some openings available to participate in the program. If you are interested, contact Wenyu Zhou at wenyuz@stanford.edu\u003c/p>\n\u003cp>This study will not be an easy one to join. To even be considered, participants need to:\u003c/p>\n\u003cp>1) Have family members that developed diabetes or have impaired fasting glucose (fasting plasma glucose >100 mg/dL)\u003c/p>\n\u003cp>2) Have a body mass index of 25 to 40 kg/m2, and be from age 35-65\u003c/p>\n\u003cp>3) NOT have major organ disease, active eating or psychiatric disorder, be pregnant or lactating, have heavy alcohol use, or use medications known to alter blood glucose.\u003c/p>\n\u003cp>4) Be highly motivated, given the fact that the study is for at least a two-year period and asks for a strong commitment to give blood samples every three months plus more often when they are sick.\u003c/p>\n\u003cfigure id=\"attachment_6855\" class=\"wp-caption alignleft\" style=\"max-width: 97px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/MikeSnyder.jpg\" rel=\"attachment wp-att-6855\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-6855\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/MikeSnyder.jpg\" alt=\"His type 2 diabetes is our gain. Image of Dr. Mike Snyder courtesy of Department of Genetics, Stanford University\" width=\"97\" height=\"144\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">His type 2 diabetes is our gain. Image of Dr. Mike Snyder courtesy of \u003ca href=\"http://genetics.stanford.edu/\">Department of Genetics\u003c/a>, Stanford University\u003c/figcaption>\u003c/figure>\n\u003cp>If you meet these criteria, then you will undergo a set of additional medical tests (like \u003ca href=\"http://www.nlm.nih.gov/medlineplus/ency/article/003466.htm\">glucose tolerance\u003c/a> for instance). If you make it through these, then you can officially join the study.\u003c/p>\n\u003cp>As part of the study, you can be involved in helping to better understand diabetes. Not only that but you will get your DNA sequenced and if you choose, you can learn what your DNA can tell you about your future health risks. (At this time you can’t get your DNA sequence but hopefully, at some point, the \u003ca href=\"http://en.wikipedia.org/wiki/Institutional_review_board\">IRB \u003c/a>will lighten up on this.)\u003c/p>\n\u003cp>Lucky (?) for me, I meet all the criteria and so I joined the study last week. Let me tell you, they are not lying about the motivation! Not only do they take what seemed an awful lot of blood, but they are also looking at the microbiomes (the bacterial populations) of various parts of my body. That means stool and urine samples and swabs from behind my ear, up my nose and from the top of my tongue. Yes, it is invasive but worth it (at least to me).\u003c/p>\n\u003cp>I love getting this constant stream of data and learning more about what my DNA says about me. I can also see what changes in my diet or exercise do to my glucose levels or if cinnamon actually helps control blood sugar and whatever else I can think of. Plus I get my DNA sequenced and get to help in gaining a better understanding of diabetes. Definitely a win-win for me.\u003c/p>\n\u003cp>And this won’t be the last of these studies. Mike will continue to plumb the depths of what it is to be Mike Snyder and so will keep getting poked and prodded for years to come. Undoubtedly lots more interesting findings are in his and our futures.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>This is really the start of the future of medicine. Through these studies we’ll learn what we need to test and how often based on a patient’s genetics and whatever else they find is important. This is just a baby step on the road to personalized medicine but at least we are on our way.\u003c/p>\n\n","blocks":[],"excerpt":"Some of the most interesting findings in science happen on fishing exhibitions. No, I don’t mean going out on a boat (although lots of cool things have been found that way); I mean just gathering lots of data and seeing what you can find.","status":"publish","parent":0,"modified":1704935288,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":30,"wordCount":1461},"headData":{"title":"Virus-Induced Type 2 Diabetes | KQED","description":"Some of the most interesting findings in science happen on fishing exhibitions. No, I don’t mean going out on a boat (although lots of cool things have been found that way); I mean just gathering lots of data and seeing what you can find.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Virus-Induced Type 2 Diabetes","datePublished":"2013-08-12T15:19:51.000Z","dateModified":"2024-01-11T01:08:08.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"sticky":false,"path":"/science/6821/virus-induced-type-2-diabetes","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_6845\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/RSV.jpg\" rel=\"attachment wp-att-6845\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-6845\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/RSV.jpg\" alt=\"For at least one man, it looks like this virus, RSV, might have set off his type 2 diabetes. Electron micrograph image courtesy of Wikimedia Commons.\" width=\"640\" height=\"365\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">For at least one man, it looks like this virus, RSV, might have set off his type 2 diabetes. Electron micrograph image courtesy of \u003ca href=\"http://en.wikipedia.org/wiki/File:Respiratory_syncytial_virus_01.jpg\">Wikimedia Commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>Some of the most interesting findings in science happen on fishing exhibitions. No, I don’t mean going out on a boat (although lots of cool things have been found that way); I mean just gathering lots of data and seeing what you can find.\u003c/p>\n\u003cp>Something really interesting came out of just such a project from the lab of Dr. Mike Snyder at Stanford University. He set out to study himself in every way possible over a period of a few years. His lab looked at his DNA, how his DNA was being used, what sorts of things were in his blood, what his immune system was doing and lots more. His lab also then determined how these things changed over the course of the experiment.\u003c/p>\n\u003cp>One of the most fascinating things to come out of this study so far was actually a bit of a lucky break (for science, not for Mike). Over the course of the experiment, Mike developed type 2 diabetes. And not only did we get to pretty much watch this happen in real time, but we also got to see that it might have been caused in a totally unexpected way—a respiratory syncytial virus (RSV) infection. To my knowledge, this is the first time the progression to type 2 diabetes has been seen to be caused by a virus and also seen in such detail.\u003c/p>\n\u003cp>Here is the data:\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/2013/08/12/virus-induced-type-2-diabetes/msglucose2/\" rel=\"attachment wp-att-6826\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-6826\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/MSglucose2.jpg\" alt=\"MSglucose2\" width=\"479\" height=\"265\">\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>There is a lot going on here so let’s break it down. We are graphing Mike’s glucose levels over time and indicating when he developed viral infections and when he changed what he ate and how much he exercised (“lifestyle changes”). In addition, his HbA1c numbers are indicated at various times. This is a measure that gets at what his glucose levels were like over the previous three months (above 6 is trouble).\u003c/p>\n\u003cp>A person is diagnosed with type 2 diabetes when his or her fasting glucose levels get above 125 mg/dL (and a person is deemed prediabetic if his or her levels are between 100 and 125). As you can see, Mike’s glucose levels are a little high but he is not even prediabetic. He might be flirting with it around day 250 but then his glucose levels come back down.\u003c/p>\n\u003cp>Then, around day 325, his glucose levels suddenly shoot up. He is now officially diabetic. His glucose levels continue to be high for a long period thereafter.\u003c/p>\n\u003cp>This sudden spike is not how most cases of type 2 diabetes are thought to happen. The usual line is that a person’s cells slowly become more resistant to insulin which makes that person’s pancreas slowly increase its insulin production. The patient’s cells need more and more insulin to get the job done.\u003c/p>\n\u003cp>After a while, the pancreas tires out and can’t keep up with the ever increasing amounts of insulin the cells demand. The result is that the patient’s glucose levels are less and less under control until type 2 diabetes develops. This is thought to be a slow, steady process.\u003c/p>\n\u003cfigure id=\"attachment_6850\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/Glucometer.jpg\" rel=\"attachment wp-att-6850\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-6850\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/Glucometer.jpg\" alt=\"All cases of type 2 diabetes might not happen in the same way. Image courtesy of Wikimedia Commons.\" width=\"200\" height=\"353\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">All cases of type 2 diabetes might not happen in the same way. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Device_to_check_for_diabetes_3.jpg\">Wikimedia Commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>Mike’s diabetes did not follow this path. Instead of slow and steady it appeared pretty suddenly, right after a severe cold caused by an RSV infection. It certainly looks as if the viral infection did something to his body that caused his pancreas to no longer be able to make enough insulin.\u003c/p>\n\u003cp>His lab was also able to see some major changes in how his genes were being used and what was in his blood right after this infection, as his type 2 diabetes was developing. The major changes were in pathways responsible for regulating his insulin levels. Something happened that caused his insulin regulation to go completely out of whack which is probably behind his rising glucose levels.\u003c/p>\n\u003cp>At around day 380, Mike radically changed his diet and exercise to try to bring his glucose levels back under control. He cut out all sugars and began to bike regularly. As you can see, his glucose levels started dropping by day 430 or so and continued to drop until they returned to normal. His diabetes is now under control.\u003c/p>\n\u003cp>We don’t know why this worked so well in Mike’s case. It may have been so effective because he was able to catch his diabetes so early or maybe because of how his diabetes developed or for some other reason.\u003c/p>\n\u003cp>We also don’t know how common it is for a virus to cause Type 2 diabetes. Most people have doctor’s appointments every few years (and some of us even less often!) and so they might miss a sudden spike like this in their glucose levels.\u003c/p>\n\u003cp>It may also be that some people have a set of genes that makes them more likely to end up with type 2 diabetes from a viral infection. Or that some people have a set of genes that make them more likely to respond to lifestyle changes if their diabetes is caught early. Or…\u003c/p>\n\u003cp>The Snyder lab is trying to get at these and many other questions by expanding the study from one to fifty participants. The study will focus on diabetes and there are still some openings available to participate in the program. If you are interested, contact Wenyu Zhou at wenyuz@stanford.edu\u003c/p>\n\u003cp>This study will not be an easy one to join. To even be considered, participants need to:\u003c/p>\n\u003cp>1) Have family members that developed diabetes or have impaired fasting glucose (fasting plasma glucose >100 mg/dL)\u003c/p>\n\u003cp>2) Have a body mass index of 25 to 40 kg/m2, and be from age 35-65\u003c/p>\n\u003cp>3) NOT have major organ disease, active eating or psychiatric disorder, be pregnant or lactating, have heavy alcohol use, or use medications known to alter blood glucose.\u003c/p>\n\u003cp>4) Be highly motivated, given the fact that the study is for at least a two-year period and asks for a strong commitment to give blood samples every three months plus more often when they are sick.\u003c/p>\n\u003cfigure id=\"attachment_6855\" class=\"wp-caption alignleft\" style=\"max-width: 97px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/MikeSnyder.jpg\" rel=\"attachment wp-att-6855\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-6855\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/08/MikeSnyder.jpg\" alt=\"His type 2 diabetes is our gain. Image of Dr. Mike Snyder courtesy of Department of Genetics, Stanford University\" width=\"97\" height=\"144\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">His type 2 diabetes is our gain. Image of Dr. Mike Snyder courtesy of \u003ca href=\"http://genetics.stanford.edu/\">Department of Genetics\u003c/a>, Stanford University\u003c/figcaption>\u003c/figure>\n\u003cp>If you meet these criteria, then you will undergo a set of additional medical tests (like \u003ca href=\"http://www.nlm.nih.gov/medlineplus/ency/article/003466.htm\">glucose tolerance\u003c/a> for instance). If you make it through these, then you can officially join the study.\u003c/p>\n\u003cp>As part of the study, you can be involved in helping to better understand diabetes. Not only that but you will get your DNA sequenced and if you choose, you can learn what your DNA can tell you about your future health risks. (At this time you can’t get your DNA sequence but hopefully, at some point, the \u003ca href=\"http://en.wikipedia.org/wiki/Institutional_review_board\">IRB \u003c/a>will lighten up on this.)\u003c/p>\n\u003cp>Lucky (?) for me, I meet all the criteria and so I joined the study last week. Let me tell you, they are not lying about the motivation! Not only do they take what seemed an awful lot of blood, but they are also looking at the microbiomes (the bacterial populations) of various parts of my body. That means stool and urine samples and swabs from behind my ear, up my nose and from the top of my tongue. Yes, it is invasive but worth it (at least to me).\u003c/p>\n\u003cp>I love getting this constant stream of data and learning more about what my DNA says about me. I can also see what changes in my diet or exercise do to my glucose levels or if cinnamon actually helps control blood sugar and whatever else I can think of. Plus I get my DNA sequenced and get to help in gaining a better understanding of diabetes. Definitely a win-win for me.\u003c/p>\n\u003cp>And this won’t be the last of these studies. Mike will continue to plumb the depths of what it is to be Mike Snyder and so will keep getting poked and prodded for years to come. Undoubtedly lots more interesting findings are in his and our futures.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>This is really the start of the future of medicine. Through these studies we’ll learn what we need to test and how often based on a patient’s genetics and whatever else they find is important. This is just a baby step on the road to personalized medicine but at least we are on our way.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/6821/virus-induced-type-2-diabetes","authors":["6177"],"categories":["science_30","science_39"],"tags":["science_233","science_326"],"featImg":"science_6826","label":"science"},"science_4323":{"type":"posts","id":"science_4323","meta":{"index":"posts_1591205157","site":"science","id":"4323","score":null,"sort":[1371147660000]},"guestAuthors":[],"slug":"opening-the-gene-box-of-a-key-ocean-species","title":"Opening the Gene Box of a Key Ocean Species","publishDate":1371147660,"format":"aside","headTitle":"Opening the Gene Box of a Key Ocean Species | KQED","labelTerm":{},"content":"\u003cfigure id=\"attachment_4324\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/EHux.gif\" rel=\"attachment wp-att-4324\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/EHux.gif\" alt=\"Emiliania huxleyi\" width=\"640\" height=\"360\" class=\"size-full wp-image-4324\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">\u003ci>Emiliania huxleyi\u003c/i> is a one-celled alga that lives inside a shell of coccoliths. Courtesy Gerhard Langer, Alfred Wegener Institute\u003c/figcaption>\u003c/figure>\n\u003cp>This week in the journal \u003ci>Nature\u003c/i>, a worldwide team of 75 scientists revealed the genetic blueprint of the one-celled alga \u003ci>Emiliania huxleyi\u003c/i>, which may be the most important species you’ve never heard of. The genomes of the domestic dog and cat are interesting, but the \u003ci>E. huxleyi\u003c/i> genome is a much bigger story. Some day this organism may become another of our partner species, as vital to us as yeast.\u003c/p>\n\u003cp>Oceanographers of all kinds know \u003ci>Emiliania huxleyi\u003c/i> by the nickname “Ehux,” and that’s what I’ll call it too. Among the marine algae, Ehux is classified as a coccolithophore, so named because it builds loose shells around itself made of coccoliths. Coccoliths, in turn, are the intricate disks seen in the photo above at high magnification. The fate of Earth’s changing climate may ride on coccoliths.\u003c/p>\n\u003cp>In the world’s atmospheric carbon cycle, the ocean is ultimately in charge. And in the ocean’s carbon cycle, Ehux is a keystone species. To make coccoliths, Ehux takes carbon dioxide dissolved in seawater and combines it with calcium ions in the water to make calcium carbonate (the mineral calcite), somehow rendering its spiky crystals into shapes elegant enough to inspire new forms of pasta. CO\u003csub>2\u003c/sub> from the air replaces what’s removed from the seawater. \u003c/p>\n\u003cp>Coccolithophores are the single largest producer of biogenic calcium carbonate on Earth, and Ehux is their leading species. Ehux grows in every part of the ocean except around the frozen poles. It’s prone to enormous blooms—bursts of reproduction that may cover areas as large as California. Ehux blooms, with their uncountable numbers of coccoliths, reflect so much light that they turn the water a milky blue that is easily monitored by satellites. \u003c/p>\n\u003cfigure id=\"attachment_4325\" class=\"wp-caption aligncenter\" style=\"max-width: 400px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/ehuxbloom.jpg\" rel=\"attachment wp-att-4325\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/ehuxbloom.jpg\" alt=\"Ehux bloom\" width=\"400\" height=\"240\" class=\"size-full wp-image-4325\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">A large bloom of \u003ci>Emiliania huxleyi\u003c/i> in the North Atlantic. NASA image\u003c/figcaption>\u003c/figure>\n\u003cp>Shed coccoliths drift down to the seafloor, and in favorable times in the geologic past they have formed beds of chalk. (The climax era of the dinosaurs, the Cretaceous Period, got its name from the thick chalk beds of Europe.) Chalk, and the coccoliths that compose it, represent carbon removed from the atmosphere. \u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Another special skill of Ehux is turning sulfur compounds into the gas dimethyl sulfide, a major ingredient in the formation of sea clouds. Its dual roles in cloud formation and CO\u003csub>2\u003c/sub> regulation put Ehux at the crux of global climate. As atmospheric carbon dioxide rises today we need to learn, as fast as possible, exactly how nature handles it. The open-access \u003ci>Nature\u003c/i> paper promises to put our hands on Ehux’s genetic toolkit.\u003c/p>\n\u003cp>What can we do with that? The possible benefits range from pure science to pure technology.\u003c/p>\n\u003cp>\u003ci>Emiliania huxleyi\u003c/i>‘s genome turns out to be as big as that of a full-grown land plant, at 141 million bases. That’s one reason the gene-mapping project took ten years. Another reason is that the genome is an extraordinarily diverse “pan genome,” with a core set of genes and a large set of optional ones suited to particular environments. The pan genome enables Ehux to cope with a wide range of limiting conditions like low nutrient levels and strong ultraviolet radiation. The research team found that Ehux strains in different oceans were less than 80 percent similar—compare that to humans, who are 99 percent similar around the world. This is the first pan genome found outside bacteria. And Ehux may also be as adept as bacteria at gene-swapping. These factors make Ehux extremely adaptable and account for its worldwide abundance.\u003c/p>\n\u003cp>We can make use of genes that control so many things. “\u003ci>E. huxleyi\u003c/i> synthesizes unusual lipids that are used as nutritional/feedstock supplements, polymer precursors and petrochemical replacements,” the authors note. If we are to master the science of making \u003ca href=\"http://science.kqed.org/quest/audio/biofuels-face-a-reality-check/\">biofuels\u003c/a> and sustainable plastics from algae, we must domesticate Ehux or a species like it. Perhaps we can also train it to build nanostructures other than coccoliths, with possible applications that include optical-electronic technology and medicine.\u003c/p>\n\u003cp>The \u003ci>Nature\u003c/i> paper, “Pan genome of the phytoplankton \u003ci>Emiliania\u003c/i> underpins its global distribution,” \u003ca href=\"http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12221.html\">is available in full to all readers\u003c/a>. It is thick reading, but dense with meaning and promise.\u003c/p>\n\u003cp>The name \u003ci>Emiliania huxleyi\u003c/i> honors achievements of two great polymaths in Earth science: \u003ca href=\"http://www.as.miami.edu/geology/emiliani\">Cesare Emiliani\u003c/a> (1922–1995), founder of paleoclimatology, and \u003ca href=\"https://en.wikipedia.org/wiki/Thomas_Huxley\">Thomas Henry Huxley\u003c/a> (1825–1895), discoverer of coccoliths. Learn more about Ehux at the \u003ca>Ehux home page\u003c/a>. \u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Several California institutions were part of this effort, most notably the Department of Energy’s \u003ca href=\"http://www.jgi.doe.gov/News/news_13_06_12.html\">Joint Genome Institute\u003c/a> in Walnut Creek. Others included Cal State San Marcos, the Craig Venter Institute, Monterey Bay Aquarium Research Institute, UC Santa Barbara and Cal State Chico.\u003c/p>\n\n","blocks":[],"excerpt":"The genome of the one-celled alga Emiliania huxleyi, the most important species you've never heard of, is now open for business.","status":"publish","parent":0,"modified":1704935630,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":14,"wordCount":825},"headData":{"title":"Opening the Gene Box of a Key Ocean Species | KQED","description":"The genome of the one-celled alga Emiliania huxleyi, the most important species you've never heard of, is now open for business.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Opening the Gene Box of a Key Ocean Species","datePublished":"2013-06-13T18:21:00.000Z","dateModified":"2024-01-11T01:13:50.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"source":"KQED Science","sourceUrl":"https://ww2.kqed.org/science/","sticky":false,"path":"/science/4323/opening-the-gene-box-of-a-key-ocean-species","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_4324\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/EHux.gif\" rel=\"attachment wp-att-4324\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/EHux.gif\" alt=\"Emiliania huxleyi\" width=\"640\" height=\"360\" class=\"size-full wp-image-4324\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">\u003ci>Emiliania huxleyi\u003c/i> is a one-celled alga that lives inside a shell of coccoliths. Courtesy Gerhard Langer, Alfred Wegener Institute\u003c/figcaption>\u003c/figure>\n\u003cp>This week in the journal \u003ci>Nature\u003c/i>, a worldwide team of 75 scientists revealed the genetic blueprint of the one-celled alga \u003ci>Emiliania huxleyi\u003c/i>, which may be the most important species you’ve never heard of. The genomes of the domestic dog and cat are interesting, but the \u003ci>E. huxleyi\u003c/i> genome is a much bigger story. Some day this organism may become another of our partner species, as vital to us as yeast.\u003c/p>\n\u003cp>Oceanographers of all kinds know \u003ci>Emiliania huxleyi\u003c/i> by the nickname “Ehux,” and that’s what I’ll call it too. Among the marine algae, Ehux is classified as a coccolithophore, so named because it builds loose shells around itself made of coccoliths. Coccoliths, in turn, are the intricate disks seen in the photo above at high magnification. The fate of Earth’s changing climate may ride on coccoliths.\u003c/p>\n\u003cp>In the world’s atmospheric carbon cycle, the ocean is ultimately in charge. And in the ocean’s carbon cycle, Ehux is a keystone species. To make coccoliths, Ehux takes carbon dioxide dissolved in seawater and combines it with calcium ions in the water to make calcium carbonate (the mineral calcite), somehow rendering its spiky crystals into shapes elegant enough to inspire new forms of pasta. CO\u003csub>2\u003c/sub> from the air replaces what’s removed from the seawater. \u003c/p>\n\u003cp>Coccolithophores are the single largest producer of biogenic calcium carbonate on Earth, and Ehux is their leading species. Ehux grows in every part of the ocean except around the frozen poles. It’s prone to enormous blooms—bursts of reproduction that may cover areas as large as California. Ehux blooms, with their uncountable numbers of coccoliths, reflect so much light that they turn the water a milky blue that is easily monitored by satellites. \u003c/p>\n\u003cfigure id=\"attachment_4325\" class=\"wp-caption aligncenter\" style=\"max-width: 400px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/ehuxbloom.jpg\" rel=\"attachment wp-att-4325\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/06/ehuxbloom.jpg\" alt=\"Ehux bloom\" width=\"400\" height=\"240\" class=\"size-full wp-image-4325\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">A large bloom of \u003ci>Emiliania huxleyi\u003c/i> in the North Atlantic. NASA image\u003c/figcaption>\u003c/figure>\n\u003cp>Shed coccoliths drift down to the seafloor, and in favorable times in the geologic past they have formed beds of chalk. (The climax era of the dinosaurs, the Cretaceous Period, got its name from the thick chalk beds of Europe.) Chalk, and the coccoliths that compose it, represent carbon removed from the atmosphere. \u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Another special skill of Ehux is turning sulfur compounds into the gas dimethyl sulfide, a major ingredient in the formation of sea clouds. Its dual roles in cloud formation and CO\u003csub>2\u003c/sub> regulation put Ehux at the crux of global climate. As atmospheric carbon dioxide rises today we need to learn, as fast as possible, exactly how nature handles it. The open-access \u003ci>Nature\u003c/i> paper promises to put our hands on Ehux’s genetic toolkit.\u003c/p>\n\u003cp>What can we do with that? The possible benefits range from pure science to pure technology.\u003c/p>\n\u003cp>\u003ci>Emiliania huxleyi\u003c/i>‘s genome turns out to be as big as that of a full-grown land plant, at 141 million bases. That’s one reason the gene-mapping project took ten years. Another reason is that the genome is an extraordinarily diverse “pan genome,” with a core set of genes and a large set of optional ones suited to particular environments. The pan genome enables Ehux to cope with a wide range of limiting conditions like low nutrient levels and strong ultraviolet radiation. The research team found that Ehux strains in different oceans were less than 80 percent similar—compare that to humans, who are 99 percent similar around the world. This is the first pan genome found outside bacteria. And Ehux may also be as adept as bacteria at gene-swapping. These factors make Ehux extremely adaptable and account for its worldwide abundance.\u003c/p>\n\u003cp>We can make use of genes that control so many things. “\u003ci>E. huxleyi\u003c/i> synthesizes unusual lipids that are used as nutritional/feedstock supplements, polymer precursors and petrochemical replacements,” the authors note. If we are to master the science of making \u003ca href=\"http://science.kqed.org/quest/audio/biofuels-face-a-reality-check/\">biofuels\u003c/a> and sustainable plastics from algae, we must domesticate Ehux or a species like it. Perhaps we can also train it to build nanostructures other than coccoliths, with possible applications that include optical-electronic technology and medicine.\u003c/p>\n\u003cp>The \u003ci>Nature\u003c/i> paper, “Pan genome of the phytoplankton \u003ci>Emiliania\u003c/i> underpins its global distribution,” \u003ca href=\"http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12221.html\">is available in full to all readers\u003c/a>. It is thick reading, but dense with meaning and promise.\u003c/p>\n\u003cp>The name \u003ci>Emiliania huxleyi\u003c/i> honors achievements of two great polymaths in Earth science: \u003ca href=\"http://www.as.miami.edu/geology/emiliani\">Cesare Emiliani\u003c/a> (1922–1995), founder of paleoclimatology, and \u003ca href=\"https://en.wikipedia.org/wiki/Thomas_Huxley\">Thomas Henry Huxley\u003c/a> (1825–1895), discoverer of coccoliths. Learn more about Ehux at the \u003ca>Ehux home page\u003c/a>. \u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Several California institutions were part of this effort, most notably the Department of Energy’s \u003ca href=\"http://www.jgi.doe.gov/News/news_13_06_12.html\">Joint Genome Institute\u003c/a> in Walnut Creek. Others included Cal State San Marcos, the Craig Venter Institute, Monterey Bay Aquarium Research Institute, UC Santa Barbara and Cal State Chico.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/4323/opening-the-gene-box-of-a-key-ocean-species","authors":["6228"],"series":["science_2625"],"categories":["science_31","science_38"],"tags":["science_323","science_327","science_326","science_325","science_309"],"featImg":"science_4324","label":"source_science_4323"}},"programsReducer":{"possible":{"id":"possible","title":"Possible","info":"Possible is hosted by entrepreneur Reid Hoffman and writer Aria Finger. 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Hosted by journalists of color, the show tackles the subject of race head-on, exploring how it impacts every part of society — from politics and pop culture to history, sports and more.\u003cbr />\u003cbr />\u003cem>Life Kit\u003c/em>, which will be in the second part of the hour, guides you through spaces and feelings no one prepares you for — from finances to mental health, from workplace microaggressions to imposter syndrome, from relationships to parenting. The show features experts with real world experience and shares their knowledge. 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As a non-partisan forum, The Club brings to the public airwaves diverse viewpoints on important topics. The Club's weekly radio broadcast - the oldest in the U.S., dating back to 1924 - is carried across the nation on public radio stations and is now podcasting. Our website archive features audio of our recent programs, as well as selected speeches from our long and distinguished history. 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