New Genome Map Tries To Capture All Human Genetic Variation

An anonymous reader shares an excerpt from MIT Technology Review: Today, researchers announced yet another version of the human genome map, which they say combines the complete DNA of 47 diverse individuals -- Africans, Native Americans, and Asians, among other groups -- into one giant genetic atlas that they say better captures the surprising genetic diversity of our species. The new map, called a "pangenome," has been a decade in the making, and researchers say it will only get bigger, creating an expanding view of the genome as they add DNA from another 300 people from around the globe. It was published in the journal Nature today. People's genomes are largely alike, but it's the hundreds of thousands of differences, often just single DNA letters, that explain why each of us is unique. The new pangenome, researchers say, should make it possible to observe this diversity in more detail than ever before, highlighting so-called evolutionary hot spots as well as thousands of surprisingly large differences, like deleted, inverted, or duplicated genes, that aren't observable in conventional studies. The pangenome relies on a mathematical concept called a graph, which you can imagine as a massive version of connect-the-dots. Each dot is a segment of DNA. To draw a particular person's genome, you start connecting the numbered dots. Each person's DNA can take a slightly different path, skipping some numbers and adding others. One payoff of the new pangenome could be better ways to diagnose rare diseases, although practical applications aren't easy to name. Instead, scientists say it's mainly giving them insight into some of the "dark matter" of the genome that's previously been hard to see, including strange regions of chromosomes that seem to share and exchange genes. For now, most biologists and doctors will stick to the existing "reference genome," the one first produced in draft form in 2001 and gradually improved. It answers most questions researchers are interested in, and all their computer tools work with it. The reason a reference genome is important is that when a new person's genome is sequenced, that sequence is projected onto the reference in order to organize and read the new data. Yet since the current reference is just one possible genome, missing bits that some people have, some information can't be analyzed and is usually ignored. Researchers call this effect "reference bias" or, more simply, the streetlamp problem. You don't see where you don't look. Officials with NIH said they hoped the new update to the genome map would make gene research more "equitable." That's because the more different your genome is from the current reference, the more information about you could be missed. The existing reference is largely the DNA of one African-American man, although it includes segments from several other people as well. "If the genome you want to analyze has sequences that are not in that reference, they will be missed in the analysis," says Deanna Church, a consultant with the business incubator General Inception, who previously held a key role at NIH managing the reference genome. "In reality, the notion that there is a 'human genome' is really the problem," she says. "The current version is the simplest model you can make. It made sense when we started ... But now we need better models."

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