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Last Updated: Oct 11, 2012 - 10:22:56 PM
Research Article
Human Genome
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Reinventing Human genome

Nov 23, 2006 - 4:27:05 PM , Reviewed by: Venkat Yelamanchili
CNVs have already been linked with susceptibility to Alzheimer's disease, kidney disease and HIV, among others, and the new map will help researchers to make connections to other conditions. "There's a general expectation that these things are quite influential," Wigler says.

[RxPG] Nearly six years after the sequence of the human genome was sketched out, one might assume that researchers had worked out what all that DNA means. But a new investigation has left them wondering just how similar one person's genome is to another's.

Geneticists have generally assumed that your string of DNA 'letters' is 99.9% identical to that of your neighbour's, with differences in the odd individual letter. These differences make each person genetically unique — influencing everything from appearance and personality to susceptibility to disease.

But hold on, say the authors of a new study published in Nature1. They have identified surprisingly large chunks of the genome that can differ dramatically from one person to the next. "Everyone has a unique pattern," says one of the lead authors, Matthew Hurles at the Wellcome Trust Sanger Institute in Cambridge, UK.

The differences in question - made up of stretches of DNA that span tens to hundreds of thousands of chemical letters — are called 'copy-number variants', or CNVs. Within a given stretch of DNA, one person may carry one copy of a DNA segment, another may have two, three or more. The region might be completely absent from a third person's genome. And sometimes the segments are shuffled up in different ways.

These variable regions received short shrift for many years. When the human genome sequence was pieced together, they were largely glossed over, because researchers were focused on finding one overarching reference sequence — and because the repetitive nature of the segments makes them hard to sequence. "It was swept under the rug," says Michael Wigler who is also mapping CNVs at Cold Spring Harbor Laboratory, New York.

The new study, led by Hurles and Stephen Scherer of the Hospital for Sick Children in Toronto, Canada, and their colleagues is the most detailed attempt to find how CNVs are scattered across the whole human genome. To do this, they compared genome chunks from 270 people of European, African or Asian ancestry.
They found nearly 1,500 such regions, taking up some 12% of the human genome. That doesn't mean that your DNA is 12% different from mine (or 88% similar), because any two people's DNA will differ at only a handful of these spots.

According to the team's back-of-the-envelope calculations, one person's DNA is probably 99.5% similar to their neighbour's. Or a bit less. "I've tried to do the calculation and it's very complicated," says Hurles. "It all depends on how you do the accounting."

The answer is also unclear because researchers think that there are many more variable blocks of sequence that are 10,000 or 1,000 letters long and were excluded from the current study. Because of limits with their methods, the new map mainly identified variable chunks larger than 50,000 letters long.

Many of these CNVs are thought to be important in our biology. The team found that 10% of human genes are spanned by these regions, meaning that they might be doubled, deleted or otherwise jumbled in a way that could help to determine whether and when we develop diseases.

CNVs have already been linked with susceptibility to Alzheimer's disease, kidney disease and HIV, among others, and the new map will help researchers to make connections to other conditions. "There's a general expectation that these things are quite influential," Wigler says.

The new map adds to a whole library of genetic cartography that already points out other landmarks in the human genome. A lot of attention has focused on mapping the places where single letters vary between individuals (single-nucleotide polymorphisms, or SNPs). Other researchers are identifying hard-to-spot regions where a segment can be flipped around so it runs backwards.

But there is plenty more for geneticists to navigate and undoubtedly more maps to come. Some will reveal the smaller regions of variation excluded from Hurle's map. Other projects are attempting to mark every single sequence that does something biologically useful, such as making proteins or packaging up DNA into chromosomes.

The precise degree to which each person's DNA differs from another may not become clear until geneticists devise a way to read through the entire genome of many different people and compare them all in detail, something that is far too expensive and time consuming today but may become possible with the advent of faster, cheaper sequencing machines.

Scherer and his team have already lined up the only two complete human genome sequences produced by the publicly funded Human Genome Project and the private company Celera. They identified both single-letter changes and small and large regions of variation and report their results in Nature Genetics

Publication: Nature: International Scientific Journal
On the web: www.nature.com 

Funding information and declaration of competing interests: Richard Redon, Shumpei Ishikawa, Karen R. Fitch, Lars Feuk, George H. Perry, T. Daniel Andrews, Heike Fiegler, Michael H. Shapero, Andrew R. Carson, Wenwei Chen, Eun Kyung Cho, Stephanie Dallaire, Jennifer L. Freeman, Juan R. González, Mònica Gratacòs, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R. MacDonald, Christian R. Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J. Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F. Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P. Carter, Hiroyuki Aburatani, Charles Lee, Keith W. Jones, Stephen W. Scherer and Matthew E. Hurles

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 Additional information about the news article
Nature, the company's flagship and the world's foremost weekly scientific journal, was launched in 1869. See www.nature.com. Nature Genetics the first Nature research journal, followed 123 years later. Now Nature Publishing Group (NPG) publishes nine Nature research journals, seven Nature Reviews journals and four Nature Clinical Practice titles.

NPG was born in 1999, incorporating the scientific journal publications of Macmillan: Nature; the Nature research journals; and NPG academic journals (formerly Stockton Press), publishers of leading society scientific, medical and technical journals. In 2000, NPG launched three Nature Reviews, www.nature.com/reviews which now comprise seven publications focused on the life sciences. The most recent addition to the portfolio is Nature Chemical Biology, publishing significant new research at the interface between chemistry and biology. In 2004, NPG launched the first four Nature Clinical Practice journals, delivering timely, authoritative interpretations of key research developments, translating the latest findings into clinical practice.

NPG is a dynamic, innovative, creative company, committed to publishing high quality, rigorously peer-reviewed research, review and reference material; timely news; and essential career and recruitment information. NPG combines strong brands, pioneering technologies and premium information for scientific researchers in the public and private sectors, government agencies, educators and the general public. A key strength of the group is its close relationship with the scientific community; by working closely with scientists, and always placing emphasis on quality rather than quantity, NPG has taken a lead in finding innovative solutions to scientists' information needs.

With a total workforce of just over 400, NPG is small enough to offer a flexible, dynamic working environment where staff are encouraged to be creative and work independently. Moreover, NPG's global presence and variety of publishing programmes offer new and exciting career development opportunities. NPG will continue to seek new ways to provide solutions to scientists' information needs and the group will continue to expand into new markets. The scientific publishing industry is at a crossroads; NPG, with its first-class staff, excellent brands, commitment to quality, and pioneering spirit, will have a leading role in this exciting future.

NPG is a subsidiary of Macmillan Publishers Ltd, a global publishing group founded in the United Kingdom in 1843. The company operates in over 70 countries around the world serving a wide variety of markets. For more information on Macmillan Publishers Ltd go to www.macmillan.com.

Macmillan is itself owned by German-based, family run company Verlagsgruppe Georg von Holtzbrinck GmbH. Its interests include book, magazine and newspaper publishing; television; radio; and new media. Further information on Verlagsgruppe Georg von Holtzbrinck GmbH can be found at www.holtzbrinck.com/eng/index.html
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