Researchers Create New Way To Locate Big Genetic Variants

December 28, 2009

(PhysOrg.com) -- Yale University researchers, analyzing hundreds of billions of bits of genetic information, have collated and standardized 2,000 signposts that mark the boundaries of large blocks of human genomic variants.

This library of genomic “breakpoints’’ was published in the Dec. 27th edition of .

sequencing, or the ordering of the billions of nucleotides that make up the genomes of living organisms, has been a key tool in modern biological research. The quest for variants that change the function of genes began by first focusing on changes, called single (SNPs) in a single genetic letter (or nucleotide). Advances in sequencing technology now enable scientists to decode the genome more rapidly and efficiently, and have paved the way for identifying large block variants, called structural variants or SVs.

These variants cause more nucleotide differences between individuals than SNPs. Some SVs, in fact, involve thousands of base pairs and can wipe out whole genes or create additional copies of other genes that can have major effects on an organism. SVs are sometimes associated with diseases such as cancer and HIV and also with developmental disorders.

Graduate students Hugo Lam and Jasmine Mu and their colleagues in the research team led by Mark Gerstein, professor of molecular biophysics and biochemistry, computer science, and bioinformatics, analyzed data from recent personal genomic studies, such as the 1000 Genomes Project, to identify precise “breakpoint” locations of SVs.

They have shown how this library of breakpoints can help researchers rapidly scan for and characterize SVs in a newly sequenced personal genome. In fact, the sequences in the library can even be put on a commercial SNP chip, which can then be used to assess SVs quickly in population studies.

Explore further: Johns Hopkins to participate in 1000 Genomes Project

Related Stories

Johns Hopkins to participate in 1000 Genomes Project

January 22, 2008

Researchers at the McKusick-Nathans Institute of Genetic Medicine (IGM) at Johns Hopkins will join other national and international scientists in the 1000 Genomes Project, an ambitious effort that will involve sequencing ...

Recommended for you

Genomes uncover life's early history

August 24, 2015

A University of Manchester scientist is part of a team which has carried out one of the biggest ever analyses of genomes on life of all forms.

Rare nautilus sighted for the first time in three decades

August 25, 2015

In early August, biologist Peter Ward returned from the South Pacific with news that he encountered an old friend, one he hadn't seen in over three decades. The University of Washington professor had seen what he considers ...

Why a mutant rice called Big Grain1 yields such big grains

August 24, 2015

(Phys.org)—Rice is one of the most important staple crops grown by humans—very possibly the most important in history. With 4.3 billion inhabitants, Asia is home to 60 percent of the world's population, so it's unsurprising ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.