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This Week in Genome Research: Sep 2, 2009

The September issue of Genome Research is available, and it's dedicated to personal genomics and genetic variation. Two papers cover the sequencing of African and Korean individuals. In one, scientists led by Kevin McKernan at Life Technologies used the SOLiD instrument to sequence an African individual, finding almost four million SNPs, 19 percent of which are new, and mapped the structural variation of the genome. Scientists from South Korea sequenced the first genome of a Korean individual, finding more than 420,000 novel SNPs.

In other interesting work, University of Utah's Lynn Jorde is senior author on a paper that analyzed more than 8,000 structural variants specific to the HuRef, finding that many of them are "mobile element-related." In fact, he and his team found that about 10 percent of indels longer than 100 base pairs are caused by mobile element-associated events.

Several new bioinformatic tools are presented in this issue, too. David Weese at the Free University of Berlin and colleagues present a new sequence mapping algorithm called RazerS. It allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance, they say, and "provides a seamless tradeoff between sensitivity and running time." Martin Krzywinski at Canada's Michael Smith Genome Sciences Center is first author on a paper that presents Circos, a visualization tool for comparing genomes. Circos, they write, "uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements."

Two more papers look at genomics and clinical research. One details the beginnings of the ClinSeq Project, a pilot program that will study the genetics behind health, disease, and drug response. Initially, the project, led by Eric Green, will enroll 1,000 patients and sequence 300 to 400 genes thought to be associated with atherosclerosis. In other work, scientists have developed the Integrating Biology and the Bedside resource that will apply electronic health recording techniques to GWAS studies.

The Scan

mRNA-Based Vaccine on the Way in China

China may soon have its own mRNA-based vaccine, according to Nature News.

Arranged Killing, Fraud Alleged by Prosecutors

The Wall Street Journal reports that prosecutors allege that the co-founder of a biotech arranged to have a business associate who threatened to expose him as a fraud killed.

Whirlwind Decade of CRISPR

The New York Times looks back at the 10 years since the University of California, Berkeley's Jennifer Doudna and her colleagues published their CRISPR paper.

PNAS Papers on Blue Cone Monochromacy Structural Variants, HIV-1 Mutant, T-ALL

In PNAS this week: structural variants linked to blue cone monochromacy, HIV-1 variants affecting the matrix protein p17, and more.