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This Week in PNAS: Jul 14, 2009

A consortium of scientists from Yale and EMBL, among others, used high-resolution analysis to study the genetics of Down syndrome in a paper published in the early online edition of PNAS this week. The scientists created a genetic map for 30 patients with rare segmental trisomies of various regions of HSA21 and found regions of 1.8 Mb -16.3 Mb likely to be involved in the development of eight of the cases, confirming the role of a single consensus region in causing severe Down syndrome.

Kenneth McNally studied genome-wide SNP changes in different varieties of rice, also in a paper in early online. Using resequencing microarrays to scan 100 Mb of a portion of the reference genome for 20 varieties, his team mapped 160,000 nonredundant SNPs. The study, they say, revealed the "breeding history and relationships among the 20 varieties" and is a model for using SNP data to improve rice.

In work led in part by Carlo Croce and NIH's Curtis Harris, researchers looked at the relationship between mutations in EGFR and lung cancer in patients who have never smoked, which is 15 percent of lung cancer cases, they say. MicroRNA expression profiling showed that miR-21 was up-regulated, and antisense experiments revealed that increased expression of miR-21 was "enhanced further by the activated EGFR signaling pathway ... and is a potential therapeutic target in both EGFR-mutant and wild-type cases," they write in the abstract.

Michigan's Arul Chinnaiyan was senior author on a paper that used paired-end transcriptome sequencing to find gene fusions in cancer. He and his team found 12 novel gene fusions in four commonly used cell lines, and they identified previously undescribed ETS gene fusions in prostate tumors. "Not only did a paired-end approach provide a greater dynamic range in comparison with single read based approaches, but it clearly distinguished the high-level 'driving' gene fusions, such as BCR-ABL1 and TMPRSS2-ERG, from potential lower level 'passenger' gene fusions," they say.

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.