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.