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Genomics In The Journals: Sep 15, 2011

NEW YORK (GenomeWeb News) – In The Lancet, members of the Australian Asthma Genetics Consortium report on two new risk loci for asthma: a SNP in the interleukin-6 receptor gene IL6R and a chromosome 11 locus that's most closely linked to allergic asthma.

The team found the loci through a genome-wide association study on 2,669 Australian asthma patients and 4,528 Australian controls, followed by replication studies and meta-analyses using data for tens of thousands more individuals, including those assessed by the GABRIEL Consortium. Because the IL6R risk variant identified seems to enhance the gene's activity, researchers reasoned that drugs such as tocilizumab that block this receptor might eventually prove useful for treating some forms of asthma.

"The IL6R association further supports the hypothesis that cytokine signaling dysregulation affects asthma risk," Queensland Institute of Medical Research investigator Manuel Ferreira, the study's corresponding author, and colleagues wrote, "and raises the possibility that an IL6R antagonist (tocilizumab) may be effective to treat the disease, perhaps in a genotype-dependent manner."

A Japanese- and German-led team used whole-exome sequencing, combined with array- and RNA-sequencing analyses, to find splicing glitches contributing to a group of blood cell production disorders known as myelodysplasia — findings they describe in Nature. Their exome sequencing experiments on matched tumor and normal samples from 29 individuals with myelodysplasia uncovered RNA splicing gene mutations in more than half of the cases. Accordingly, the team decided to screen for splicing-related alterations and do more extensive splicing analyses in hundreds more myelodysplasia tumor samples. In so doing, they found that some 45 to 85 percent of myelodysplasia patients showed some sort of RNA splicing defect, though the prevalence of these mutations varied depending on the myelodysplasia subtype.

Researchers used the Illumina GAIIx platform to sequence 246 suspicious genes (1.43 million bases of DNA) in 11 unrelated individuals from Israeli Jewish and Palestinian Arab families in an effort to find mutations behind hereditary hearing loss. The search led to hearing loss-associated mutations in CDH23, MYO15A, TECTA, WFS1, and TMC1 genes, including a TMC1 risk allele that was subsequently found in 34 percent of the hearing loss cases that they tested in individuals of Moroccan Jewish ancestry. By evaluating genes implicated in the discovery stage of the study in others with hearing loss, the researchers tracked down hearing loss-related mutations in 20 more individuals. The study is appearing in a special, exome sequencing-focused issue of Genome Biology.

"Our two-tier approach allowed us to scan exons of genes thought to be involved in hereditary deafness and their flanking sequences," senior author Karen Avraham, a human molecular genetic and biochemistry researcher at Tel Aviv University, said in a statement. "This meant that we were able to quickly target specific genes and find multiple mutations responsible for hearing loss."

Non small-cell lung cancer tumors from smokers have more copy number changes than those from non-smokers or light smokers, according to a study in the early, online edition of the Proceedings of the National Academy of Sciences. American and Norwegian researchers brought together smoking history information and copy number data for hundreds of non small-cell tumor samples. The team found that individuals in the group classified as heavy smokers had more copy number changes, specifically gains, in their tumors than individuals in the light smoker and non-smoker group. On the other hand, tumors in the light smoker/non-smoker group were more likely to be copy number losses affecting non-coding sequences.

"The discrepancy between gains and losses suggests that different mechanisms may exist for the genome impact of cigarette smoking," Harvard School of Public Heath researcher David Christiani, the study's senior author, and colleagues explained. "For gains, smoking executes its oncogenic effect by increasing the event of [copy number] changes. In contrast, for losses smoking does not increase [copy number alteration] events but increases the proportion of genes being affected."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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