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Genomics In The Journals: Sep 29, 2011

NEW YORK (GenomeWeb News) – Members of the IBC 50K CAD Consortium report in PLoS Genetics that they have identified new genetic variants involved in coronary artery disease in individuals of European or South Asian ancestry through a large candidate gene association study.

Using a custom gene array, researchers assessed around 2,100 genes suspected of contributing to CAD in nearly 15,600 individuals in CAD and almost 35,000 unaffected controls. They then attempted to replicate dozens of potentially associated loci in 17,121 more cases and roughly 40,500 controls. This gene-centric association approach yielded new CAD-associated variants in and around five genes, including variants that affected CAD risk in both Europeans and South Asians.

"This is one of the first genetic studies of CAD to include a significant proportion of subjects of South Asian origin, an ethnic group that has a higher risk of CAD," University of Cambridge researcher John Danesh, co-corresponding author on the study, said in a statement. "Our study shows that many of the genes that affect risk of CAD do so similarly in European Caucasians as in South Asians."


In Nature Genetics, a large international research team describes the genome-wide association meta-analysis that they used to track down sites in the genome contributing to lung function. From genotyped or imputed SNP data for 48,201 individuals of European descent enrolled through almost two-dozen past studies, the researchers found new loci linked to lung function traits — specifically forced expiratory volume in one second and the ratio of this FEV1 to forced vital capacity. They subsequently verified 16 of the new loci in tens of thousands more individuals. Those involved in the study say these and other genetic variants may eventually lead to better understanding and treating of some lung diseases related to the lung functions that they focused on for this study, including chronic obstructive pulmonary disease.

"We now need to take the knowledge gained from this study to do two things: firstly to learn more about the function of genes which contribute to the risk of developing lung diseases such as COPD, and secondly to try and develop strategies to use genetic information to improve the clinical care provided to individual patients," co-senior author Ian Hall, a University of Nottingham therapeutics and molecular medicine researcher, said in a statement.


Recurrent mutations in the RNA splicing-related gene called SF3B1 contribute to myelodysplasia, a group of chronic blood cancers that can precede leukemia, according to a New England Journal of Medicine study. Members of the International Cancer Genome Consortium's Chronic Myelodysplasia Disorders Working Group did exome sequencing on nine individuals with myelodysplasia followed by targeted gene sequencing in thousands of myelodysplasia or other cancer samples to track down the myelodysplasia-associated SF3B1 mutations. Their findings suggest the gene is mutated in roughly one-fifth of myelodysplasias, leading to an altered form of red blood cells in the bone marrow that are known as ring sideroblasts.

"[O]ur analysis showed that patients with the SF3B1 mutation had a better overall chance of survival compared to those without the mutation," Wellcome Trust Sanger Institute researcher Elli Papaemmanuil, the study's first author, said in a statement. "This suggests that the SF3B1 mutations drive a more benign form of myelodysplasia."


Stanford University researchers used a method they call "chromatin isolation by RNA purification" (ChIRP), combined with deep DNA sequencing, to find sequences and sites in the genome where long intergenic non-coding RNAs bind. The ChIRP approach, which the researchers describe in a Molecular Cell study, involves grabbing lncRNAs of interest using tiled oligonucleotides. Because these regulatory RNAs are often associated with chromatin interacting proteins and DNA, they were able to sequence DNA commingling with the ChIRP-bound lncRNAs to find lncRNA binding sites. The team demonstrated the feasibility of this strategy, mapping occupancy sites for the mammalian lncRNAs TERC and HOTAIR and a Drosophila lncRNA called roX2.

"Taken together, our research shows that our technique is widely applicable and can vastly enrich our understanding of how regulatory RNAs unlock the genome in many very specific ways," Stanford University researcher Howard Chang, the study's senior author, said in a statement.


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

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