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Genomics In The Journals: Oct 27, 2011

NEW YORK (GenomeWeb News) – Japanese researchers did a genome-wide association study involving thousands of individuals from Japan to track down variants near the chromosome 10 gene LBX1 that increase the risk of a spinal curvature condition called adolescent idiopathic scoliosis. Because adolescent idiopathic scoliosis is 10 times more common in females than males, all 1,050 cases and 1,474 controls who were genotyped for the GWAS were female. The top three candidate SNPs found in the discovery stage of the study — all in a linkage disequilibrium block on chromosome 10 — were subsequently verified in 326 more adolescent idiopathic scoliosis cases and another 9,823 controls. The findings appear in Nature Genetics.

In the Proceedings of the National Academy of Sciences, researchers from the Fred Hutchinson Cancer Research Center, the University of Washington, and Duke University describe the combined nuclease digestion and paired-end sequencing strategy that they used to look at chromatin patterns in the genome of the budding yeast Saccharomyces cerevisiae. By modifying the protocol for preparing Illumina paired-end libraries, the team reported, they were able to look at bits of DNA as small as 25 base pairs, allowing them to map nucleosome, sub-nucleosome, and transcription factor occupancy patterns in the model organism.

In Genome Biology, a Chinese research team reports that it has sequenced the 516 million base draft genome of Clonorchis sinensis, a liver fluke that infects humans who have consumed undercooked fish containing the parasite. Over time, C. sinensis infections can result in diseases of the liver, gall bladder, or bile duct disease, including a form of bile duct cancer. Although the team identified more than 16,000 predicted protein-coding genes in the fluke genome, many corresponding to metabolic machinery, they did not find genes coding for some critical fatty acid biosynthesis components — genes that are also missing from the genomes of two other liver flukes.

"This means that liver flukes evolved to use their host's fatty acids before the species separated," corresponding author Xinbing Yu, a parasitology and tropical disease researcher at Sun Yat-sen University in China, said in a statement. "Genomic information is not only able to help us understand evolution but the sequence of C. sinensis is helping us understand liver fluke biology."

Genetic variants in at least three genes can influence an individual's risk of developing early stent thrombosis, a serious complication that can occur in those with coronary stent implants, according to a Journal of the American Medical Association study by French and American researchers. The group looked at whether 23 variants in 15 genes could predict early stent thrombosis events, using genotype and other data for 123 patients who had and 246 patients who had not experienced this complication. Results of the case-control study, conducted at 10 French hospitals over more than three years, indicate that four variants in CYP2C19, ABCB1, and ITGB3 genes that influence response to the blood thinner clopidogrel or affect blood platelet function are also associated with early stent thrombosis.

"Our research indicates that early stent thrombosis is strongly related to ineffectiveness of clopidogrel in certain patients," co-first author Jean-Sebastien Hulot, director of pharmacogenomics and personalized therapeutics for Mount Sinai School of Medicine's Cardiovascular Research Center, said in a statement. "Now that we have a clearer understanding of the mechanism behind the development of stent thrombosis, we can take preventive measures to protect our patients from this deadly complication."

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

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