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Genomics In The Journals: Oct 4, 2012

NEW YORK (GenomeWeb News) – An international team reports on efforts to sequence and begin analyzing a draft genome sequence for the Puerto Rican parrot, Amazona vittata, in GigaScience, an effort that was supported by local community funding.

Using DNA from a female Puerto Rican parrot, researchers generated sequence covering more than three-quarters of the parrot's 1.58 billion base pair genome to a depth of almost 27-fold. The study's authors are optimistic that the genome sequence will serve as a resource for coming up with new tools to support breeding and management programs for the critically endangered bird.

"Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species," corresponding author Taras Oleksyk, with the University of Puerto Rico-Mayagüez, and colleagues wrote, "and aid in ongoing and future conservation efforts."

In Nature Genetics, a large international team led by investigators in China outlines findings from a genome-wide association study of prostate cancer in the Han Chinese population. Through a multi-stage GWAS that involved almost 4,500 Han Chinese men with prostate cancer and more than 8,900 unaffected controls from the same population, the researchers identified prostate cancer-associated sites in the genome that were known from past studies in other populations. They also narrowed in on two new prostate cancer-linked loci. The first fell near the RAD23B and KLF4 genes on chromosome 9. The other locus, found on chromosome 19, was subsequently deemed to be in linkage disequilibrium with a germline deletion that lops off almost all of the exons in an inflammatory response regulating gene called LILRA3.

Researchers from China and Japan used comparative genomics to explore the genetic basis of rice domestication in a new Nature study.

The team sequenced plants from nearly 450 wild rice (Oryza rufipogon) accessions from different parts of the world, comparing these genomes to those of cultivated rice from 1,083 cultivated O. sativa indica and O. sativa japonica varieties. With that sequence data, the researchers were able to discern and map variants in the rice genome as well as their relationship to domestication events. For instance, their analysis uncovered dozens of apparent selective sweeps that seem to coincide with rice domestication. Together, the data suggest that rice from the japonica sub-species were first to be domesticated, likely springing from a wild rice population in southern China's Guangxi province. Cultivation of the indica sub-species, on the other hand, seems to have started more recently, apparently as the result of breeding between O. sativa japonica plants and wild rice plants native to other parts of Asia.

"The understanding of past domestication, including the selections on critical traits and the recent rapid speciation, will further guide future breeding efforts," authors of that study say. "Moreover, the great diversity in the wild rice populations, which have much more natural allelic variation than domesticated rice, will further facilitate breeding to modify crops in the post-domestication era."

A German-led group reporting in the journal Diabetes looked at the metabolomic profiles in blood samples that might foretell the onset of type 2 diabetes.

The researchers used mass spectrometry to measure the concentrations of 163 metabolites in blood samples collected from thousands of then-healthy participants through several large prospective population studies. They then looked at whether the levels of any of these blood sample metabolites corresponded to type 2 diabetes development over an average of seven years of follow-up. In the process, the team defined 14 metabolites whose levels coincided with the eventual onset of type 2 diabetes. In at least one of the cohorts considered, the levels of two metabolites were also linked to insulin sensitivity and secretion profiles, suggesting that metabolite markers might eventually help in predicting diabetes risk or managing related conditions prior to disease onset.

"In addition to simple sugars, the 14 identified metabolites include various protein components and choline-containing phospholipids which play a role in the structure of cell membranes and in the transport of blood lipids," German Institute of Human Nutrition researcher Anna Floegel, the study's lead author, said in a statement. "Our findings particularly indicate a previously unknown role of phospholipids in type 2 diabetes development."

A team based at Brigham and Women's Hospital, Harvard University, and elsewhere has discovered a new risk variant for uterine leiomyomata, commonly known as uterine fibroids, in a fatty acid synthase gene called FASN.

As they explain in the American Journal of Human Genetics, the researchers did a genome-wide SNP linkage analyses involving more than 1,100 individuals from families affected by uterine fibroids, along with genome-wide association and meta-analyses based on thousands more unrelated cases and controls. The search led to a SNP with genome-wide significant ties to uterine fibroids in FASN — a gene that the researchers subsequently found expressed at elevated levels in uterine fibroid samples compared with samples of typical muscle tissue from the wall of the uterus.

In a statement, the study's senior author Cynthia Morton, director of Brigham and Women's Hospital's Center for Uterine Fibroids, explained that the findings are promising, as the "[i]dentification of genetic risk factors may provide valuable insight into medical management."

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

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.