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Genomics In The Journals: Dec 1, 2011

NEW YORK (GenomeWeb News) – An international research team has conducted a meta-analysis of genome-wide association studies to gain a better understanding of the genetics of blood cell formation. The team, led by researchers from the Institute of Genetic Epidemiology at the Helmholtz Center Munich and the University of Cambridge, assessed data from studies that included around 68,000 individuals of European, South Asian, and East Asian ancestry and identified 68 genomic loci associated with platelet count and platelet volume. They further examined the role of the genes identified in the fruit fly and zebrafish, identifying 11 of the genes as novel regulators of blood cell formation.

"We anticipate that these resources will help to advance megakaryopoiesis research, to address key questions in blood stem-cell biology and to propose new targets for the treatment of haematological disorders," the researchers concluded in their paper, which is published in this week's issue of Nature.

Researchers from Massachusetts General Hospital have discovered that a small percentage of glioblastomas contain amplification of multiple receptor tyrosine kinase genes, specifically EGFR, MET, and PDGFA. The research team mined data from the Cancer Genome Atlas and discovered that 5 percent of the glioblastoma samples contained two or three of the genes at the same time, a finding they called surprising.

The also further screened 350 glioblastoma samples compiled by the NGH Department of Pathology for amplification and found extra copies of two or three of the genes in 16 of the cases. They reported their findings this week in the online version of Cancer Cell.

"This new type of genetic variation within a tumor has not been described before — probably because of the technical limitations of whole-genome analysis," author John Iafrate, an MGH researcher and associate professor of pathology at Harvard Medical School, said in a statement. "We now need to perform functional experiments to explore interactions between subpopulations within a tumor and determine to what extent this may occur in other types of tumors."

Two researchers have offered suggestions for improving validation practices in a variety of 'omics research disciplines in a perspective article published in Science. John Ioannidis of Stanford University and Muin Khoury of the Office of Public Health Genomics at the US Centers for Disease Control and Prevention outline the challenges for researchers in validating discoveries and reproducing results from 'omics research. They offer several strategies intended to enhance validation practices and utility of such information including increased availability of public data and protocols, funding incentives from federal agencies, and reproducibility rewards or penalties.

They also noted that as 'omics technologies are used for clinical purposes, "randomized clinical trials are need to assess whether 'omics information improves patient outcomes."

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

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Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

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GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

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