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This Week in Nature: Jan 28, 2010

In the advance, online edition of Nature Genetics this week, National Cancer Institute investigators Stephen Chanock and Patricia Hartge led a team of researchers who did a genome-wide association study to find variants linked to pancreatic cancer risk. The GWAS involved 3,851 cases and 3,934 controls from a dozen prospective studies and turned up eight SNPs at three loci on chromosomes 1, 5, and 13, including a chromosome 5 locus previously implicated in other cancer types.

An international research team reports that they have identified genetic variants associated with Arabidopsis lyrata adaptation to soils containing high heavy metal levels. By re-sequencing pooled DNA from plants adapted to this so-called serpentine soil and pooled DNA from non-serpentine soil grown A. lyrata, the researchers found genetic polymorphisms linked to serpentine soil adaptation. Among them: variants affecting loci involved in heavy metal detoxification and mineral transport.

A Harvard University-led team reports in Nature Medicine online that they have used an integrated genomics approach to find a region on chromosome 8 that's often over-expressed or amplified in treatment-resistant, recurrent breast cancer. In their follow-up experiments, the researchers show that knocking down either of the two genes in this region — YWHAZ or LAPTM4B — makes tumor cells sensitive to anthracycline-based chemotherapy.

Finally, today's online edition of Nature is scheduled to include a paper on stem cell reprogramming by a Stanford University team. By testing a set of 19 candidate genes, the researchers demonstrated that they could directly program mouse embryonic and post-natal fibroblasts to become neurons using three transcription factors — and without first generating pluripotent cells. "Generation of [induced neuronal] cells from non-neural lineages could have important implications for studies of neural development, neurological disease modeling, and regenerative medicine," they write.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

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.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

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

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.