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Amos Tanay and Eitan Yaffe report methods to correct biases in the Hi-C method for mapping chromosomal contacts on a genome-wide scale. Their analysis of Hi-C data shows interchromosomal aggregation of hypersensitive sites, transcriptionally active foci and other epigenetic markers of active chromatin.
Timothy Bishop and colleagues of the GenoMEL Consortium report a genome-wide association study for melanoma, identifying three new susceptibility loci.
Fanni Gergely, Geoffrey Woods and colleagues identify a disease-associated CEP63 mutation in a family with primary microcephaly. They further show that CEP63 and CEP152 interact and form a discrete ring around the proximal end of the parental centriole, implicating this complex in the regulation of centrosome number.
Mark Daly, Manuel Rivas and colleagues used next-generation sequencing to study the coding exons of 56 genes from regions previously associated with Crohn's disease. Follow-up analyses in independent case-control series confirmed association of many newly discovered rare variants with disease risk.
Stuart MacGregor and colleagues report the results of a genome-wide association study for melanoma susceptibility in an Australian population. They identify a new melanoma susceptibility locus on chromosome 1.
Patrick Sulem, Daniel Gudbjartsson, Bragi Walters and colleagues identify two low-frequency variants associated with serum uric acid levels and gout in the Icelandic population. The variants were discovered by whole-genome sequencing and are associated with two- to threefold differences in disease risk.
Using a combination of whole-genome sequencing, haplotype sharing and the genealogies of the Icelandic population, Thorunn Rafnar, Kari Stefansson and colleagues identified a rare coding mutation in the gene of a BRCA1-interacting factor, BRIP1, that confers a high relative risk of ovarian cancer.
Jim Lupski and colleagues report characterization of complex genomic rearrangements at the MECP2 and PLP1 loci. They show that all the complex rearrangement products share a common genomic organization wherein the triplicated segment is inverted and located between directly oriented duplicated genomic segments; these structures are mediated by inverted repeats that can be separated by over 300 kb.
Dirk Schübeler and colleagues report an experimental strategy to identify genetic elements that autonomously determine DNA methylation states in murine stem cells. They identified promoter sequences that supported proper de novo methylation during differentiation and determined that this activity is contained within small methylation-determining regions.
Shireen Lamandé and colleagues report mutations in TRPV4 in familial digital arthropathy-brachydactyly (FDAB), which is characterized by osteoarthropathy of the fingers and toes. TRPV4 is a cation channel, and functional experiments suggest mutant proteins are not localized properly to the cell surface.
Fostering scientific progress and ensuring that the community has access to human exome data can be difficult to do when faced with the divergent interests of patients, data generators, data funders and potential data users. We support the archiving of sensitive datasets in secure repositories with appropriate mechanisms in place to control access.
Two new studies describe germline mutations in BAP1 in putatively dissimilar cancer-related syndromes. The spectrum of neoplasms associated with these germline mutations suggest that BAP1 has an important tumor suppressor function in multiple tissues.