Volume 43 Issue 10, October 2011

Two new studies take distinct population genetic approaches to analyzing whole-genome sequencing data sets in order to estimate human demographic parameters. These papers refine our understanding of the relationships among human populations while illustrating both the possibilities and the statistical challenges of fitting demographic models to whole-genome data sets.

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.

Several new studies report mutations in the gene GATA2 in three different familial syndromes characterized by predisposition to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Before the onset of MDS and AML, patients with similar GATA2 mutations had distinct hematological abnormalities.

Sahar Mansour and colleagues report alterations in the transcription factor GATA2 in eight pedigrees with Emberger disorder, which is characterized by primary lymphedema and predispositon to acute myeloid leukemia. Most of the heterozygous variants lead to frameshift mutations and premature termination of GATA2.

João Barata and colleagues identify somatic gain-of-function IL7R mutations in childhood T-cell acute lymphoblastic leukemia. The mutations result in constitutive receptor activation, implicating the IL-7R pathway as a potential therapeutic target in a subset of T-ALL cases.

Joshua Bis, Christopher O'Donnell and colleagues report a meta-analysis of genome-wide association studies from the CHARGE Consortium that identifies loci associated with carotid intima media thickness and plaque. These are established measures of subclinical atherosclerosis that predict future cardiovascular disease events.

Duncan Odom and colleagues map Pol III occupancy genome-wide in liver tissue from six mammals. The analysis showed variable binding of Pol III at individual tRNA genes that nevertheless led to conserved expression of amino acid isotypes.

Detlef Weigel and colleagues report results from the first phase of the Arabidopsis 1001 Genomes Project, based on short-read sequencing of 80 geographically diverse strains. This collection of strains has been made available to the scientific community, and the authors show that the identified polymorphisms in these strains can be useful for imputation and genome-wide association studies.

Matthew Meyerson and colleagues report the whole-genome sequencing of primary colorectal tumors and matched adjacent non-tumor tissue from nine individuals with colorectal cancer. They identify a recurrent VTI1A-TCF7L2 fusion in 3% of colorectal cancers.

The Schizophrenia Psychiatric Genome-Wide Association Study Consortium reports five genetic loci newly associated with risk of schizophrenia, involving 17,836 cases of schizophrenia and 33,859 healthy controls. The new locus with the strongest support of association was located within an intron for microRNA 137, a known regulator of neuronal development. Four other genome-wide significant loci for schizophrenia contain predicted targets of MIR137, suggesting that disruption to pathways involving MIR137 may be an etiologic mechanism in schizophrenia.

The Psychiatric GWAS Consortium Bipolar Disorder Working Group reports a large-scale genome-wide association study of 7,481 individuals with bipolar disorder with replication in 4,493 cases. The Consortium identifies a new susceptibility locus near ODZ4 and replicates a known association near CACNA1C for bipolar disorder.

John Chambers and colleagues report a genome-wide association study for type 2 diabetes in individuals of south Asian ancestry. They identify six loci newly associated with type 2 diabetes.

Yoon Shin Cho and colleagues report a genome-wide association study for nine metabolic traits in east Asians. They identify ten new loci that are associated with these traits.

Dianna Milewicz and colleagues report a genome-wide association study of sporadic thoracic aortic aneurysm and dissection. They identify an associated locus on 15q21 spanning the FBN1 gene.

Michiaki Kubo and colleagues report a genome-wide association study for age-related macular degeneration in individuals of Japanese ancestry. They identify two genetic loci newly associated with this disease.

Paul Elliott, Martin Tobin, Cornelia van Duijn and colleagues report a genome-wide association study for pulse pressure and mean arterial pressure, identifying six new loci influencing these two traits.

Hamish Scott and colleagues report that germline mutations in GATA2 segregate with myelodysplastic syndrome and acute myeloid leukemia in four pedigrees. The resulting alterations occur in a conserved zinc finger DNA-binding domain of GATA2.

Thomas Wiesner and colleagues report that germline mutations in BAP1 predispose to melanocytic tumors ranging histopathologically from epithelioid nevi to atypical melanocytic proliferations. Some BAP1 mutation carriers also developed uveal or cutaneous melanomas.

Joseph Testa, Michele Carbone and colleagues report that germline mutations in BAP1 predispose to malignant mesothelioma and uveal melanoma. They further hypothesize that mesothelioma predominates in BAP1 mutation carriers following exposure to asbestos.

Andrea Ventura and colleagues report germline hemizygous deletions in the miR-17~92 cluster in individuals with features overlapping Feingold syndrome. Mice with targeted deletions in miR17~92 also display growth and skeletal defects.

Adam Siepel and colleagues estimate key parameters for ancient human demography using a Bayesian analysis of the whole-genome sequences of six individuals from diverse populations. They present new methods for coalescent-based inference of demographic parameters as well as a custom pipeline for genotype inference.

The Brassica rapa Genome Sequencing Project Consortium reports the draft genome of the B. rapa accession Chiifu-401-42, an inbred Chinese cabbage line. The B. rapa genome should provide a useful reference genome for the Brassica species, which include many important oil and vegetable crops.