NATURE GENETICS
October 2011 Volume 43 Number 10, pp 921 - 1040
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EDITORIAL
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Capture and release p921
doi:10.1038/ng.961
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.
http://links.ealert.nature.com/ctt?kn=74&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
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NEWS AND VIEWS
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Whole-genome sequencing data offer insights into human demography
pp923 - 925
Jonathan K Pritchard
doi:10.1038/ng.953
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.
http://links.ealert.nature.com/ctt?kn=71&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Germline BAP1 mutations and tumor susceptibility pp925 - 926
Alisa M Goldstein
doi:10.1038/ng.956
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.
http://links.ealert.nature.com/ctt?kn=77&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
GATA2 mutations lead to MDS and AML pp926 - 927
R. Katherine Hyde and P. Paul Liu
doi:10.1038/ng.949
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.
http://links.ealert.nature.com/ctt?kn=86&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
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RESEARCH HIGHLIGHTS
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Sexually dimorphic digits p928
http://links.ealert.nature.com/ctt?kn=94&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Selfish switch in honeybee workers p928
http://links.ealert.nature.com/ctt?kn=89&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
A surprising role for FOXO p928
http://links.ealert.nature.com/ctt?kn=90&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
MED12 mutations and uterine fibroids p928
http://links.ealert.nature.com/ctt?kn=85&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Maternal imprinting defect p928
http://links.ealert.nature.com/ctt?kn=88&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
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BRIEF COMMUNICATION
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Mutations in GATA2 cause primary lymphedema associated with a predisposition
to acute myeloid leukemia (Emberger syndrome) pp929 - 931
Pia Ostergaard et al.
doi:10.1038/ng.923
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.
Abstract: http://links.ealert.nature.com/ctt?kn=117&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=84&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
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ARTICLES
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Oncogenic IL7R gain-of-function mutations in childhood T-cell acute
lymphoblastic leukemia pp932 - 939
Priscila P Zenatti et al.
doi:10.1038/ng.924
Joao 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.
Abstract: http://links.ealert.nature.com/ctt?kn=118&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=66&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Meta-analysis of genome-wide association studies from the CHARGE consortium
identifies common variants associated with carotid intima media thickness
and plaque pp940 - 947
Joshua C Bis et al.
doi:10.1038/ng.920
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.
Abstract: http://links.ealert.nature.com/ctt?kn=119&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=113&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Pol III binding in six mammals shows conservation among amino acid
isotypes despite divergence among tRNA genes pp948 - 955
Claudia Kutter et al.
doi:10.1038/ng.906
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.
Abstract: http://links.ealert.nature.com/ctt?kn=121&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=105&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Whole-genome sequencing of multiple Arabidopsis thaliana populations
pp956 - 963
Jun Cao et al.
doi:10.1038/ng.911
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.
Abstract: http://links.ealert.nature.com/ctt?kn=120&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=95&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
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LETTERS
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Genomic sequencing of colorectal adenocarcinomas identifies a recurrent
VTI1A-TCF7L2 fusion pp964 - 968
Adam J Bass et al.
doi:10.1038/ng.936
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.
Abstract: http://links.ealert.nature.com/ctt?kn=123&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=42&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Genome-wide association study identifies five new schizophrenia loci
pp969 - 976
doi:10.1038/ng.940
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.
Abstract: http://links.ealert.nature.com/ctt?kn=122&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=39&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Large-scale genome-wide association analysis of bipolar disorder identifies
a new susceptibility locus near ODZ4 pp977 - 983
doi:10.1038/ng.943
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.
Abstract: http://links.ealert.nature.com/ctt?kn=127&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=43&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Genome-wide association study in individuals of South Asian ancestry
identifies six new type 2 diabetes susceptibility loci pp984 - 989
Jaspal S Kooner et al.
doi:10.1038/ng.921
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.
Abstract: http://links.ealert.nature.com/ctt?kn=124&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=34&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Large-scale genome-wide association studies in east Asians identify new
genetic loci influencing metabolic traits pp990 - 995
Young Jin Kim et al.
doi:10.1038/ng.939
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.
Abstract: http://links.ealert.nature.com/ctt?kn=130&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=57&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Genome-wide association study identifies a susceptibility locus for
thoracic aortic aneurysms and aortic dissections spanning FBN1 at 15q21.1
pp996 - 1000
Scott A LeMaire et al.
doi:10.1038/ng.934
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.
Abstract: http://links.ealert.nature.com/ctt?kn=129&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=63&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Genome-wide association study identifies two susceptibility loci for
exudative age-related macular degeneration in the Japanese population
pp1001 - 1004
Satoshi Arakawa et al.
doi:10.1038/ng.938
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.
Abstract: http://links.ealert.nature.com/ctt?kn=136&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=51&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Genome-wide association study identifies six new loci influencing pulse
pressure and mean arterial pressure pp1005 - 1011
Louise V Wain et al.
doi:10.1038/ng.922
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.
Abstract: http://links.ealert.nature.com/ctt?kn=137&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=55&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Heritable GATA2 mutations associated with familial myelodysplastic
syndrome and acute myeloid leukemia pp1012 - 1017
Christopher N Hahn et al.
doi:10.1038/ng.913
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.
Abstract: http://links.ealert.nature.com/ctt?kn=148&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=93&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Germline mutations in BAP1 predispose to melanocytic tumors
pp1018 - 1021
Thomas Wiesner et al.
doi:10.1038/ng.910
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.
Abstract: http://links.ealert.nature.com/ctt?kn=146&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=10&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Germline BAP1 mutations predispose to malignant mesothelioma
pp1022 - 1025
Joseph R Testa et al.
doi:10.1038/ng.912
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.
Abstract: http://links.ealert.nature.com/ctt?kn=143&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=87&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Germline deletion of the miR-17~92 cluster causes skeletal and
growth defects in humans pp1026 - 1030
Loic de Pontual et al.
doi:10.1038/ng.915
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.
Abstract: http://links.ealert.nature.com/ctt?kn=141&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=1&ms=MzcxMTUxNDcS1&r=MTc2NTE5MD...
Bayesian inference of ancient human demography from individual
genome sequences pp1031 - 1034
Ilan Gronau et al.
doi:10.1038/ng.937
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.
Abstract: http://links.ealert.nature.com/ctt?kn=140&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=79&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
The genome of the mesopolyploid crop species Brassica rapa
pp1035 - 1039
Xiaowu Wang et al.
doi:10.1038/ng.919
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.
Abstract: http://links.ealert.nature.com/ctt?kn=147&ms=MzcxMTUxNDcS1&r=MTc2NTE5...
Article: http://links.ealert.nature.com/ctt?kn=31&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
----------------------
ERRATUM
----------------------
Erratum: Common variants in P2RY11 are associated with narcolepsy
p1040
Birgitte R Kornum et al.
doi:10.1038/ng1011-1040b
http://links.ealert.nature.com/ctt?kn=24&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
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CORRIGENDA
----------------------
Corrigendum: Identification of an imprinted master trans regulator
at the KLF14 locus related to multiple metabolic phenotypes p1040
Kerrin S Small et al.
doi:10.1038/ng1011-1040c
http://links.ealert.nature.com/ctt?kn=19&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
Genome-wide association analyses identifies a susceptibility locus
for tuberculosis on chromosome 18q11.2 p1040
Thorsten Thye et al.
doi:10.1038/ng1011-1040a
http://links.ealert.nature.com/ctt?kn=21&ms=MzcxMTUxNDcS1&r=MTc2NTE5M...
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