May 2011 Volume 43 Number 5, pp 389 - 499
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----------------------
EDITORIAL
----------------------
No second thoughts about data access p389
doi:10.1038/ng.827
More data than we can handle is no excuse to give up our efforts to
promote data access, but it may make us think about new ways to make it sustainable.
http://links.ealert.nature.com/ctt?kn=74&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
----------------------
CORRESPONDENCE
----------------------
Defining rare variants by their frequencies in controls may increase
type I error pp391 - 392
Mathieu Lemire
doi:10.1038/ng.818
http://links.ealert.nature.com/ctt?kn=71&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Bias due to selection of rare variants using frequency in controls pp392 - 393
Richard D Pearson
doi:10.1038/ng.816
http://links.ealert.nature.com/ctt?kn=79&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Bias due to selection of rare variants using frequency in controls pp394 - 395
Christopher T Johansen, Jian Wang and Robert A Hegele
doi:10.1038/ng.817
http://links.ealert.nature.com/ctt?kn=75&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
----------------------
NEWS AND VIEWS
----------------------
Cattle gain stature pp397 - 398
Peter M Visscher and Michael E Goddard
doi:10.1038/ng.819
Identifying causal variants for complex traits and understanding their
function remain arduous tasks. A new study combines the advantages of gene
mapping in livestock with elegant genetic and functional analyses to address
these challenges and identifies candidate regulatory variants affecting
stature in cattle.
http://links.ealert.nature.com/ctt?kn=86&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
High-throughput identification of genetic interactions in HIV-1 pp398 - 400
Daniel M Weinreich
doi:10.1038/ng.820
A study characterizes the in vitro replicative capacity of over 70,000
clinical isolates of HIV-1 in the absence of drugs, or in the presence
of one of 15 individual drugs. The largest survey of the effects of
mutations on fitness undertaken in any organism, this study finds
extensive pairwise interactions among over 1,800 variable sites
identified through sequencing the protease and reverse transcriptase genes.
http://links.ealert.nature.com/ctt?kn=93&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Estimating the mutation rate of Mycobacterium tuberculosis during infection pp400 - 401
David R Sherman and Sebastien Gagneux
doi:10.1038/ng.815
Current models of Mycobacterium tuberculosis latency presume very low
mycobacterial replication and mutation rates. In contrast to these models,
a study reporting whole-genome sequencing of mycobacteria isolated from
infected macaques shows that the mutational capacity of M. tuberculosis
during latency is not reduced, a finding with important implications for
tuberculosis research and control.
http://links.ealert.nature.com/ctt?kn=85&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
----------------------
RESEARCH HIGHLIGHTS
----------------------
Research highlights p403
doi:10.1038/ng.829
http://links.ealert.nature.com/ctt?kn=84&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
----------------------
ARTICLES
----------------------
Variants modulating the expression of a chromosome domain encompassing PLAG1
influence bovine stature pp405 - 413
Latifa Karim et al.
doi:10.1038/ng.814
Michel Georges and colleagues report fine mapping and functional characterization
of a quantitative trait locus with a large effect on bovine stature. They show
that the likely causal variants at this locus modulate expression of a
chromosomal domain encompassing PLAG1 and several other genes.
Abstract: http://links.ealert.nature.com/ctt?kn=32&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=91&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
High conservation of transcription factor binding and evidence for combinatorial
regulation across six Drosophila species pp414 - 420
Qiye He et al.
doi:10.1038/ng.808
Julia Zeitlinger, Alexander Stark and colleagues report genome-wide binding
profiles for the transcription factor Twist across six Drosophila species.
They find that the binding pattern is highly conserved across species,
suggesting strong functional constraints at the enhancers that Twist regulates.
Abstract: http://links.ealert.nature.com/ctt?kn=24&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=113&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Glycerol-3-phosphate is a critical mobile inducer of systemic immunity in plants pp421 - 427
Bidisha Chanda et al.
doi:10.1038/ng.798
Pradeep Kachroo and colleagues show that glycerol-3-phosphate is a critical mobile
inducer of systemic acquired resistance in plants.
Abstract: http://links.ealert.nature.com/ctt?kn=25&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=104&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
----------------------
LETTERS
----------------------
Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated
with Alzheimer's disease pp429 - 435
Paul Hollingworth et al.
doi:10.1038/ng.803
Julie Williams, Michael Owen and colleagues report staged follow-up and
meta-analyses of genome-wide association studies for Alzheimer's disease
from the GERAD+ consortium. They identify common variants at ABCA7 and
MS4A6A/MS4A4E associated with Alzheimer's disease and support for
several additional susceptibility loci.
Abstract: http://links.ealert.nature.com/ctt?kn=26&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=109&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with
late-onset Alzheimer's disease pp436 - 441
Adam C Naj et al.
doi:10.1038/ng.801
Gerard Schellenberg and colleagues report a genome-wide association study
of late-onset Alzheimer's disease (LOAD), as part of the Alzheimer Disease
Genetics Consortium. They identify common variants in MS4A4/MS4A6E, CD2AP,
CD33 and EPHA1 associated with LOAD.
Abstract: http://links.ealert.nature.com/ctt?kn=20&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=95&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Exome sequencing identifies GRIN2A as frequently mutated in melanoma pp442 - 446
Xiaomu Wei et al.
doi:10.1038/ng.810
Yardena Samuels and colleagues report the sequencing of 14 melanoma exomes.
They identify a recurrent mutation in TRRAP in 4% of cases as well as
mutations in GRIN2A in 33% of tumors.
Abstract: http://links.ealert.nature.com/ctt?kn=21&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=41&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
A genome-wide association study identifies three loci associated with
susceptibility to uterine fibroids pp447 - 450
Pei-Chieng Cha et al.
doi:10.1038/ng.805
Yusuke Nakamura and colleagues report a genome-wide association study for uterine
fibroids. They identify three loci associated with susceptibility to this benign tumor.
Abstract: http://links.ealert.nature.com/ctt?kn=22&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=45&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Genome-wide association study identifies a common variant associated with risk of
endometrial cancer pp451 - 454
Amanda B Spurdle et al.
doi:10.1038/ng.812
Amanda Spurdle and colleagues report results of a genome-wide association study
of endometrial cancer. They identify a risk variant near HNF1B that has
previously been associated with increased risk of prostate cancer and with
reduced risk of type 2 diabetes.
Abstract: http://links.ealert.nature.com/ctt?kn=23&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=39&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Genome-wide association study identifies a susceptibility locus for HCV-induced
hepatocellular carcinoma pp455 - 458
Vinod Kumar et al.
doi:10.1038/ng.809
Koichi Matsuda and colleagues report a genome-wide association study for
hepatitis C virus-induced hepatocellular carcinoma. They identify a
susceptibility locus at MICA in individuals of Japanese ancestry.
Abstract: http://links.ealert.nature.com/ctt?kn=119&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=57&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Common variation in GPC5 is associated with acquired nephrotic syndrome pp459 - 463
Koji Okamoto et al.
doi:10.1038/ng.792
Eisei Noiri and colleagues show that intronic variants in GPC5 are
associated with acquired nephrotic syndrome. They further show that
knockdown of Gpc5 in mice confers resistance to podocyte injury in two
different models of experimentally induced nephrosis.
Abstract: http://links.ealert.nature.com/ctt?kn=121&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=59&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
High-resolution characterization of a hepatocellular carcinoma genome pp464 - 469
Yasushi Totoki et al.
doi:10.1038/ng.804
Tatsuhiro Shibata and colleagues report the sequencing of a hepatocellular
carcinoma. The authors identified 63 somatic non-synonymous substitutions
and 22 somatic chromosomal rearrangements in this liver tumor.
Abstract: http://links.ealert.nature.com/ctt?kn=122&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=50&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Mutant nucleophosmin and cooperating pathways drive leukemia initiation
and progression in mice pp470 - 475
George S Vassiliou et al.
doi:10.1038/ng.796
George Vassiliou, Allan Bradley and colleagues perform a Sleeping Beauty
transposon mutagenesis screen to identify insertions that cooperate with
mutant Npm1 to produce acute myeloid leukemia (AML) in mice. They observed
mutually exclusive integrations in Csf2, Flt3 or Rasgrp1 in a high percentage
of cases, providing insights into the molecular pathogenesis of this AML subtype.
Abstract: http://links.ealert.nature.com/ctt?kn=124&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=53&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change pp476 - 481
Tina T Hu et al.
doi:10.1038/ng.807
Detlef Weigel and colleagues report the genome sequence of Arabidopsis lyrata.
In comparison with the much smaller genome of A. thaliana, from which A. lyrata
diverged about 10 million years ago, they find that the reduction in genome size
is attributed to a large number of deletions across the genome.
Abstract: http://links.ealert.nature.com/ctt?kn=123&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=13&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium
tuberculosis during latent infection pp482 - 486
Christopher B Ford et al.
doi:10.1038/ng.811
Sarah Fortune and colleagues report the whole-genome sequencing of
Mycobacterium tuberculosis strains isolated from cynomolgus macaques
with either active, latent or early reactivation disease. They estimate
a similar mutation rate for these disease states in vivo, as well as for
the bacterium in vitro. This suggests that M. tuberculosis has a greater
mutational rate during latent and early reactivation disease than previously
predicted and may be able to acquire drug resistance during these states.
Abstract: http://links.ealert.nature.com/ctt?kn=126&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=83&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase pp487 - 489
Trevor Hinkley et al.
doi:10.1038/ng.795
Sebastian Bonhoeffer, Christos Petropoulos and colleagues report a
systems analysis of the fitness landscape of HIV-1 protease and reverse
transcriptase. They use a dataset of over 70,000 virus samples, isolated
from HIV-1 subtype B infected individuals, assayed for in vitro
replicative capacity alone or under drug selection.
Abstract: http://links.ealert.nature.com/ctt?kn=125&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=90&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
----------------------
TECHNICAL REPORT
----------------------
A framework for variation discovery and genotyping using next-generation
DNA sequencing data pp491 - 498
Mark A DePristo et al.
doi:10.1038/ng.806
Mark DePristo and colleagues report an analytical framework to discover
and genotype variation using whole exome and genome resequencing data
from next-generation sequencing technologies. They apply these methods
to low-pass population sequencing data from the 1000 Genomes Project.
Abstract: http://links.ealert.nature.com/ctt?kn=127&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=5&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
----------------------
CORRIGENDA
----------------------
Corrigendum: Genome-wide association study of systemic sclerosis
identifies CD247 as a new susceptibility locus p499
Timothy R D J Radstake et al.
doi:10.1038/ng0511-499a
http://links.ealert.nature.com/ctt?kn=2&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
Corrigendum: TTC21B contributes both causal and modifying alleles
across the ciliopathy spectrum p499
Erica E Davis et al.
doi:10.1038/ng0511-499b
http://links.ealert.nature.com/ctt?kn=29&m=36557924&r=MTc2NTYxNjY4OQS2&b=2&j=MTAwMTY2NDYzS0&mt=1&rt=0
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