November 2010 Volume 42 Number 11, pp 915 - 1030
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Joint Focus from Nature Biotechnology and The Pharmacogenomics
The MicroArray Quality Control II papers
Building on its original work assessing the technical performance of
DNA microarray technology, the MicroArray Quality Control (MAQC)
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researchers, has set out to investigate the capabilities and
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prediction.
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----------------------
EDITORIAL
----------------------
Discussing standards p915
doi:10.1038/ng1110-915
Whereas plans for data generation and public release can be agreed
upon between data producers and their funders, community standards
for the reporting, analysis and publication of high throughput data
require wider discussion and broad consensus.
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----------------------
CORRESPONDENCE
----------------------
The Archon Genomics X PRIZE for whole human genome sequencing
pp917 - 918
Larry Kedes and Edison T Liu
doi:10.1038/ng1110-917
http://links.ealert.nature.com/ctt?kn=71&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
No evidence for lateral gene transfer between salmonids and
schistosomes pp918 - 919
Christoph Grunau and Jarome Boissier
doi:10.1038/ng1110-918
http://links.ealert.nature.com/ctt?kn=79&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Marker papers and data citation p919
Jane Peterson and Joseph Campbell
doi:10.1038/ng1110-919
http://links.ealert.nature.com/ctt?kn=75&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Lack of evidence for DNA methylation of Invader4 retroelements in
Drosophila and implications for Dnmt2-mediated epigenetic
regulation pp920 - 921
Matthias Schaefer and Frank Lyko
doi:10.1038/ng1110-920
http://links.ealert.nature.com/ctt?kn=86&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Reply to "Lack of evidence for DNA methylation of Invader4
retroelements in Drosophila and implications for Dnmt2-mediated
epigenetic regulation" p921
Sameer Phalke, Olaf Nickel and Gunter Reuter
doi:10.1038/ng1110-921
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----------------------
NEWS AND VIEWS
----------------------
A common mechanism for microcephaly pp923 - 924
Bernd Wollnik
doi:10.1038/ng1110-923
New studies employing high-throughput parallel sequencing have revealed
WDR62 mutations in individuals with microcephaly associated with a
broad range of malformations of cortical development. These findings
establish that WDR62 acts as a molecular link between proliferation
and migration in neurogenesis.
http://links.ealert.nature.com/ctt?kn=89&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Glutamate receptors and learning and memory pp925 - 926
Jozef Gecz
doi:10.1038/ng1110-925
Glutamate receptors have long been implicated in neurological processes
underpinning learning and memory. A new study now shows that mutations
in genes encoding glutamate receptor subunits can cause variable
neurodevelopmental phenotypes including intellectual disability and
epilepsy.
http://links.ealert.nature.com/ctt?kn=83&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Genome-wide association studies coming of age in rice pp926 - 927
Richard M Clark
doi:10.1038/ng1110-926
A new study reports the next-generation sequencing of 517 rice genomes,
each to approximately onefold coverage. By leveraging sequence
information across rice lines and by imputing missing genotypes, a
haplotype map (HapMap) was constructed and used for genome-wide
association studies in this major crop.
http://links.ealert.nature.com/ctt?kn=68&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
----------------------
RESEARCH HIGHLIGHTS
----------------------
Research highlights p929
doi:10.1038/ng1110-929
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----------------------
ARTICLES
----------------------
Whole-genome sequencing and comprehensive variant analysis of a
Japanese individual using massively parallel sequencing pp931 - 936
Akihiro Fujimoto et al.
doi:10.1038/ng.691
Tatsuhiko Tsunoda and Hidewaki Nakagawa report the genome sequence of a
Japanese male individual generated with high-throughput sequencing
technology. Their analyses reveal a number of novel single nucleotide
variants, insertions, deletions and other variants.
Abstract: http://links.ealert.nature.com/ctt?kn=30&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=102&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Association analyses of 249,796 individuals reveal 18 new loci
associated with body mass index pp937 - 948
Elizabeth K Speliotes et al.
doi:10.1038/ng.686
Ruth Loos and colleagues report results of a large genome-wide
association study for body mass index. They identify 18 new loci
associated with this trait, some of which map near key hypothalamic
regulators of energy balance.
Abstract: http://links.ealert.nature.com/ctt?kn=23&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=106&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Meta-analysis identifies 13 new loci associated with waist-hip ratio
and reveals sexual dimorphism in the genetic basis of fat distribution
pp949 - 960
Iris M Heid et al.
doi:10.1038/ng.685
Cecilia Lindgren and colleagues report results of a large-scale
genome-wide association study for waist-to-hip ratio, a measure of
body fat distribution. They identify 13 new loci associated with this
trait, several of which show stronger effects in women than in men.
Abstract: http://links.ealert.nature.com/ctt?kn=24&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=95&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Genome-wide association studies of 14 agronomic traits in rice
landraces pp961 - 967
Xuehui Huang et al.
doi:10.1038/ng.695
Bin Han and colleagues performed low-coverage sequencing of 517 rice
landraces and constructed a high-density haplotype map of the rice
genome. They have used this resource to carry out genome-wide
association studies for 14 agronomic traits and identify 80 loci with
strong association signals.
Abstract: http://links.ealert.nature.com/ctt?kn=25&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=107&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
----------------------
LETTERS
----------------------
Resequencing of 200 human exomes identifies an excess of low-frequency
non-synonymous coding variants pp969 - 972
Yingrui Li et al.
doi:10.1038/ng.680
Jun Wang and colleagues report the targeted capture and resequencing of
the exomes of 200 Danish individuals at an average coverage of 12-fold.
They identify an excess of low frequency non-synonymous variants that
goes beyond previous predictions.
Abstract: http://links.ealert.nature.com/ctt?kn=19&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=47&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Meta-analysis of three genome-wide association studies identifies
susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13
and 20q13.33 pp973 - 977
Richard S Houlston et al.
doi:10.1038/ng.670
Ian Tomlinson, Richard Houlston, Malcolm Dunlop and colleagues report
results of a large genome-wide association study of colorectal cancer.
They identify four new risk loci and suggest that many more loci of
similar effect size are likely to exist.
Abstract: http://links.ealert.nature.com/ctt?kn=20&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=38&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
A multi-stage genome-wide association study of bladder cancer
identifies multiple susceptibility loci pp978 - 984
Nathaniel Rothman et al.
doi:10.1038/ng.687
Montserrat Garcia-Closas and colleagues report a genome-wide association
study for bladder cancer. They identify three new susceptibility loci on
chromosomes 22q13.1, 19q12 and 2q37.1.
Abstract: http://links.ealert.nature.com/ctt?kn=21&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=37&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
A genome-wide association study identifies new psoriasis susceptibility
loci and an interaction between HLA-C and ERAP1 pp985 - 990
Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2
doi:10.1038/ng.694
Richard Trembath, Peter Donnelly and colleagues report a genome-wide
association study identifying six new psoriasis susceptibility loci.
They also identify a statistical interaction between HLA-C and ERAP1
in psoriasis susceptibility.
Abstract: http://links.ealert.nature.com/ctt?kn=22&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=62&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Genome-wide association study identifies a psoriasis susceptibility
locus at TRAF3IP2 pp991 - 995
Eva Ellinghaus et al.
doi:10.1038/ng.689
Andre Franke and colleagues report a genome-wide association study for
psoriasis vulgaris in a German cohort with replication in German and
North American psoriasis cohorts. They identify variants in TRAF3IP2,
encoding a protein involved in IL-17 mediated T-cell immune response,
associated with psoriasis.
Abstract: http://links.ealert.nature.com/ctt?kn=116&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=63&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Common variants at TRAF3IP2 are associated with susceptibility to
psoriatic arthritis and psoriasis pp996 - 999
Ulrike Huffmeier et al.
doi:10.1038/ng.688
Andre Reis and colleagues report a genome-wide association study
identifying a susceptibility locus at TRAF3IP2 for psoriatic
arthritis and psoriasis.
Abstract: http://links.ealert.nature.com/ctt?kn=117&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=54&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Genome-wide association analysis identifies three psoriasis
susceptibility loci pp1000 - 1004
Philip E Stuart et al.
doi:10.1038/ng.693
James Elder and colleagues report meta-analyses of two psoriasis
genome-wide association studies with replication in additional
cohorts. They make use of imputation using both the HapMap and
initial 1000 Genomes Project datasets and identify three new
psoriasis susceptibility loci.
Abstract: http://links.ealert.nature.com/ctt?kn=118&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=16&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Association analyses identify six new psoriasis susceptibility loci
in the Chinese population pp1005 - 1009
Liang-Dan Sun et al.
doi:10.1038/ng.690
Xue-Jun Zhang and colleagues report genome-wide association analyses
identifying six new susceptibility loci in the Chinese population.
Abstract: http://links.ealert.nature.com/ctt?kn=120&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=11&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
WDR62 is associated with the spindle pole and is mutated in human
microcephaly pp1010 - 1014
Adeline K Nicholas et al.
doi:10.1038/ng.682
C Geoffrey Woods and colleagues used targeted capture followed by
massively parallel sequencing to identify mutations in WDR62 in
microcephaly. WDR62 associates with the spindle pole during mitosis,
and mutant WDR62 proteins fail to localize to spindle poles in
dividing neural progenitors.
Abstract: http://links.ealert.nature.com/ctt?kn=119&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=85&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Mutations in WDR62, encoding a centrosome-associated protein, cause
microcephaly with simplified gyri and abnormal cortical architecture
pp1015 - 1020
Timothy W Yu et al.
doi:10.1038/ng.683
Christopher Walsh and colleagues used targeted high-throughput
sequencing to identify mutations in WDR62 in human microcephaly.
The authors report that WDR62 is a centrosomal protein.
Abstract: http://links.ealert.nature.com/ctt?kn=122&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=87&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA
receptors cause variable neurodevelopmental phenotypes pp1021 - 1026
Sabine Endele et al.
doi:10.1038/ng.677
Kerstin Kutsche and colleagues report that mutations in GRIN2A and
GRIN2B cause variable neurodevelopmental phenotypes including mental
retardation and epilepsy. GRIN2A and GRIN2B encode regulatory subunits
of N-methyl-D-aspartate (NMDA) receptors, which mediate excitatory
neurotransmission in the brain.
Abstract: http://links.ealert.nature.com/ctt?kn=121&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=78&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Genome-wide patterns of genetic variation among elite maize inbred
lines pp1027 - 1030
Jinsheng Lai et al.
doi:10.1038/ng.684
Jun Wang and colleagues report the resequencing of sixite maize inbred
lines. The authors identified over 1 million SNPs and 30,000 insertion
or deletion polymorphisms in this agricultural crop.
Abstract: http://links.ealert.nature.com/ctt?kn=124&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=28&m=35925986&r=MTc2NTYxNjY4OQS2&b=2&j=ODUxODQyNjkS1&mt=1&rt=0
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FOCUS ON EPIGENETICS
This Focus summarizes the progress that has been made in characterizing
the epigenetic basis of disease and developmental pathways, and
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