October 2010 Volume 42 Number 10, pp 811 - 914
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EDITORIAL
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A question of benefit p811
doi:10.1038/ng1010-811
Newborn screening panels for genetic diseases are now nearly uniform across the United States, and expanded
panels now test for diseases for which there is no known treatment. This expansion of newborn screening raises
questions about whether traditional assumptions of implied consent are appropriate.
http://links.ealert.nature.com/ctt?kn=33&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
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CORRESPONDENCE
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Public data archives for genomic structural variation pp813 - 814
Deanna M Church et al.
doi:10.1038/ng1010-813
http://links.ealert.nature.com/ctt?kn=27&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Gene-environment interaction influences the reactivity of autoantibodies to citrullinated antigens in rheumatoid
arthritis pp814 - 816
Diane van der Woude et al.
doi:10.1038/ng1010-814
http://links.ealert.nature.com/ctt?kn=28&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Reply to "Gene-environment interaction influences the reactivity of autoantibodies to citrullinated
antigens in rheumatoid arthritis" p816
Karin Lundberg et al.
doi:10.1038/ng1010-816
http://links.ealert.nature.com/ctt?kn=29&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Reassessing the TARBP2 mutation rate in hereditary nonpolyposis colorectal cancer pp817 - 818
Pilar Garre et al.
doi:10.1038/ng1010-817
http://links.ealert.nature.com/ctt?kn=22&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Reply to "Reassessing the TARBP2 mutation rate in hereditary nonpolyposis colorectal cancer" p818
Sonia A Melo and Manel Esteller
doi:10.1038/ng1010-818
http://links.ealert.nature.com/ctt?kn=23&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
----------------------
NEWS AND VIEWS
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GWAS identifies a common breast cancer risk allele among BRCA1 carriers pp819 - 820
Peter Kraft and Christopher A Haiman
doi:10.1038/ng1010-819
A genome-wide association study conducted among women with deleterious BRCA1 mutations has identified a common
allele associated with breast cancer risk in BRCA1 carriers and estrogen receptor-negative breast cancer in the
general population. This suggests that genetic association studies focused on particular subtypes may provide
further insight into complex diseases.
http://links.ealert.nature.com/ctt?kn=24&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
PRDM9 marks the spot pp821 - 822
Gil McVean and Simon Myers
doi:10.1038/ng1010-821
A new study demonstrates that PRDM9 variation in humans leads to profound differences in the activity of
hotspots for both allelic recombination and genomic instability. Although PRDM9 is found to play a role in many
more human hotspots than previously suspected, the search remains for additional, undetermined factors involved
in defining hotspot locations and intensities.
http://links.ealert.nature.com/ctt?kn=25&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Harvesting the apple genome pp822 - 823
James Giovannoni
doi:10.1038/ng1010-822
The genome sequence of the domesticated apple has been assembled and compared to previously sequenced plant
genomes. The genetic sequence of the 17 apple chromosomes shows evidence of a recent genome duplication that
may have spawned the additional gene family members needed for the evolution and development of the unique
fruit structure of the apple termed the pome.
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----------------------
RESEARCH HIGHLIGHTS
----------------------
Research highlights p825
doi:10.1038/ng1010-825
http://links.ealert.nature.com/ctt?kn=139&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental
retardation syndrome pp827 - 829
Peter M Krawitz et al.
doi:10.1038/ng.653
Peter Robinson and colleagues performed exome sequencing on three siblings to identify mutations in PIGV in
Hyperphosphatasia-Mental Retardation (HPMR) syndrome.
Abstract: http://links.ealert.nature.com/ctt?kn=140&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=145&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes
pp830 - 831
Michael F Hammer et al.
doi:10.1038/ng.651
Michael Hammer and colleagues follow two recent conflicting reports regarding the ratio of X-linked to autosomal
nucleotide diversity by examining this question in a larger resequencing dataset and in publicly available
sequence data from six human genomes. They suggest that the patterns of nucleotide diversity are influenced by
local selection near genes that more strongly affects the X chromosome than the autosomes.
Abstract: http://links.ealert.nature.com/ctt?kn=143&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=147&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
----------------------
ARTICLES
----------------------
The genome of the domesticated apple (Malus X domestica Borkh.) pp833 - 839
Riccardo Velasco et al.
doi:10.1038/ng.654
Riccardo Velasco and colleagues report the genome sequence of the 'Golden Delicious' domesticated apple. These
data shed new insight into the genomic events that preceded the origin of this crop.
Abstract: http://links.ealert.nature.com/ctt?kn=146&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=150&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy
pp840 - 850
Edgar A Otto et al.
doi:10.1038/ng.662
Friedhelm Hildebrandt and colleagues combine homozygosity mapping with candidate exome capture and
high-throughput sequencing to identify SDCCAG8 mutations as the cause of a retinal-renal ciliopathy. They
further show that SDCCAG8 localizes to centrioles and that its depletion causes renal cysts and cell polarity
defects.
Abstract: http://links.ealert.nature.com/ctt?kn=148&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=154&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency
pp851 - 858
Sarah E Calvo et al.
doi:10.1038/ng.659
Vamsi Mootha and colleagues report high-throughput targeted sequencing of 103 candidate genes in 103 individuals
with human mitochondrial complex I deficiency. They identify two genes newly associated with complex I deficiency
and are able to provide genetic diagnoses in 22% of their previously unsolved cases.
Abstract: http://links.ealert.nature.com/ctt?kn=153&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=157&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
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LETTERS
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PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans
pp859 - 863
Ingrid L Berg et al.
doi:10.1038/ng.658
Alec Jeffreys and colleagues report that variation at PRDM9 in humans influences sperm recombination hotspot
activity, independent of a consensus binding motif, as well as meiotic genome instability.
Abstract: http://links.ealert.nature.com/ctt?kn=158&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=171&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes
at UBE2E2 and C2CD4A-C2CD4B pp864 - 868
Toshimasa Yamauchi et al.
doi:10.1038/ng.660
Toshimasa Yamauchi and colleagues report results of a genome-wide association study of type 2 diabetes in the
Japanese population. They identify new risk loci at UBE2E2 and C2CD4A-C2CD4B and show that the latter is also
associated with type 2 diabetes risk in Europeans.
Abstract: http://links.ealert.nature.com/ctt?kn=166&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=164&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Genome-wide association study of migraine implicates a common susceptibility variant on 8q22.1 pp869 - 873
doi:10.1038/ng.652
Arno Palotie, Verneri Anttila and colleagues report a genome-wide association study of migraine. They identify
a variant on chromosome 8q22.1 associated with risk of migraine.
Abstract: http://links.ealert.nature.com/ctt?kn=162&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=161&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24
pp874 - 879
Ellen L Goode et al.
doi:10.1038/ng.668
Simon Gayther and colleagues report a genome wide association study for ovarian cancer. They identify two new
susceptibility loci at 2q31 and 8q24 and two suggestive susceptibility loci at 3q25 and 17q21.
Abstract: http://links.ealert.nature.com/ctt?kn=170&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=169&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Common variants at 19p13 are associated with susceptibility to ovarian cancer pp880 - 884
Kelly L Bolton et al.
doi:10.1038/ng.666
Paul Pharoah and colleagues report a genome-wide association study for survival time after diagnosis of
epithelial ovarian cancer and a parallel analysis of susceptibility to epithelial ovarian cancer. They
identified two SNPs at 19p13.11 that associated with susceptibility to the serous subtype of epithelial
ovarian cancer.
Abstract: http://links.ealert.nature.com/ctt?kn=168&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=167&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone
receptor-negative breast cancer in the general population pp885 - 892
Antonis C Antoniou et al.
doi:10.1038/ng.669
Fergus Couch and colleagues report a genome-wide association study for modifiers of breast cancer susceptibility
in BRCA1 mutation carriers. They identify a locus at 19p13 associated with breast cancer risk in BRCA1 mutation
carriers, and further replication studies identify this locus as associated with estrogen receptor-negative
breast cancer in the general population.
Abstract: http://links.ealert.nature.com/ctt?kn=85&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=56&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Variation in TP63 is associated with lung adenocarcinoma susceptibility in Japanese and Korean populations
pp893 - 896
Daiki Miki et al.
doi:10.1038/ng.667
Yataro Daigo and colleagues report a genome-wide association study for lung adenocarcinoma in Japanese and
Korean populations, identifying a susceptibility locus at TP63.
Abstract: http://links.ealert.nature.com/ctt?kn=54&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=53&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14
pp897 - 901
Abbas M Solouki et al.
doi:10.1038/ng.663
Caroline Klaver and colleagues report a genome-wide association study for myopia and refractive error in the
general population, identifying a susceptibility locus at 15q14.
Abstract: http://links.ealert.nature.com/ctt?kn=62&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=61&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
A genome-wide association study for myopia and refractive error identifies a susceptibility locus at 15q25
pp902 - 905
Pirro G Hysi et al.
doi:10.1038/ng.664
Christopher Hammond and colleagues report a genome-wide association study for myopia and refractive error,
identifying a susceptibility locus at 15q25.
Abstract: http://links.ealert.nature.com/ctt?kn=60&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=59&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma pp906 - 909
Gudmar Thorleifsson et al.
doi:10.1038/ng.661
Gudmar Thorleifsson and colleagues report a genome-wide association study for primary open angle glaucoma,
identifying a susceptibility locus near CAV1 and CAV2.
Abstract: http://links.ealert.nature.com/ctt?kn=65&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=64&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Keratin 17 promotes epithelial proliferation and tumor growth by polarizing the immune response in skin
pp910 - 914
Daryle DePianto, Michelle L Kerns, Andrzej A Dlugosz and Pierre A Coulombe
doi:10.1038/ng.665
Pierre Coulombe and colleagues show that ablation of keratin 17 in mice delays the initiation of skin tumors
driven by constitutive Hedgehog signaling. Mice lacking keratin 17 show reduced skin inflammation and an altered
cytokine profile, suggesting an immunomodulatory role in regulating Hedgehog-driven skin tumorigenesis.
Abstract: http://links.ealert.nature.com/ctt?kn=63&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=36&m=35833013&r=MTc2NTYxNjY4OQS2&b=2&j=ODMwMzA5MDUS1&mt=1&rt=0
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