September 2010 Volume 42 Number 9, pp 729 - 810
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EDITORIAL
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Cite site p729
doi:10.1038/ng0910-729
We now have adapted our preprint archive, Nature Precedings, to host project descriptions,
community standards papers and funder policies. Citable project descriptions provide a guide
to the resources available and create a mechanism to give data producers citation credit.
http://links.ealert.nature.com/ctt?kn=71&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
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NEWS AND VIEWS
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Infectious diseases not immune to genome-wide association pp731 - 732
Paul I W de Bakker and Amalio Telenti
doi:10.1038/ng0910-731
Two genome-wide association studies for meningococcal disease and tuberculosis identify new loci
associated with susceptibility to these infectious diseases. They highlight a role for the acquired
and innate immune systems in host control of several human pathogens and demonstrate that denser
genotyping platforms and population-specific reference panels are necessary for genetic studies in
African populations.
http://links.ealert.nature.com/ctt?kn=68&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Putting a finger on the switch pp733 - 734
James J Bieker
doi:10.1038/ng0910-733
The transition from fetal to adult beta-like globin expression is a key step in the maturation of
the red blood cell lineage. Two new studies show that the KLF1 zinc finger protein uses direct and
indirect means to regulate the final switch from fetal to adult globin expression and that monoallelic
loss of KLF1 expression leads to persistence of fetal hemoglobin.
http://links.ealert.nature.com/ctt?kn=72&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Variable evolutionary signatures at the heart of enhancers pp734 - 735
Ross C Hardison
doi:10.1038/ng0910-734
What is the best way to identify regulatory DNA sequences such as enhancers, promoters, insulators
and silencers? A new study shows that specific binding by a coactivator protein identifies enhancers
that are invisible to common detection methods based on evolutionary constraint.
http://links.ealert.nature.com/ctt?kn=90&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
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RESEARCH HIGHLIGHTS
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Research highlights p737
doi:10.1038/ng0910-737
http://links.ealert.nature.com/ctt?kn=87&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome
18q11.2 pp739 - 741
Thorsten Thye et al.
doi:10.1038/ng.639
Adrian Hill and colleagues report a genome-wide association study for tuberculosis in cohorts from
Ghana and The Gambia. They identify a host susceptibility loci for pulmonary tuberculosis disease at 18q11.2.
Abstract: http://links.ealert.nature.com/ctt?kn=11&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=76&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
KLF1 regulates BCL11A expression and gamma- to beta-globin gene switching pp742 - 744
Dewang Zhou et al.
doi:10.1038/ng.637
Tim Townes and colleagues show that knockdown of KLF1 in human and mouse adult erythroid progenitors
results in reduced BCL11A levels and increased fetal hemoglobin expression. These findings suggest a
potential strategy to activate fetal hemoglobin expression in individuals with beta-thalassemia or
sickle cell disease.
Abstract: http://links.ealert.nature.com/ctt?kn=6&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=83&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
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ARTICLE
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A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk pp745 - 750
Francesca Antonacci et al.
doi:10.1038/ng.643
Evan Eichler and colleagues identify a large, complex structural polymorphism at 16p12.1 in a region
previously associated with neurocognitive disease. They further show that the region has experienced
dynamic structural evolution in primates and that disease-associated microdeletions arise on the more
common human haplotype.
Abstract: http://links.ealert.nature.com/ctt?kn=7&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=64&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
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LETTERS
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Genome-wide association study identifies five new susceptibility loci for prostate cancer in the
Japanese population pp751 - 754
Ryo Takata et al.
doi:10.1038/ng.635
Hidewaki Nakagawa and colleagues report a genome-wide association study for prostate cancer in a
Japanese population. They replicate previously associated loci and identify five new susceptibility loci.
Abstract: http://links.ealert.nature.com/ctt?kn=3&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=109&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular
carcinoma in chronic hepatitis B virus carriers pp755 - 758
Hongxing Zhang et al.
doi:10.1038/ng.638
Gangqiao Zhou and colleagues report a genome-wide association study for hepatocellular carcinoma in
chronic hepatitis B virus carriers, identifying a new susceptibility locus at chromosome 1p36.22.
Abstract: http://links.ealert.nature.com/ctt?kn=5&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=101&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies
susceptibility loci at PLCE1 and C20orf54 pp759 - 763
Li-Dong Wang et al.
doi:10.1038/ng.648
Li Dong Wang and colleagues report a genome wide association study for esophageal squamous cell carcinoma
in the Chinese population. They identify two risk loci at PLCE1 and C20orf54.
Abstract: http://links.ealert.nature.com/ctt?kn=1&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=92&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell
carcinoma pp764 - 767
Christian C Abnet et al.
doi:10.1038/ng.649
Christian Abnet and colleagues report genome-wide association studies for gastric adenocarcinoma and
esophageal squamous cell carcinoma in a Chinese population. They identified a new shared risk locus
in the PLCE1 gene at 10q23.
Abstract: http://links.ealert.nature.com/ctt?kn=2&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=42&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
A genome-wide association study identifies four susceptibility loci for keloid in the Japanese population
pp768 - 771
Mitsuko Nakashima et al.
doi:10.1038/ng.645
Yusuke Nakamura and colleagues report a genome-wide association study of keloid, a dermal fibroproliferative
growth, in the Japanese population. Their work identifies common variants at four loci associated with
susceptibility to keloid formation.
Abstract: http://links.ealert.nature.com/ctt?kn=29&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=39&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Genome-wide association study identifies variants in the CFH region associated with host susceptibility
to meningococcal disease pp772 - 776
doi:10.1038/ng.640
Sonia Davila and colleagues report a genome-wide association study for meningococcal disease. They identify
variants in the CFH region associated with susceptibility to meningococcal disease.
Abstract: http://links.ealert.nature.com/ctt?kn=28&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=74&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency pp777 - 780
Ricardo C Ferreira et al.
doi:10.1038/ng.644
Lennart Hammarstrom, Tim Behrens and colleagues report the results of a genome wide association study of
selective immunoglobulin A deficiency, the most common form of primary immunodeficiency in humans. They
validated previously known HLA haplotype associations and identified a new risk variant in IFIH1.
Abstract: http://links.ealert.nature.com/ctt?kn=31&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=38&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease
pp781 - 785
Taye H Hamza et al.
doi:10.1038/ng.642
Haydeh Payami and colleagues report results of a genome-wide association study for Parkinson's disease.
They identify common variants in the HLA region associated with the late-onset sporadic form of the disease
and replicate published associations with SNCA, MAPT and GAK.
Abstract: http://links.ealert.nature.com/ctt?kn=30&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=57&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy
pp786 - 789
Hyun Hor et al.
doi:10.1038/ng.647
Mehdi Tafti and colleagues identify new HLA class II haplotypes that are strongly protective against
narcolepsy. Their analyses suggest a virtually causal role for the HLA region in determining narcolepsy
susceptibility.
Abstract: http://links.ealert.nature.com/ctt?kn=24&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=59&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome pp790 - 793
Sarah B Ng et al.
doi:10.1038/ng.646
Jay Shendure and colleagues report exome sequencing of ten individuals with Kabuki syndrome. They identify
mutations in MLL2, encoding a Trithorax-group histone methyltransferase, as causal for this rare autosomal
dominant malformation disorder.
Abstract: http://links.ealert.nature.com/ctt?kn=25&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=50&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Germline CBL mutations cause developmental abnormalities and predispose to juvenile myelomonocytic leukemia
pp794 - 800
Charlotte M Niemeyer et al.
doi:10.1038/ng.641
Charlotte Niemeyer, Mignon Loh and colleagues report that germline mutations at CBL are associated with
developmental abnormalities and predispose individuals to juvenile myelomonocytic leukemia.
Abstract: http://links.ealert.nature.com/ctt?kn=26&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=53&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Haploinsufficiency for the erythroid transcription factor KLF1 causes hereditary persistence of fetal
hemoglobin pp801 - 805
Joseph Borg et al.
doi:10.1038/ng.630
Sjaak Philipsen and colleagues report that haploinsufficiency for KLF1 causes hereditary persistence of
fetal hemoglobin in a large Maltese family. They further show that KLF1 is a key activator of BCL11A,
which suppresses the expression of fetal hemoglobin.
Abstract: http://links.ealert.nature.com/ctt?kn=21&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=118&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
ChIP-Seq identification of weakly conserved heart enhancers pp806 - 810
Matthew J Blow et al.
doi:10.1038/ng.650
Len Pennacchio and colleagues used ChIP-Seq with the enhancer-associated protein p300 to identify 3,000
candidate cardiac transcriptional enhancers in embryonic mice at E11.5. Notably, most candidate heart
enhancers at this time point are not deeply evolutionarily conserved.
Abstract: http://links.ealert.nature.com/ctt?kn=22&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=86&m=35745399&r=MTc2NTYxNjY4OQS2&b=2&j=ODA3Mzk2NjkS1&mt=1&rt=0
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