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Alison Klein and colleagues report a genome-wide meta-analysis to identify loci associated with pancreatic cancer risk. They identify associated variants at 17q25.1, 3q29, 7p13 and 2p13.3.
Jianxin Ma and colleagues report the identification of a gene variant selected for during the domestication of soybean that causes permeable seed coats, in contrast to the hard seed coats of its wild ancestors. The identified gene, GmHs1-1, is predicted to encode a calcineurin-like metallophosphatase, although its cellular function remains unknown.
Steven McCarroll, Joel Hirschhorn and colleagues identify eight common structural forms of the human amylase locus. They measured amylase gene copy number in ~3,500 individuals and detected no association with BMI and obesity.
Hannes Helgason, Kari Stefansson and colleagues report an association study of gastric cancer susceptibility based on whole-genome sequencing in the Icelandic population. They find that loss-of-function variants in ATM confer risk of gastric cancer.
Lauri Aaltonen, Jussi Taipale and colleagues report frequent mutation of CTCF- and cohesin-binding sites (CBSs) in multiple cancer types. They find that the frequency of CBS mutations in microsatellite-stable colorectal cancer is 1.5 times higher than that of other known cancer mutational targets.
Chengcai Chu and colleagues show that genetic variation in NRT1.1B/OsNPF6.5 contributes to nitrate-use divergence between two main subspecies of Asian cultivated rice. Their findings may help to improve nitrogen-use efficiency in plant production.
Yukinori Okada, Michiaki Kubo and colleagues report the construction of a new HLA imputation reference panel for the Japanese population. They apply this resource to analyze the association of the HLA region with Graves' disease and find that variants in multiple class I and class II HLA genes contribute independently to disease risk.
Yao Zhao, Yongyong Shi and colleagues performed a genome-wide association study on sporadic pituitary adenoma in the Han Chinese population. They identify three new susceptibility loci.
Andrew Crosby, David Silver and colleagues show that a partially inactivating mutation in MFSD2A causes a non-lethal microcephaly syndrome with symptoms that include intellectual disability, spasticity and absent speech. Their findings indicate an essential role for lysophosphatidylcholine uptake in human brain development and function.
Joseph Gleeson, David Silver and colleagues show that inactivating mutations in MFSD2A, which encodes an essential transporter of long-chain fatty acids in brain, cause a lethal microcephaly syndrome. These results establish a link between the activity of this transporter and human brain growth.
Geoffrey Woods, Jan Senderek and colleagues show that biallelic mutations in PRDM12 cause congenital insensitivity to pain. They further show that PRDM12 is expressed in nociceptors and their progenitors and participates in sensory neuron development in Xenopus.
Hong-Xuan Lin, Ji-Ping Gao, Jun-Xiang Shan and colleagues show that natural variation in a proteasome α2 subunit gene contributes to thermotolerance in African rice. Their follow-up studies suggest that the variant allele protects cells from heat stress by enhancing the elimination of cytotoxic denatured proteins and maintaining heat-response processes.
Shamil Sunyaev, Paul de Bakker and colleagues report an analysis of 11,020 de novo mutations from the whole-genome sequences of Dutch families sequenced as part of the Genome of the Netherlands project. They identify correlations related to paternal age and genic content and develop an empirical human mutation rate map.
Kajsa Paulsson and colleagues performed whole-genome and/or whole-exome sequencing of 51 cases of high hyperdiploid pediatric acute lymphoblastic leukemia, which is characterized by a massive nonrandom gain of chromosomes. They found that high hyperdiploidy arose early during leukemogenesis and was the main leukemogenic event.
Friedrich Luft and colleagues identify missense mutations in PDE3A in six unrelated families with an autosomal dominant syndrome marked by severe hypertension and brachydactyly. They further show that the mutations result in gain of enzymatic function, leading to increased vascular smooth muscle cell proliferation and vessel wall hyperplasia.
Roland Kuiper and colleagues identify a homozygous germline nonsense mutation in the base-excision repair gene NTHL1 in three families with recessive inheritance of adenomatous polyposis.
Eric Boerwinkle and colleagues carried out exome sequencing on 8,554 individuals and tested loss-of-function variants for association with 20 phenotypes related to common chronic diseases. They identified several new associations and illustrate the value of applying exome sequencing to a large sample of deeply phenotyped individuals.
Kerstin Kutsche, Marco Tartaglia and colleagues show that missense mutations in KCNH1 and ATP6V1B2 cause Zimmermann-Laband syndrome, a disorder characterized by facial dysmorphism, intellectual disability, digit anomalies and hypertrichosis. Functional studies indicate that the KCNH1 mutations lead to altered channel activity.
Mohammad Akbari and colleagues report that rare truncating mutations in RECQL are associated with breast cancer susceptibility. RECQL encodes a helicase that helps prevent double-stranded DNA breaks by stabilizing stalled or regressed replication forks.
Sarah Fortune, Meindert Lamers and colleagues show that, unlike Escherichia coli, Mycobacterium tuberculosis uses an exonuclease domain in polymerase DnaE1 to proofread DNA replication. Importantly, this proofreading mechanism renders mycobacteria sensitive to nucleoside analogs, a class of small molecules used to treat viral infections and cancer.