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Jessica Okosun, Csaba Bödör and colleagues performed whole-genome or whole-exome sequencing on 10 follicular lymphoma and transformed follicular lymphoma pairs, followed by deep sequencing of 28 target genes in an additional 122 cases. They identify recurrent mutations in linker histone genes and genes involved in JAK-STAT signaling, NF-κB signaling and B cell development.
Ludwine Messiaen and colleagues report the identification of constitutional LZTR1 mutations in individuals with schwannomatosis, an autosomal dominant inherited disorder of multiple schwannomas.
Michael Duchen, Francesco Muntoni, Eamonn Sheridan and colleagues show that loss-of-function mutations in MICU1 cause a recessive disorder characterized by proximal myopathy, learning difficulties and progressive extrapyramidal motor deficits. The mutations alter mitochondrial calcium homeostasis, leading to mitochondrial damage and dysfunction.
David Adams and colleagues identify inactivating mutations in CUX1 in diverse human cancers. They validate CUX1 as a tumor suppressor using mouse and Drosophila cancer models, and show that CUX1 deficiency activates phosphoinositide 3-kinase signaling through transcriptional downregulation of a PI3K inhibitor.
Roy Kishony and colleagues sequenced the genomes of Burkholderia dolosa isolates from patients with cystic fibrosis, using colony resequencing and deep population sequencing approaches to allow comparisons of multiple isolates from each individual. They identify extensive intrastrain genomic diversity and show specific signatures of selection acting on the pathogen within individual patients.
Nada Jabado, Jacek Majewski, Annie Huang and colleagues show that embryonal tumors with multilayered rosettes are characterized by a recurrent fusion of TTYH1 with the C19MC microRNA cluster. They further show that this fusion results in massive overexpression of a brain-specific isoform of DNMT3B, suggesting that this pediatric brain tumor is driven by epigenetic reactivation of an early developmental neurogenesis program.
Florent Soubrier and colleagues identify biallelic mutations in EIF2AK4 as a major cause of pulmonary veno-occlusive disease, a rare form of pulmonary hypertension. EIF2AK4 encodes a serine-threonine kinase, and the disease-causing mutations are predicted to result in loss of protein function.
Richard Houlston and colleagues report results of a genome-wide association study of chronic lymphocytic leukemia. They validate several new susceptibility loci for this disease, including variants near POT1, TERC and TERT.
Jung-Hyun Lee, Jong Bhak and their colleagues report the whole-genome sequencing and de novo assembly of a male minke whale genome, as well as the genome sequences of three additional minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Their comparative analysis across cetaceans provides insights into adaptation to an aquatic lifestyle.
Klaus Bønnelykke and colleagues identify a common variant in CDHR3 associated with early childhood asthma with severe exacerbations. CDHR3 encodes a cell adhesion protein expressed at high levels in airway epithelium, suggesting a role for altered epithelial integrity in asthma pathogenesis.
Sérgio Sousa and colleagues show that Lenz-Majewski syndrome, a disorder featuring generalized craniotubular hyperostosis, results from de novo gain-of-function mutations in PTDSS1. The mutations lead to increased phophatidylserine synthesis, suggesting a link between phosphatidylserine production and bone metabolism.
Wolfgang Busch and colleagues report results of a genome-wide association study of developmental cell–type traits in Arabidopsis. They identify a new F-box gene, KUK, as a regulator of root meristem and cell length and show the feasibility of applying genome-wide association to the study of cellular traits.
Andrew Hattersley, Jorge Ferrer and colleagues use epigenomic annotation of pancreatic progenitor cells to guide the interpretation of whole-genome sequences from individuals with isolated pancreatic agenesis. They show that recessive mutations in a distal developmental enhancer of PTF1A cause pancreatic agenesis and abolish enhancer activity.
Xuejun Zhang, Jun Wang and colleagues report the application of exome sequencing to a large collection of psoriasis cases and controls. They identify seven common and low-frequency nonsynonymous variants within known psoriasis susceptibility genes that are associated with psoriasis risk.
Matthew Meyerson and colleagues report whole-exome and whole-genome sequencing of 55 small intestine neuroendocrine tumors. They identify recurrent somatic mutations in CDKN1B, implicating cell cycle dysregulation in the pathogenesis of these tumors.
Laura Wood, Kenneth Kinzler, Nickolas Papadopoulos, Aldo Scarpa and colleagues report exome sequencing of intrahepatic cholangiocarcinomas. They identify recurrent somatic mutations in BAP1, ARID1A and PBRM1.
Arul Chinnaiyan and colleagues report the results of prospective clinical sequencing of 11 estrogen receptor–positive metastatic breast cancers. They identify ESR1 mutations affecting the ligand-binding domain in six hormone-resistant metastatic breast cancers and show that the mutant estrogen receptors are constitutively active and continue to be responsive to anti-estrogen therapies in vitro.
Bin Tean Teh, Patrick Tan, Steven Rozen, Irinel Popescu and colleagues report exome sequencing of cholangiocarcinomas, including cases caused by liver fluke (Opisthorchis viverrini) infection and cases caused by non–O. viverrini etiologies. They identify recurrent somatic mutations in BAP1 and ARID1A and demonstrate different mutation patterns in liver fluke infection–related and non-infection-related cancers.
Adrienne Flanagan and colleagues identify distinct driver mutations in H3F3A and H3F3B in chondroblastoma and giant cell tumor of bone. The mutations occur in over 90% of tumors and exhibit a high degree of tumor type specificity.
Guo-Liang Xu, Duanqing Pei and colleagues show that during induced pluripotent cell reprogramming Tet1 regulates 5-hydroxymethylcytosine levels at loci critical for mesenchymal-to-epithelial transition in a vitamin C–dependent fashion. They also show that Tet1 either enhances or inhibits somatic cell reprogramming, depending on the absence or presence of vitamin C, respectively.