Volume 45 Issue 2, February 2013

Attempts to elucidate the mechanism underpinning the genetic association between IFNL3, previously called IL28B, and clearance of hepatitis C virus have, by and large, been unsuccessful. A study in this issue suggests that a new gene, IFNL4, may be responsible.

Our understanding of inherited risk factors for colorectal cancer (CRC) is incomplete. A new study reports the identification of germline CRC risk variants that adversely affect the proofreading function of DNA polymerases encoded by POLE and POLD1.

Soumya Raychaudhuri and colleagues report a broadly applicable method that uses chromatin marks, specifically H3K4me3, to identify critical cell types to fine map complex trait variants.

Matthew Meyerson and colleagues report exome sequencing of solitary fibrous tumor (SFT), a rare mesenchymal tumor. They identify a NAB2-STAT6 fusion in 55% of cases.

William Harbour, Anne Bowcock and colleagues identify recurrent mutations at codon 625 of SF3B1 in uveal melanomas. These mutations occur in low-grade tumors and are associated with favorable prognosis.

Ian Tomlinson and colleagues report the identification of germline variants in POLE and POLD1 that are susceptibility alleles for colorectal cancer. POLE and POLD1 encode DNA polymerases that function in DNA replication.

Anna Köttgen and colleagues report genome-wide association studies for serum urate in over 140,000 individuals from the Global Urate Genetics Consortium (GUGC). They identify 18 loci newly associated with serum urate concentrations and confirm 10 known loci, characterize their associations with gout and include a network analysis suggesting a role for inhibins-activins pathways in regulating urate homeostasis.

Stuart Macregor, Tien Wong and colleagues report meta-analyses that identify 16 new loci associated with central corneal thickness. They also identify two loci associated with risk of developing keratoconus, a common corneal ectasia.

Ludmila Prokunina-Olsson, Thomas O'Brien and colleagues report the discovery of a new gene, INFL4, encoding interferon-λ4, that is upstream of INFL3 (IL28B). A compound dinucleotide frameshift genetic variant in INFL4 creates the full-length INFL4 protein and is more strongly associated with hepatitis C virus clearance in individuals of African ancestry than rs12979860, a known variant associated with clearance.

Roland Brosch and colleagues report whole-genome sequencing of tubercle bacilli with smooth colony morphology, also known as Mycobacterium canetti and/or Mycobacterium prototuberculosis, obtained from humans with tuberculosis from geographically diverse regions. Their comparative genomic analysis with Mycobacterium tuberculosis and other M. tuberculosis complex members identifies extensive recombination and provides insights into the evolution of mycobacteria. The authors also report that tubercle bacilli with smooth colony morphology show reduced persistence and virulence compared to M. tuberculosis strains in infection experiments in mice.

Arul Chinnaiyan and colleagues identify NAB2-STAT6 fusions in 52 of 52 solitary fibrous tumor cases. Overexpression of this fusion induced cell proliferation, which could be suppressed by knockdown of EGR1.

Stein Aerts, Jan Cools and colleagues report exome sequencing of T-cell acute lymphoblastic leukemia. They identify recurrent somatic mutations in CNOT3 and ribosome genes RPL5 and RPL10.

Wei Zheng and colleagues report genome-wide analyses in east Asians and identify three new loci associated with colorectal cancer risk.

Karen Mohlke, Markku Laakso, Michael Boehnke and colleagues report the first application of the Illumina HumanExome Beadchip array, examining association with insulin and glycemic traits in 8,229 nondiabetic Finnish males from the population-based Metabolic Syndrome in Men (METSIM) study. They identify low-frequency coding variants at both known and newly associated loci with insulin processing and secretion.

Daniel Kastner and colleagues report genome-wide association analyses for Behçet's disease, a condition characterized by episodic inflammation of the skin and eyes and an important cause of blindness. They identify four loci newly associated with Behçet's disease, an epistatic interaction between HLA-B*51 and ERAP1 and overlap with loci previously associated to related inflammatory disorders.

Jenefer Blackwell, Peter Donnelly and colleagues report a genome-wide association study for visceral leishmaniasis using studies from India and Brazil, with replication in an additional Indian study. They identify common variants at the HLA-DRB1–HLA-DQA1 HLA class II region associated with susceptibility to visceral leishmaniasis.

Michal Minczuk, Wolfram Kunz and colleagues report that loss-of-function mutations in MGME1 impair mitochondrial DNA replication and cause a multisystemic mitochondrial disease. Their functional studies show that MGME1 encodes a RecB-type exonuclease that cleaves single-stranded DNA and processes DNA flap substrates.

Minsheng You and colleagues report the whole-genome sequence of the diamondback moth, Plutella xylostella. Their transcriptome analysis from different life stages, together with comparative genomic and phylogenetic analysis, provides insights into herbivore evolution and insect adaptation to plant feeding and detoxification.