Letters in 2017

Sekar Kathiresan and colleagues perform a genome-wide association test for coronary artery disease (CAD) using data from the UK Biobank. They identify 15 new loci and perform phenome-wide association scanning, implicating insulin resistance pathways and transendothelial migration of leukocytes in CAD.

Sven van der Lee, Julie Williams, Gerard Schellenberg and colleagues identify rare coding variants in PLCG2, ABI3 and TREM2 associated with Alzheimer's disease. These genes are highly expressed in microglia and provide additional evidence that the microglia-mediated immune response contributes to the development of Alzheimer's disease.

Hugh Watkins and colleagues meta-analyze data from the UK Biobank along with recent genome-wide association studies for coronary artery disease. They identify 13 new loci that were genome-wide significant and 243 loci at a 5% false discovery rate.

Kumarasamy Thangaraj, David Reich and colleagues identify 81 South Asian groups descended from extreme founder events, including 14 with a census size of over 1 million people, thus providing an opportunity to test for and decrease the burden of recessive genetic diseases in these populations.

Jeff Hasty and colleagues use an endonuclease from S. cerevisiae along with quorum sensing from A. fischeri to produce sustained cycling of DNA plasmid concentration across a colony of E. coli cells. This copy number modulation system enables dynamic regulation of gene circuit elements without the need for specially engineered promoters.

Junko Takita, Seishi Ogawa and colleagues profile 121 cases of pediatric T cell acute lymphoblasic leukemia (T-ALL) and identify recurrent SPI1 (PU.1) gene fusions. They find that these SPI1 fusions correlated with poor survival, retained transcriptional activity and, in a mouse stem cell model, enhanced cell proliferation.

Rogier Versteeg, Johan van Nes and colleagues report that neuroblastomas comprise two cell types, mesenchymal and adrenergic, that have different responses to chemotherapeutic agents in vitro. Using ChIP–seq and expression profiling of pairs of phenotypically divergent isogenic cell lines, they identify candidate transcription factors for regulation of the two cell states.

Kari Stefansson and colleagues identify a nonsense mutation in RBM12 segregating with psychosis in an extended Icelandic pedigree and an independent frameshift mutation in RBM12 segregating with psychosis in a Finnish family. They further show that carriers of the Icelandic mutation who are unaffected by psychosis exhibit a psychiatric disorder and cognitive test battery profile resembling that of patients with schizophrenia.

Ian Alexander and colleagues characterize a liver-specific enhancer–promoter element that is found in the genome of wild-type adeno-associated virus type 2 (AAV2), from which gene transfer vectors have been derived. They suggest that these sequences could provide a possible link between AAV integration events in the liver and gene dysregulation and pathogenesis.

Ralph McGinnis, Valgerdur Steinthorsdottir, Linda Morgan and colleagues perform a genome-wide association study in the offspring of preeclampsia pregnancies and identify variants in the fetal genome near FLT1 that are associated with risk of preeclampsia. FLT1 is known to encode an isoform of placental origin implicated in the pathology of preeclampsia, providing biological support for the association of this locus with preeclampsia risk.

Christopher Amos and colleagues perform genome-wide association analysis for lung cancer using cohorts genotyped on the OncoArray and combing these with existing data. They identify 18 loci, 10 of which are new, finding heterogeneity across the different lung cancer subtypes, and explore candidate genes through eQTL analysis in lung tissue.

Clare Turnbull and colleagues report discovery of 19 new susceptibility loci for testicular germ cell tumor (TGCT) and provide evidence for a network of physical interactions between TGCT risk variants and candidate causal genes. Their findings implicate widespread disruption of developmental transcriptional regulators in TGCT susceptibility, consistent with failed primordial germ cell differentiation as an initiating step in oncogenesis.

Katherine Nathanson, Peter Kanetsky and colleagues present a meta-analysis of five genome-wide association studies of testicular germ cell tumor (TGCT). They identify eight new susceptibility loci and new independent signals at two previously reported loci, providing further clues to the etiology of TGCT.

Nazneen Rahman, Geert Kops and colleagues report the identification of biallelic loss-of-function mutations in TRIP13 in six individuals with Wilms tumor who presented with features of mosaic variegated aneuploidy. They show that TRIP13-mutant cells show spindle assembly checkpoint defects and suggest that mechanisms leading to aneuploidy may contribute directly to increased cancer risk.

Yuta Kochi and colleagues perform expression quantitative trait loci (eQTL) analysis on five subsets of immune cells individually sorted from blood from 105 individuals. They develop an integrated analysis pipeline of expression and epigenomic data along with gene association to identify cell-specific candidate causal genes and apply this to rheumatoid arthritis.

Danielle Posthuma and colleagues perform a large meta-analysis for intelligence and determine genetic overlap with several neuropsychiatric and metabolic traits. They find 15 new significant loci and implicate 40 new genes, most of which are predominantly expressed in the brain.

Cecilia Lo and colleagues report the recovery of mice with hypoplastic left heart syndrome (HLHS) from a large mutagenesis screen. They find genetic heterogeneity among HLHS mice and functionally validate mutations in two genes, Sap130 and Pcdha, as contributing to HLHS in a combinatorial manner.

Joanna Howson and colleagues perform a genome-wide association study and meta-analysis for coronary artery disease in large, trans-ancestry cohorts. They identify 15 new loci and correlate these regions with cell-type-specific gene expression and plasma protein levels to find novel pathways and potential mechanisms of disease.

Igor Grigoriev and colleagues perform single-molecule real-time sequencing on 16 diverse fungal species to evaluate levels of adenine methylation (6mA). They find that almost 3% of all adenines are methylated in early-diverging fungi, and they identify clusters of methylated adenines that are enriched at transcription start sites of active genes.

Stephen Tapscott and colleagues report that human DUX4, which is linked to facioscapulohumeral dystrophy, and mouse DUX activate genes associated with cleavage-stage embryos, including retrotransposons, in muscle cells. They suggest that the ancestral DUX4-regulated genes characteristic of cleavage-stage embryos are driven by conventional promoters, whereas divergence of the DUX4 and DUX homeodomains correlates with retrotransposon specificity.