Volume 51 Issue 3, March 2019

The origin of strawberry is truly global, involving both natural processes and human intervention. The strawberry genome sequence provides support for an influential hypothesis of genome dominance.

Genomic analysis of 151 diploid potatoes and three potato populations produced by self-crossing identifies 344,831 deleterious substitutions and 15 genomic regions with severe segregation distortions, providing the basis for genome design of potato inbred lines.

Genome-wide association analyses identify 28 new susceptibility loci for type 2 diabetes in the Japanese population. Transethnic comparisons highlight the key role of beta cell dysfunction in type 2 diabetes across different ancestry groups.

Genome-wide association analyses identify 57 loci associated with insomnia symptoms and provide evidence of shared genetic architecture between insomnia and cardiometabolic, behavioral, psychiatric and reproductive traits.

Genome-wide analyses in >1 million individuals identify new loci and pathways associated with insomnia. The findings implicate key brain areas and cell types in the neurobiology of insomnia and highlight potential targets for developing new treatments.

Genome-wide meta-analysis of clinically diagnosed Alzheimer’s disease (AD) and AD-by-proxy (71,880 AD cases, 383,378 controls) identifies new loci and functional pathways that contribute to AD risk.

Large genome-wide meta-analysis of clinically diagnosed late-onset Alzheimer’s disease (LOAD) from 94,437 individuals identifies new LOAD risk loci and implicates Aβ formation, tau protein binding, immune response and lipid metabolism.

A genome-wide-association meta-analysis of 18,381 austim spectrum disorder (ASD) cases and 27,969 controls identifies five risk loci. The authors find quantitative and qualitative polygenic heterogeneity across ASD subtypes.

New methods for multivariate genome-wide-association meta-analysis (GWAMA) applied to four well-being spectrum traits identifies 304 association loci, representing a 26% increase in the number of signals, as compared with four univariate analyses.

A transancestral exome-wide association study for body-fat distribution identifies protein-coding variants that are significantly associated with waist-to-hip ratio adjusted for body mass index.

Sequencing of the MHC region in the Japanese population provides insight into population-specific allelic and structural variability. These data enable discovery and fine-mapping of genotype–phenotype associations across 52 phenotypes.

A genome-wide association study in more than 400,000 individuals identifies 139 new signals for lung function. These variants can predict chronic obstructive pulmonary disease in independent, transancestral cohorts.

Genome-wide analysis of chronic obstructive pulmonary disease identifies 82 loci, 35 of which are new. Integration of gene expression and genomic annotation data shows enrichment of signals in lung tissue, smooth muscle and several lung cell types.

Genomic analysis of 551 esophageal adenocarcinomas identifies new driver mutations and biomarkers associated with poor prognosis. More than 50% of esophageal adenocarcinomas contain sensitizing events for CDK4/CDK6 inhibitors, thus providing an evidence base for targeted therapeutics.

Oncogenic gain-of-function EZH2 mutations alter gene–promoter interactions and lead to silencing 1,034 of genes within topologically associating domains, thus resulting in inactivation of multiple tumor-suppressor genes.

scRepli-seq measures DNA replication timing in single cells on the basis of copy number. Applying haplotype-resolved scRepli-seq to mESCs establishes basic principles of replication-timing conservation and heterogeneity among populations of cells.

Chromosome-scale assembly for the cultivated octoploid strawberry (Fragaria × ananassa) uncovers the origin and evolutionary processes that shaped this complex allopolyploid, providing a useful resource for genome-wide analyses and molecular breeding.

This study presents the genomes of 2,101 emm28 Streptococcus pyogenes invasive strains, of which 492 were transcriptionally profiled, and 50 were assessed for virulence. GWAS, eQTL analysis, and study of isogenic mutant strains identified an intergenic region that alters global transcript profiles and bacterial virulence.

This comprehensive pancancer analysis of RNA-sequencing data from bulk tumors defines the landscape of tumor-infiltrating B cell–receptor repertoires and highlights new mechanisms of tumor immune evasion through genetic alterations.

UTMOST (unified test for molecular signatures) is a method for cross-tissue gene expression imputation for transcriptome-wide association analyses. Cross-tissue TWAS using UTMOST identifies new candidate genes for late-onset Alzheimer’s disease.