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The authors present an integrative framework for identifying structural variants (SVs) in cancer that applies optical mapping, Hi-C, and whole-genome sequencing. They find SVs affecting distal regulatory sequences, DNA replication, and three-dimensional chromatin structure.
Signed linkage disequilibrium profile regression is a new method for detecting directional effects of genomic annotations on disease risk. The results implicate new causal disease genes and can suggest mechanisms underlying the effects of causal genes on disease.
Genome-wide analyses identify 42 risk loci for diverticular disease, 39 of which are new. Genes in associated regions are enriched for expression in connective tissue cell types and are coexpressed with genes involved in vascular and mesenchymal biology.
Analysis of sequencing data from 249 cancer patients with clinically annotated outcomes to immune checkpoint therapy identifies correlates of treatment response. The results highlight complexity in identifying events that generate an immunoresponsive tumor environment.
Analysis of GTEx, cancer and autism data sets shows that cis-regulatory variation can modify the penetrance of coding variants. Deleterious coding variants on regulatory haplotypes resulting in high expression are enriched in disease cohorts and selected against in general populations.
This study identifies a set of critical dependency genes in MYCN-amplified neuroblastoma that make up the oncogenic transcriptional regulatory circuitry underlying cell state and tumor survival.
The authors identify copy number signatures from shallow whole-genome sequencing of high-grade serous ovarian cancer (HGSOC) cases. HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in genomic aberration.
Genome-wide polygenic risk scores derived from GWAS data for five common diseases can identify subgroups of the population with risk approaching or exceeding that of a monogenic mutation.
Analysis of summary statistics from 32 GWAS datasets using a new likelihood-based approach evaluates polygenicity across different traits. Effect-size distributions predict the sample sizes needed to explain the SNP-based heritability of traits.
Relatedness disequilibrium regression is a new method for estimating heritability that removes environmental bias by taking advantage of variation in relatedness due to random Mendelian segregation.
ASMC is a new method to estimate coalescence times using SNP array or sequencing data. When applied to data from the UK Biobank or Genome of the Netherlands, ASMC detects signals of recent positive selection and background selection.
SAIGE (Scalable and Accurate Implementation of GEneralized mixed model) is a generalized mixed model association test that can efficiently analyze large data sets while controlling for unbalanced case-control ratios and sample relatedness, as shown by applying SAIGE to the UK Biobank data for > 1,400 binary phenotypes.
Two BAH-domain-containing proteins (SHL and EBS) form a complex with EMF1, reading and effecting the H3K27me3 mark in Arabidopsis. The BAH-EMF1c complex thus shows PRC1-like functions in higher plants.
EBS, which prevents premature flowering in Arabidopsis, is shown to bind H3K27me3 and H3K4me3 via different domains. Disruption of either EBS–H3K27me3 or EBS–H3K4me3 interaction induces early floral transition.
Large-scale association analyses identify 142 independent risk variants for atrial fibrillation. Pathway and functional enrichment analyses suggest that many of the putative risk genes act via cardiac structural remodeling.
Sequencing and de novo assembly of the maize W22 reference genome enable accurate placement of Mutator (Mu) and Dissociation (Ds) transposable element insertions, providing a foundation for maize functional genomics and transposon biology.
The de novo genome assembly of maize line Mo17 and comparative analysis with other sequenced maize lines show extensive gene-order variations. This study provides insights into maize evolution and has implications for improving maize hybrid lines.
Coding variants in peptidylglycine α-amidating monooxygenase (PAM) associated with type 2 diabetes risk negatively impact overall PAM activity via defects in expression and catalytic function, resulting in reduced insulin content and altered dynamics of insulin secretion.
A combined analysis of participants from the UK Biobank and the International Glaucoma Genetic Consortium identifies 85 new loci for intraocular pressure (IOP). Pathway analysis uncovers new pathways associated with both IOP and glaucoma.
A coupled knockdown-editing screen shows that CRISPR–Cas9 editing in human cells requires the Fanconi anemia pathway, which acts by diverting double-strand break repair away from non-homologous end joining toward single-strand template repair.