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Pan-cancer genomic analyses based on HLA affinity predictions show that apparent neoantigen depletion signals in untreated tumors become negligible after correction for trinucleotide-based mutational signatures.
Short- and long-term cultures of human stem-cell-derived neurons reveal that a pattern of restricted selection of clustered protocadherin isoforms, pre-established in pluripotent cells, distinguishes immature from mature neurons.
Analysis of whole-genome sequences from more than 3,500 metastatic tumors identifies mutational signatures associated with different chemotherapies and provides estimates of the relative contribution of different treatments to tumor mutational burden.
Genome-wide meta-analysis with individuals of East Asian or European ancestry identifies 176 loci associated with schizophrenia. Despite consistent genetic effects across populations, polygenic risk models trained in one population have reduced performance in the other population.
Popular crop plants have been bred and selected for desirable taste and color traits. Genomic approaches are increasingly being used to provide insights into the origins, evolution and biology of our favorite foods. Large-scale sequencing efforts have brought agriculture genomics into the big-data era, leading to sweet rewards.
A fundamental problem in rare-disease diagnostics is the lack of consensus as to which genes have sufficient evidence to attribute causation. To address this issue, we have created PanelApp (https://panelapp.genomicsengland.co.uk), a publicly available knowledge base of curated virtual gene panels.
Two genetic studies uncover how domestication changed fruit quality traits in melon and watermelon. The studies combine population genomic and quantitative genetic tools to study crop evolution and provide breeders with comprehensive variation maps.
Genome-wide analyses in 19,629 individuals identify 365 independent variants associated with brain volumetric phenotypes. The study provides insight into the overlapping genetic architecture of brain volume measures and cognitive and mental health traits.
Genome-wide analysis of venous thromboembolism identifies 22 new risk loci and facilitates construction of a polygenic risk score. Comparison to arterial vascular disease highlights shared pathophysiology and potential therapeutic strategies.
Analysis of whole-genome sequencing and expression data for 17 tissues identifies short tandem repeats whose repeat number is associated with gene expression (eSTRs). Specific eSTRs are implicated in different complex traits through colocalization analysis with known genome-wide association study signals.
Cytokine-induced regulatory changes in human pancreatic islets illustrate the β-cell chromatin dynamics in response to a proinflammatory environment and implicate a role for islet enhancers in type 1 diabetes.
A comprehensive map of genomic variation in melon derived from resequencing of 1,175 accessions sheds light on the population structure and domestication history of melon and agronomic traits for melon breeding.
An improved watermelon reference genome and whole-genome resequencing of 414 cultivated and wild accessions provide insights into fruit quality traits and dessert watermelon evolution.
The rare loss-of-function allele p.Arg138* in SLC30A8 (encoding ZnT8) mediates protection against type 2 diabetes (T2D) through promoting better insulin secretion and enhanced glucose responsiveness, suggesting ZnT8 as a target for T2D treatment.
Genome-wide analyses identify variants near HDAC9 associated with abdominal aortic calcification and other cardiovascular phenotypes. Functional work shows that HDAC9 promotes an osteogenic vascular smooth muscle cell phenotype, enhancing calcification and reducing contractility.
A generic framework for providing participant information and implementing a tiered consent process for health genomic research in Africa can help to harness global health benefits from sharing and meta-analysis of African genomic data while simultaneously respecting and upholding the autonomy and individual choices of African research participants.
The authors explore the impact of nonsense-mediated mRNA decay (NMD) on human genetic disease and cancer immunotherapy by applying the rules of NMD across the genome as a resource called NMDetective.
Genome-wide analysis identifies variants associated with the volume of seven different subcortical brain regions defined by magnetic resonance imaging. Implicated genes are involved in neurodevelopmental and synaptic signaling pathways.