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Near-gapless and haplotype-resolved genome assemblies of the dwarfing ‘M9’ and semi-vigorous ‘MM106’ rootstocks and a major apple cultivar ‘Fuji’ provide insights into the genetic basis of rootstock-induced dwarfing traits.
An open-source automated algorithm called DeepFlow enables large-scale derivation of aortic flow measurements, and genetic analysis of aortic flow, structural and functional traits demonstrates a causal relationship between aortic size and aortic valve regurgitation.
Achieving a diagnosis for Indigenous people living with a rare, often genetic, disease is crucial for equitable healthcare. The International Rare Disease Research Consortium convened a global Task Force to bridge the gap in diagnosing Indigenous rare diseases, and identify solutions to tackle the health inequity faced by Indigenous people.
Understanding clinical heterogeneity in attention deficit hyperactivity disorder (ADHD) is important for improving personalized care and long-term outcomes. A study exploits the large scale and breadth of phenotyping of the iPSYCH cohort to link clinical heterogeneity to genetic heterogeneity in ADHD.
Fluorescence-activated nuclear sorting combined with deep profiling shows that Huntington’s disease repeat expansions arise in specific cell types and are associated with elevated MSH2 and MSH3, which promote expansions in vitro by inhibiting excision of CAG slip-outs by FAN1.
Bottom-up in vitro reconstitution of ~10-kb chromatin domains shows that nucleosome positioning, rather than loop extrusion or transcription, determines domain formation in yeast.
Causal-TWAS (cTWAS) is a statistical framework that adjusts for genetic confounders in transcriptome-wide association studies. Application of cTWAS on common traits leads to reliable detection of candidate causal genes.
GIFT fine-maps candidate causal genes in a transcription-wide association study by conditioning on predicted expression of nearby genes, leading to improved statistical power and enhanced mapping resolution when applied to complex traits.
Multi-omic analysis of single nuclei from 12 human placentas collected during early-stage and late-stage pregnancy characterizes syncytiotrophoblast diversity. Gene regulatory network analysis implicates candidate lineage regulators such as STAT5A and CEBPB.
This Review explores mechanistic theories of aging, discusses challenges in establishing causality of these mechanisms and suggests that genetically informed investigation will help address this gap.
Skin color is highly variable in Africans, but the underlying molecular mechanisms remain poorly understood. Using population genetics and functional genomics, we identified key genetic variants, regulatory elements and genes that affect skin pigmentation, an adaptive trait, which provides valuable insights into the mechanisms underlying human skin color diversity and evolution.
The genetic background of pediatric acute myeloid leukemia (AML) does not fit with classification systems developed for adult AML. This study investigates the genetic background of pediatric AML and proposes a genomic framework for improved classification and risk stratification based on the driver alterations.
A combination of single-cell imaging and dynamic polymer simulation shows that stacked boundary conformation facilitates cis-regulatory elements communication across topologically associating domain (TAD) borders at the Pitx1 locus in developing mouse limbs.
ZmWAKL, which encodes a cell-wall-associated receptor kinase-like protein, regulates quantitative disease resistance to gray leaf spot in maize through the ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module.
Inherited polygenic scores for blood cell traits are associated with an increased risk of JAK2V617F clonal expansion and influence clinical phenotypes in individuals with myeloproliferative neoplasms.
Genome-wide association analysis of triglycerides to high-density lipoprotein cholesterol (TG:HDL-C) ratio within the UK Biobank identifies candidate insulin resistance-associated loci linked to metabolic pathways and insulin biology. A polygenic risk score derived from these results shows an association with multiple cardiometabolic traits.
A new method allows selection of matched controls from an external pool of samples without genotype sharing. This method has been implemented in an online repository containing 39,472 exome sequencing controls that can be used for association analyses.
Massively parallel reporter assays identify 165 functional variants associated with skin pigmentation in ethnically diverse Africans. Functional characterization of eight variants demonstrates their impact in regulating melanin levels and validates CYB561A3 as a novel gene involved in melanogenesis and pigmentation.