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Loss of NECTIN1 is a frequent event in human melanoma and is associated with metastasis. NECTIN1 depletion modulates a switch from cell–cell adhesion to cell–matrix adhesion in response to low levels of IGF1 signaling from the microenvironment.
Nanopore sequencing is used to profile chromatin accessibility and DNA methylation on DNA molecules over 100 kb. Phasing analysis at the H19/IGF2 locus identifies a primate-specific enhancer driving biallelic IGF2 expression in specific cellular contexts.
Implementation of a genomics-informed prebreeding strategy in a global winter wheat collection enhances the use of genebank accessions and uncovers the value of genetic resources for wheat improvement.
Heterozygous de novo gain-of-function mutations in KCNK3, which encodes the two-pore-domain K+ channel TASK-1, cause a channelopathy characterized by developmental delay with sleep apnea.
The ion channel NALCN regulates cell shedding in mice and enhances metastasis in mouse models of cancer. Disseminated cells without oncogenic mutations form normal structures at secondary sites, suggesting that cell shedding is a physiological process that is hijacked during tumorigenesis.
The sc-linker is an analysis framework that combines genome-wide association study summary statistics, epigenomics and single-cell transcriptomes to identify disease-critical cell types and cellular processes across tissues and states.
Cross-disorder genetic association analyses identify five loci differentiating attention-deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). Individuals diagnosed with both ADHD and ASD are double-loaded with genetic risk for both disorders.
Analyses of population-level variation in gene and enhancer expression in the human brain characterize the gene–enhancer regulome and the regulatory mechanisms of transcribed enhancers in neuropsychiatric diseases.
Single-cell DNA sequencing data are generated from human neurons using primary template-directed amplification and analyzed using SCAN2, an improved genotyping tool. Indels are enriched in neuronal regulatory elements and may be deleterious.
SAIGE-GENE+ performs set-based rare variant association tests with improved type 1 error control and computational efficiency by collapsing ultra-rare variants and conducting multiple tests corresponding to different minor allele frequency cutoffs and annotations.
Multi-modality single-cell sequencing determines genotype, transcriptome and methylome information in cells from individuals with DNMT3A R882 mutated clonal hematopoiesis, allowing for the comparison of mutant and wild-type cells from the same individuals.
A high-quality genome assembly of pea cultivar ZW6 and pan-genome analyses provide insights into pea genome evolution and domestication as well as genomic resources for pea improvement.
Random segregation of extrachromosomal DNA contributes to intratumoral heterogeneity and facilitates the rapid adaptation of human tumor cells to anticancer drugs.
Multi-ancestry meta-analyses of genome-wide association studies for self-reported physical activity during leisure time, leisure screen time, sedentary commuting and sedentary behavior at work identify 99 loci associated with at least one of these traits.
Cistrome-wide association study (CWAS) is an approach for nominating variants that impact traits through effects on chromatin state. CWAS performed on 307 prostate cistromes identifies candidate loci for prostate cancer and androgen-related traits.
METTL3-dependent RNA N6-methyladenosine (m6A) deposition can lead to DNA demethylation. The m6A reader FXR1 recruits DNA 5-methylcytosine dioxygenase TET1 to chromatin, which is linked to chromatin accessibility and gene transcription.
scDRS associates individual cells in scRNA-seq with disease by scoring single-cell transcriptomes using GWAS gene signatures. Applied to 74 GWAS and 1.3 million single-cell profiles, scDRS identifies specific cellular subpopulations associated with these diseases.
A genomic and transcriptomic analysis of 2,754 childhood acute lymphoblastic leukemias identifies 376 putative driver genes, and associations between disease subtypes and prognosis.
Analyses of gene–environment correlations across geographic regions for 56 complex traits in UK Biobank suggest that both passive and active sources of gene–environment correlation affect genetic association signals.