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Showing 1–50 of 68 results
Advanced filters: Author: Stella Zhu Clear advanced filters
  • A large-scale mouse study reveals that while existing epigenomic data detect many developmental enhancers, a substantial fraction is missed - highlighting the need for expanded resources to fully annotate enhancers genome-wide.

    • Brandon J. Mannion
    • Stella Tran
    • Len A. Pennacchio
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-11
  • A genome-wide association meta-analysis study of blood lipid levels in roughly 1.6 million individuals demonstrates the gain of power attained when diverse ancestries are included to improve fine-mapping and polygenic score generation, with gains in locus discovery related to sample size.

    • Sarah E. Graham
    • Shoa L. Clarke
    • Cristen J. Willer
    Research
    Nature
    Volume: 600, P: 675-679
  • A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

    • Mari E. K. Niemi
    • Juha Karjalainen
    • Chloe Donohue
    ResearchOpen Access
    Nature
    Volume: 600, P: 472-477
  • A large genome-wide association study of more than 5 million individuals reveals that 12,111 single-nucleotide polymorphisms account for nearly all the heritability of height attributable to common genetic variants.

    • Loïc Yengo
    • Sailaja Vedantam
    • Joel N. Hirschhorn
    ResearchOpen Access
    Nature
    Volume: 610, P: 704-712
  • Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

    • Athanasios Kousathanas
    • Erola Pairo-Castineira
    • J. Kenneth Baillie
    ResearchOpen Access
    Nature
    Volume: 607, P: 97-103
  • Analysis of 97,691 high-coverage human blood DNA-derived whole-genome sequences enabled simultaneous identification of germline and somatic mutations that predispose individuals to clonal expansion of haematopoietic stem cells, indicating that both inherited and acquired mutations are linked to age-related cancers and coronary heart disease.

    • Alexander G. Bick
    • Joshua S. Weinstock
    • Pradeep Natarajan
    Research
    Nature
    Volume: 586, P: 763-768
  • Rajderkar et al. provide a genome-wide compendium of transcriptional enhancers active in human craniofacial development, along with single-cell resources for studies of mammalian craniofacial morphogenesis.

    • Sudha Sunil Rajderkar
    • Kitt Paraiso
    • Axel Visel
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-18
  • While GWAS have uncovered susceptibility loci for B-cell precursor acute lymphoblastic leukemia (BCP-ALL), much of the heritable risk remains undiscovered. Here, the authors perform a meta-analysis of two existing BCP-ALL GWAS together with an unpublished GWAS to identify risk loci at 8q24.21 and 2q22.3.

    • Jayaram Vijayakrishnan
    • James Studd
    • Richard S. Houlston
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-9
  • GWAS have identified more than 500 genetic loci associated with blood lipid levels. Here, the authors report a genome-wide analysis of interactions between genetic markers and physical activity, and find that physical activity modifies the effects of four genetic loci on HDL or LDL cholesterol.

    • Tuomas O. Kilpeläinen
    • Amy R. Bentley
    • Ruth J. F. Loos
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-11
  • A genome-wide association study including over 76,000 individuals with schizophrenia and over 243,000 control individuals identifies common variant associations at 287 genomic loci, and further fine-mapping analyses highlight the importance of genes involved in synaptic processes.

    • Vassily Trubetskoy
    • Antonio F. Pardiñas
    • Jim van Os
    Research
    Nature
    Volume: 604, P: 502-508
  • Reduced glomerular filtration rate (eGFR) is a hallmark of chronic kidney disease. Here, Pattaro et al. conduct a meta-analysis to discover several new loci associated with variation in eGFR and find that genes associated with eGFR loci often encode proteins potentially related to kidney development.

    • Cristian Pattaro
    • Alexander Teumer
    • Caroline S. Fox
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-19
  • Carotid intima-media thickness (cIMT) and plaque are associated with subclinical atherosclerosis and coronary heart disease (CHD). Here, the authors identify and prioritize genetic loci for cIMT and plaque by GWAS and colocalization approaches and further demonstrate genetic correlation with CHD and stroke.

    • Nora Franceschini
    • Claudia Giambartolomei
    • Christopher J. O’Donnell
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-14
  • Genome wide association studies have identified multiple loci associated with risk of developing prostate cancer but the functional significance of many of these are unknown. Here, after generating models to predict methylation, the authors identify CpG methylation sites associated with prostate cancer.

    • Lang Wu
    • Yaohua Yang
    • Stella Koutros
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-11
  • Although the common genetic variants contributing to blood lipid levels have been studied, the contribution of rare variants is less understood. Here, the authors perform a rare coding and noncoding variant association study of blood lipid levels using whole genome sequencing data.

    • Margaret Sunitha Selvaraj
    • Xihao Li
    • Pradeep Natarajan
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-18
  • The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.

    • Daniel Taliun
    • Daniel N. Harris
    • Gonçalo R. Abecasis
    ResearchOpen Access
    Nature
    Volume: 590, P: 290-299
  • The influence of X chromosome genetic variation on blood lipids and coronary heart disease (CHD) is not well understood. Here, the authors analyse X chromosome sequencing data across 65,322 multi-ancestry individuals, identifying associations of the Xq23 locus with lipid changes and reduced risk of CHD and diabetes mellitus.

    • Pradeep Natarajan
    • Akhil Pampana
    • Gina M. Peloso
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-14
  • Mutagenesis of 23 ultraconserved enhancers and examination of their activities in transgenic mouse reporter assays show that overall their regulatory properties are robust to mutation. Manipulation of endogenous loci in mice corroborates reporter assay data.

    • Valentina Snetkova
    • Athena R. Ypsilanti
    • Diane E. Dickel
    Research
    Nature Genetics
    Volume: 53, P: 521-528
  • Using data from a single time point, passenger-approximated clonal expansion rate (PACER) estimates the fitness of common driver mutations that lead to clonal haematopoiesis and identifies TCL1A activation as a mediator of clonal expansion.

    • Joshua S. Weinstock
    • Jayakrishnan Gopakumar
    • Siddhartha Jaiswal
    Research
    Nature
    Volume: 616, P: 755-763
  • The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.

    • Tim H. H. Coorens
    • Ji Won Oh
    • Yuqing Wang
    Reviews
    Nature
    Volume: 643, P: 47-59
  • Similarities in cancers can be studied to interrogate their etiology. Here, the authors use genome-wide association study summary statistics from six cancer types based on 296,215 cases and 301,319 controls of European ancestry, showing that solid tumours arising from different tissues share a degree of common germline genetic basis.

    • Xia Jiang
    • Hilary K. Finucane
    • Sara Lindström
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-23
  • John Chambers, Jaspal Kooner, Pim van der Harst, Shyong Tai, Paul Elliott, Jiang He, Norihiro Kato and colleagues performed a genome-wide association study of blood pressure phenotypes in individuals of European, East Asian and South Asian ancestry. They find trait-associated SNPs at 12 loci, some of which are associated with methylation at nearby CpG sites.

    • Norihiro Kato
    • Marie Loh
    • John C Chambers
    Research
    Nature Genetics
    Volume: 47, P: 1282-1293
  • Multiple myeloma is a cancer of the plasma cells, and the complete aetiology of the disease is still unclear. Here the authors perform an additional GWAS analysis followed by a meta-analysis with existing GWAS and replication genotyping and identify 6 novel risk loci and utilise gene expression, epigenetic profiling and in situ Hi-C data to further our understanding of MM susceptibility.

    • Molly Went
    • Amit Sud
    • Stephen N. Thibodeau
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-10
  • Timblin et al. demonstrate that LPS or hydroxyoestrogen-induced mitochondrial stress triggers mitohormesis in macrophages, restraining inflammatory gene activation by suppressing oxidative metabolism.

    • Greg A. Timblin
    • Kevin M. Tharp
    • Kaoru Saijo
    Research
    Nature Metabolism
    Volume: 3, P: 618-635
  • A study shows that clonal haematopoiesis of indeterminate potential is associated with an increased risk of chronic liver disease specifically through the promotion of liver inflammation and injury.

    • Waihay J. Wong
    • Connor Emdin
    • Pradeep Natarajan
    Research
    Nature
    Volume: 616, P: 747-754
  • STAAR is a powerful rare variant association test that incorporates variant functional categories and complementary functional annotations using a dynamic weighting scheme based on annotation principal components. STAAR accounts for population structure and relatedness and is scalable for analyzing large whole-genome sequencing studies.

    • Xihao Li
    • Zilin Li
    • Xihong Lin
    Research
    Nature Genetics
    Volume: 52, P: 969-983
  • Most studies of the genetics of the metabolome have been done in individuals of European descent. Here, the authors integrate genomics and metabolomics in Black individuals, highlighting the value of whole genome sequencing in diverse populations and linking circulating metabolites to human disease.

    • Usman A. Tahir
    • Daniel H. Katz
    • Robert E. Gerszten
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-16
  • Ludmila Prokunina-Olsson and colleagues report a fine-mapping and association analysis of germline variants in the APOBEC3 region associated with cancer risk. They identify two variants with differential effects in bladder and breast cancer, and their in vitro results suggest that environmental exposures may induce tissue-specific APOBEC mutagenesis and contribute to oncogenesis in carriers of APOBEC3 risk variants.

    • Candace D Middlebrooks
    • A Rouf Banday
    • Ludmila Prokunina-Olsson
    Research
    Nature Genetics
    Volume: 48, P: 1330-1338
  • Fernando Rivadeneira and colleagues in the Genetic Factors for Osteoporosis Consortium report a large-scale meta-analysis identifying new loci associated with bone mineral density (BMD) and risk of fracture. Thirty-two new loci are found to be associated with BMD, and 6 loci confer higher risk for low-trauma bone fracture.

    • Karol Estrada
    • Unnur Styrkarsdottir
    • Fernando Rivadeneira
    Research
    Nature Genetics
    Volume: 44, P: 491-501
  • Platelet aggregation is associated with myocardial infarction and stroke. Here, the authors have conducted a whole genome sequencing association study on platelet aggregation, discovering a locus in RGS18, where enhancer assays suggest an effect on activity of haematopoeitic lineage transcription factors.

    • Ali R. Keramati
    • Ming-Huei Chen
    • Andrew D. Johnson
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-13
  • Pooling participant-level genetic data into a single analysis can result in variance stratification, reducing statistical performance. Here, the authors develop variant-specific inflation factors to assess variance stratification and apply this to pooled individual-level data from whole genome sequencing.

    • Tamar Sofer
    • Xiuwen Zheng
    • Kenneth M. Rice
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-14
  • The cellular heterogeneity in brain obscures the identification of robust cellular regulatory networks. Here the authors integrate genome-wide chromosome conformation data from sorted neurons and glia, with transcriptomic and enhancer profiles, to characterize cell-type-specific gene regulatory landscapes in the human brain, and provide insights into cell-type-specific gene regulatory networks in brain disorders.

    • Benxia Hu
    • Hyejung Won
    • Daniel H. Geschwind
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-13
  • Classical Hodgkin lymphoma is a cancer that originates in lymph nodes. Little is known about its genetic susceptibility. Here, the authors combined existing and new genome-wide association studies to identify risk loci for classical Hodgkin lymphoma at 6q22.33, and nodular sclerosis Hodgkin lymphoma at 3q28, 6q23.3, 10p14, 13q34, 16p13.13.

    • Amit Sud
    • Hauke Thomsen
    • Richard S. Houlston
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-11
  • Stella Hubbart et al. show that over-expression of the photoprotective protein gene psbS leads to enhanced canopy-level radiation use efficiency and grain yield in rice. The results demonstrate that alterations to photoprotection and light-harvesting processes could be used to improve yield in rice crops.

    • Stella Hubbart
    • Ian R. A. Smillie
    • Erik H. Murchie
    ResearchOpen Access
    Communications Biology
    Volume: 1, P: 1-12
  • Genome-wide analysis of self-reported dyslexia identifies 42 associated loci, including 27 not previously associated with cognitive traits. Dyslexia shows genetic correlation with ambidexterity but not neuroanatomical measures of language-related circuitry.

    • Catherine Doust
    • Pierre Fontanillas
    • Michelle Luciano
    ResearchOpen Access
    Nature Genetics
    Volume: 54, P: 1621-1629
  • The Cancer Genome Atlas Network describe their multifaceted analyses of primary breast cancers, shedding light on breast cancer heterogeneity; although only three genes (TP53, PIK3CA and GATA3) are mutated at a frequency greater than 10% across all breast cancers, numerous subtype-associated and novel mutations were identified.

    • Daniel C. Koboldt
    • Robert S. Fulton
    • Jacqueline D. Palchik
    ResearchOpen Access
    Nature
    Volume: 490, P: 61-70
  • An analysis of 16 health-related quantitative traits in approximately 350,000 individuals reveals statistically significant associations between genome-wide homozygosity and four complex traits (height, lung function, cognitive ability and educational attainment); in each case increased homozygosity associates with a decreased trait value, but no evidence was seen of an influence on blood pressure, cholesterol, or ten other cardio-metabolic traits.

    • Peter K. Joshi
    • Tonu Esko
    • James F. Wilson
    Research
    Nature
    Volume: 523, P: 459-462