Evidence map›Paper›PMID 37986808›Full record

ArticlebioRxiv : the preprint server for biology2023

Transcriptomics and chromatin accessibility in multiple African population samples.

Marianne K DeGorter, Page C Goddard, Emre Karakoc, Soumya Kundu, Stephanie M Yan, Daniel Nachun, Nathan Abell, Matthew Aguirre, Tommy Carstensen, Ziwei Chen and 22 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 13 citations in OpenAlex.

  1. Article
  2. Human Riboviruses: A Comprehensive Study.Journal of molecular evolution · 2025
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

32 authors at 10 institutions in 7 countries.

Marianne K DeGorterDepartment of Pathology, Stanford University, Stanford, CA.ORCID 0000-0001-7592-752X
Page C GoddardDepartment of Genetics, Stanford University, Stanford, CA.ORCID 0000-0001-8187-5316
Emre KarakocHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.ORCID 0000-0002-2324-8127
Soumya KunduDepartment of Computer Science, Stanford University, Stanford CA.ORCID 0000-0001-5182-5326
Stephanie M YanDepartment of Biology, Johns Hopkins University, Baltimore.ORCID 0000-0002-6880-465X
Daniel NachunDepartment of Pathology, Stanford University, Stanford, CA.ORCID 0000-0002-0271-1135
Nathan AbellDepartment of Genetics, Stanford University, Stanford, CA.ORCID 0000-0003-1098-5395
Matthew AguirreDepartment of Biomedical Data Science, Stanford University, Stanford, CA.ORCID 0000-0001-9069-6475
Tommy CarstensenHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.ORCID 0000-0002-3672-9931
Ziwei ChenDepartment of Computer Science, Stanford University, Stanford CA.ORCID 0000-0002-1479-5057
Matthew DurrantDepartment of Biology, Johns Hopkins University, Baltimore.ORCID 0000-0001-8433-1760
Vikranth R DwaracherlaDepartment of Electrical Engineering, Stanford University, Stanford, CA.
Karen FengDepartment of Biomedical Data Science, Stanford University, Stanford, CA.ORCID 0000-0001-5763-300X
Michael J GloudemansDepartment of Biomedical Data Science, Stanford University, Stanford, CA.ORCID 0000-0002-9924-9943
Naiomi HunterDepartment of Genetics, Stanford University, Stanford, CA.ORCID 0000-0002-1728-8421
Mohana P S MoorthyDepartment of Computer Science, Stanford University, Stanford CA.
Cristina PomillaHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.ORCID 0000-0002-2581-8365
Kameron B RodriguesDepartment of Pathology, Stanford University, Stanford, CA.ORCID 0000-0002-0270-3688
Courtney J SmithDepartment of Genetics, Stanford University, Stanford, CA.
Kevin S SmithDepartment of Pathology, Stanford University, Stanford, CA.ORCID 0000-0003-2432-1928
Rachel A UngarDepartment of Genetics, Stanford University, Stanford, CA.ORCID 0000-0002-2214-959X
Brunilda BalliuDepartment of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA and Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA.ORCID 0000-0001-8953-804X
Jacques FellaySchool of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland and Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.ORCID 0000-0002-8240-939X
Paul FlicekDepartment of Genetics, University of Cambridge, Cambridge, UK.ORCID 0000-0002-3897-7955
Paul J McLarenSexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Canada and Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.ORCID 0000-0001-6019-7018
Brenna HennDepartment of Anthropology, University of California Davis, Davis CA and Genome Center, University of California Davis, Davis CA.ORCID 0000-0003-4998-287X
Rajiv C McCoyDepartment of Biology, Johns Hopkins University, Baltimore.ORCID 0000-0003-0615-146X
Lauren SugdenDepartment of Mathematics and Computer Science, Dusquesne University, Pittsburgh, PA.ORCID 0000-0003-3495-8359
Anshul KundajeDepartment of Genetics, Stanford University, Stanford, CA.ORCID 0000-0003-3084-2287
Manjinder S SandhuDepartment of Medicine, University of Cambridge, Cambridge, UK.
Deepti GurdasaniWilliam Harvey Research Institute, Queen Mary University of London, London, UK; Kirby Institute, University of New South Wales, Australia; School of Medicine, University of Western Australia, Australia.ORCID 0000-0001-9996-6929
Stephen B MontgomeryDepartment of Pathology, Stanford University, Stanford, CA.ORCID 0000-0002-5200-3903
Stanford University · USJohns Hopkins University · USNovo Nordisk (Denmark) · DKUniversity of Cambridge · GBDuquesne University · USÉcole Polytechnique Fédérale de Lausanne · CHPublic Health Agency of Canada · CAQueen Mary University of London · GBUniversity of California, Davis · USUniversity of California, Los Angeles · US

Funding

INSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2M
POSTDOCTORAL TRAINING IN MEDICAL INFORMATION SCIENCEST15LM007033 · NLM · STANFORD UNIVERSITY · PI SYLVIA KATINA PLEVRITIS · 1985 to 2026
$25.5M
Decoding the regulatory architecture of the human genome across cell types, individuals and diseaseU01HG009431 · NHGRI · STANFORD UNIVERSITY · PI PRITCHARD, JONATHAN K · 2017 to 2021
$3.5M
Function and fitness consequences of human genetic variationR35GM133747 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Rajiv Champion McCoy · 2019 to 2026
$3.3M
Investigating the role of structural variation in hominin evolution.F31HG012495 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI YAN, STEPHANIE M · 2022 to 2023
$86k
NHGRI NIH HHS F31 HG012495NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG009431NIGMS NIH HHS R35 GM133747NLM NIH HHS T15 LM007033
6 · The paper itself

Abstract

Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.

Identifiers

PMID37986808
PMCPMC10659267
OpenAlexW4388424823

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.