Evidence map›Paper›PMID 36085083›Full record

ArticleGenome medicine2022

Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative.

Ruth Johnson, Yi Ding, Vidhya Venkateswaran, Arjun Bhattacharya, Kristin Boulier, Alec Chiu, Sergey Knyazev, Tommer Schwarz, Malika Freund, Lingyu Zhan and 16 more

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In one paragraph

Article in Genome medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 37 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed, 2 pooled it
–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

37 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
  2. Pooled it
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  8. SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores.bioRxiv : the preprint server for biology · 2026
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  12. Common and rare variant genetic contributions in African Americans with autism.medRxiv : the preprint server for health sciences · 2025
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  16. Review
  17. Article
  18. Big data in sarcoidosis.Current opinion in pulmonary medicine · 2024
    Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

26 authors.

Ruth JohnsonDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA. ruthjohnson@g.ucla.edu.ORCID http://orcid.org/0000-0002-1929-0998
Yi DingDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Vidhya VenkateswaranDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Arjun BhattacharyaDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Kristin BoulierBioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Alec ChiuBioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Sergey KnyazevDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Tommer SchwarzDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Malika FreundDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Lingyu ZhanMolecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Kathryn S BurchDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Christa CaggianoDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Brian HillDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Nadav RakoczDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Brunilda BalliuDepartment of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Christopher T DennyDivision of Hematology/Oncology, Department of Pediatrics, Gwynne Hazen Cherry Memorial Laboratories, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Jae Hoon SulDepartment of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Noah ZaitlenProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Valerie A ArboledaDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Eran HalperinDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Sriram SankararamanDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Manish J ButteDepartment of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
UCLA Precision Health Data Discovery Repository Working Group, UCLA Precision Health ATLAS Working Group
Clara LajonchereProgram in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Daniel H GeschwindDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Bogdan PasaniucDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA. pasaniuc@g.ucla.edu.

Funding

UCLA Clinical Translational Science InstituteUL1TR001881 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARLEEN F. BROWN, ARASH NAEIM · 2016 to 2026
$118.1M
CARDIOVASCULAR SCIENTIST TRAINING PROGRAMT32HL007895 · NHLBI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SHIVKUMAR, KALYANAM, WATSON, KAROL E · 1998 to 2023
$9.2M
Training Grant in Genomic Analysis and InterpretationT32HG002536 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Valerie A Arboleda, Harold Pimentel · 2002 to 2026
$8.6M
Methods for Genome-wide Association Studies in Admixed PopulationsR01HG006399 · NHGRI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L · 2011 to 2024
$6.3M
Elucidation of the genetic mechanisms driving prostate tumorigenesis through integrative computational and functional approachesR01CA251555 · NCI · DANA-FARBER CANCER INST · PI FREEDMAN, MATTHEW L, PASANIUC, BOGDAN · 2021 to 2025
$3.4M
Genomic Approaches to Population Health in Multi-Ethnic Hospital SystemsR01HG011345 · NHGRI · UNIVERSITY OF COLORADO DENVER · PI ARBOLEDA, VALERIE A, GIGNOUX, CHRISTOPHER R · 2020 to 2023
$3.1M
Unraveling correlations between Mendelian and common disease using functional genomicsDP5OD024579 · OD · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARBOLEDA, VALERIE A · 2017 to 2021
$1.9M
Statistical Models for Dissecting Human Population Admixture and its Role in Evolution and DiseaseR35GM125055 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SANKARARAMAN, SRIRAM · 2017 to 2021
$1.6M
UCLA Dental Specialty PhD ProgramK12DE027830 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Yvonne L Kapila · 2018 to 2026
$1.5M
NCATS NIH HHS UL1 TR001881NCI NIH HHS R01 CA251555NHGRI NIH HHS R01 HG006399NHGRI NIH HHS R01 HG011345NHGRI NIH HHS T32 HG002536NHLBI NIH HHS T32 HL007895NIDCR NIH HHS K12 DE027830NIGMS NIH HHS R35 GM125055NIH HHS DP5 OD024579
6 · The paper itself

Abstract

backgroundLarge medical centers in urban areas, like Los Angeles, care for a diverse patient population and offer the potential to study the interplay between genetic ancestry and social determinants of health. Here, we explore the implications of genetic ancestry within the University of California, Los Angeles (UCLA) ATLAS Community Health Initiative-an ancestrally diverse biobank of genomic data linked with de-identified electronic health records (EHRs) of UCLA Health patients (N=36,736).

methodsWe quantify the extensive continental and subcontinental genetic diversity within the ATLAS data through principal component analysis, identity-by-descent, and genetic admixture. We assess the relationship between genetically inferred ancestry (GIA) and >1500 EHR-derived phenotypes (phecodes). Finally, we demonstrate the utility of genetic data linked with EHR to perform ancestry-specific and multi-ancestry genome and phenome-wide scans across a broad set of disease phenotypes.

resultsWe identify 5 continental-scale GIA clusters including European American (EA), African American (AA), Hispanic Latino American (HL), South Asian American (SAA) and East Asian American (EAA) individuals and 7 subcontinental GIA clusters within the EAA GIA corresponding to Chinese American, Vietnamese American, and Japanese American individuals. Although we broadly find that self-identified race/ethnicity (SIRE) is highly correlated with GIA, we still observe marked differences between the two, emphasizing that the populations defined by these two criteria are not analogous. We find a total of 259 significant associations between continental GIA and phecodes even after accounting for individuals' SIRE, demonstrating that for some phenotypes, GIA provides information not already captured by SIRE. GWAS identifies significant associations for liver disease in the 22q13.31 locus across the HL and EAA GIA groups (HL p-value=2.32×10

conclusionsOverall, our results explore the interplay between SIRE and GIA within a disease context and underscore the utility of studying the genomes of diverse individuals through biobank-scale genotyping linked with EHR-based phenotyping.

Indexed as

Electronic Health RecordsPublic HealthAsian PeopleBiological Specimen BanksGenomicsHumansBiobankElectronic health recordsGenetic ancestryGenome-wide association studiesPhenome-wide association studies

Identifiers

PMID36085083
PMCPMC9461263

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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.