Evidence map›Paper›PMID 37490908›Full record

ArticleAmerican journal of human genetics2023

Genotype error due to low-coverage sequencing induces uncertainty in polygenic scoring.

Ella Petter, Yi Ding, Kangcheng Hou, Arjun Bhattacharya, Alexander Gusev, Noah Zaitlen, Bogdan Pasaniuc

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in American journal of human genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Beyond predictive RAmerican journal of human genetics · 2025
    Article
  5. Article
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

7 authors.

Ella PetterDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: ellapetter@ucla.edu.
Yi DingBioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kangcheng HouBioinformatics Interdepartmental Program, 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.
Alexander GusevDana-Farber Cancer Institute, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
Noah ZaitlenBioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, UCLA, Los Angeles, CA, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Bogdan PasaniucBioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: pasaniuc@ucla.edu.

Funding

Polygenic Risk Scores for Diverse Populations - Bridging Research and Clinical CareR01HL151152 · NHLBI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI Christy Leigh Avery, Jennifer Below · 2020 to 2026
$12.3M
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
PRS Center for Admixed Populations (CAPE)U01HG011715 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI Eimear Elizabeth Kenny, Leslie A Lange · 2021 to 2026
$5.2M
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
Characterizing non-coding somatic and germline variant interactions in ovarian cancerR01CA244569 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI GAYTHER, SIMON ANDREW, GUSEV, ALEXANDER · 2020 to 2024
$3.3M
Quantifying and Characterizing the shared genetic contribution to common cancersU01CA194393 · NCI · UNIVERSITY OF WASHINGTON · PI KRAFT, PETER, LINDSTROEM, SARA · 2015 to 2023
$3.0M
Integration of genetic, gene expression and environmental data to inform biological basis of mammographic densityR01CA244670 · NCI · UNIVERSITY OF WASHINGTON · PI LINDSTROEM, SARA · 2021 to 2024
$1.8M
Leveraging cross-cancer shared heritability to better understand the genetic architecture of cancerR01CA194393 · NCI · UNIVERSITY OF WASHINGTON · PI KRAFT, PETER, LINDSTROEM, SARA · 2020 to 2022
$1.6M
NCI NIH HHS R01 CA194393NCI NIH HHS R01 CA244569NCI NIH HHS R01 CA244670NCI NIH HHS R01 CA251555NCI NIH HHS U01 CA194393NHGRI NIH HHS R01 HG006399NHGRI NIH HHS U01 HG011715NHLBI NIH HHS R01 HL151152
6 · The paper itself

Abstract

Polygenic scores (PGSs) have emerged as a standard approach to predict phenotypes from genotype data in a wide array of applications from socio-genomics to personalized medicine. Traditional PGSs assume genotype data to be error-free, ignoring possible errors and uncertainties introduced from genotyping, sequencing, and/or imputation. In this work, we investigate the effects of genotyping error due to low coverage sequencing on PGS estimation. We leverage SNP array and low-coverage whole-genome sequencing data (lcWGS, median coverage 0.04×) of 802 individuals from the Dana-Farber PROFILE cohort to show that PGS error correlates with sequencing depth (p = 1.2 × 10

Indexed as

GenomicsPolymorphism, Single NucleotideGenotypeUncertaintyWhole Genome Sequencingeffect sizesgenotype errorlcWGSPGSPGS errorrisk stratificationuncertainty

Identifiers

PMID37490908
PMCPMC10432141

What Socratic holds

Textmetadata
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 Socratic graph.