Evidence map›Paper›PMID 36782330›Full record

ArticleGenome biology2023

BIGKnock: fine-mapping gene-based associations via knockoff analysis of biobank-scale data.

Shiyang Ma, Chen Wang, Atlas Khan, Linxi Liu, James Dalgleish, Krzysztof Kiryluk, Zihuai He, Iuliana Ionita-Laza

Abstract read
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In one paragraph

Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
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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

8 authors.

Shiyang MaDepartment of Biostatistics, Columbia University, New York, NY, USA.
Chen WangDepartment of Biostatistics, Columbia University, New York, NY, USA.
Atlas KhanDivision of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
Linxi LiuDepartment of Statistics, University of Pittsburgh, Pittsburgh, PA, USA.
James DalgleishDepartment of Biostatistics, Columbia University, New York, NY, USA.
Krzysztof KirylukDivision of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
Zihuai HeQuantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, USA.
Iuliana Ionita-LazaDepartment of Biostatistics, Columbia University, New York, NY, USA. ii2135@columbia.edu.

Funding

Statistical and computational methods for integrative analysis of Alzheimer's Disease geneticsR01AG066206 · NIA · STANFORD UNIVERSITY · PI HE, ZIHUAI · 2019 to 2023
$3.5M
Novel Statistical methods for DNA Sequencing Data, and applications to Autism.R01MH095797 · NIMH · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI IONITA, IULIANA · 2012 to 2022
$3.1M
Multi-omics approaches for gene discovery in Alzheimer's Disease.RF1AG072272 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI IONITA, IULIANA, WEI, YING · 2021 to 2021
$1.6M
NIA NIH HHS R01 AG066206NIA NIH HHS RF1 AG072272NIMH NIH HHS R01 MH095797
6 · The paper itself

Abstract

We propose BIGKnock (BIobank-scale Gene-based association test via Knockoffs), a computationally efficient gene-based testing approach for biobank-scale data, that leverages long-range chromatin interaction data, and performs conditional genome-wide testing via knockoffs. BIGKnock can prioritize causal genes over proxy associations at a locus. We apply BIGKnock to the UK Biobank data with 405,296 participants for multiple binary and quantitative traits, and show that relative to conventional gene-based tests, BIGKnock produces smaller sets of significant genes that contain the causal gene(s) with high probability. We further illustrate its ability to pinpoint potential causal genes at [Formula: see text] of the associated loci.

Indexed as

Biological Specimen BanksGenetic TestingChromatinChromosome MappingGenome-Wide Association StudyHumansPhenotypePolymorphism, Single NucleotideChromatinAlgorithmic leveragingFine-mappingGene-based associationsKnockoff statisticsUK Biobank

Identifiers

PMID36782330
PMCPMC9926792

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Registered trials

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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.