Evidence map›Paper›PMID 36945429›Full record

ArticlebioRxiv : the preprint server for biology2023

A deep population reference panel of tandem repeat variation.

Helyaneh Ziaei Jam, Yang Li, Ross DeVito, Nima Mousavi, Nichole Ma, Ibra Lujumba, Yagoub Adam, Mikhail Maksimov, Bonnie Huang, Egor Dolzhenko and 12 more

Abstract 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. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Helyaneh Ziaei JamDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Yang LiDepartment of Medicine, University of California San Diego, La Jolla, CA.
Ross DeVitoDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Nima MousaviDepartment of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA.
Nichole MaDepartment of Medicine, University of California San Diego, La Jolla, CA.
Ibra LujumbaThe African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Yagoub AdamCovenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria.
Mikhail MaksimovDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Bonnie HuangDepartment of Bioengineering, University of California San Diego, La Jolla, CA.
Egor DolzhenkoIllumina Incorporated, San Diego, California 92122, USA.
Yunjiang QiuIllumina Incorporated, San Diego, California 92122, USA.
Fredrick Elishama KakemboThe African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Habi JosephThe African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Blessing OnyidoDepartment of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria.
Jumoke AdeyemiDepartment of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria.
Mehrdad BakhtiariDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Jonghun ParkDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Sara JavadzadehDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Daudi JjingoThe African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Ezekiel AdebiyiCovenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria.
Vineet BafnaDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Melissa GymrekDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA.

Funding

H3ABioNet: informatics solutions for H3AfricaU24HG006941 · NHGRI · UNIVERSITY OF CAPE TOWN · PI MULDER, NICOLA · 2017 to 2021
$12.9M
Genetic & Social Determinants of Health: Center for Admixture Science and TechnologyRM1HG011558 · NHGRI · YALE UNIVERSITY · PI FRAZER, KELLY A, GYMREK, MELISSA · 2021 to 2025
$11.2M
eLwazi Open Science Data Platform for AfricaU2CEB032224 · NIBIB · UNIVERSITY OF CAPE TOWN · PI SKELTON, MICHELLE · 2021 to 2025
$11.2M
Systematic characterization of tandem repeat variants contributing to complex traitsR01HG010885 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Alon Goren, Melissa Gymrek · 2020 to 2026
$4.8M
Refining Mendelian disease analysis via detection of clinically relevant repeat variantsR01HG010149 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna, Vikas Bansal · 2018 to 2026
$4.5M
Computational methods for detecting patterns of complex genomic variationR01GM114362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2016 to 2026
$3.1M
WEST AFRICAN SUSTAINABLE LEADERSHIP AND INNOVATION TRAINING IN BIOINFORMATICS RESEARCH (WASLITBRe)U2RTW010679 · FIC · COVENANT UNIVERSITY · PI ADEBIYI, EZEKIEL FEMI, AMOAKO-YIRENKYI, PETER · 2017 to 2021
$1.4M
NURTURING GENOMICS AND BIOINFORMATICS RESEARCH CAPACITY IN AFRICA (BRecA)U2RTW010672 · FIC · MAKERERE UNIVERSITY COLLEGE OF HEALTH SCIENCES · PI JJINGO, DAUDI, KATEETE, DAVID PATRICK · 2017 to 2022
$1.3M
FIC NIH HHS U2R TW010672FIC NIH HHS U2R TW010679NHGRI NIH HHS R01 HG010149NHGRI NIH HHS R01 HG010885NHGRI NIH HHS RM1 HG011558NHGRI NIH HHS U24 HG006941NIBIB NIH HHS U2C EB032224NIGMS NIH HHS R01 GM114362
6 · The paper itself

Abstract

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3,550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

Identifiers

PMID36945429
PMCPMC10028971

What OpenQuestion holds

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LicenceCC BY-NC
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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.