Evidence map›Paper›PMID 36747613›Full record

ArticlebioRxiv : the preprint server for biology2024

A harmonized public resource of deeply sequenced diverse human genomes.

Zan Koenig, Mary T Yohannes, Lethukuthula L Nkambule, Xuefang Zhao, Julia K Goodrich, Heesu Ally Kim, Michael W Wilson, Grace Tiao, Stephanie P Hao, Nareh Sahakian and 12 more

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

Article in bioRxiv : the preprint server for biology, 2024. 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, 48 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors at 2 institutions in 2 countries.

Zan KoenigStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Mary T YohannesStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Lethukuthula L NkambuleStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Xuefang ZhaoProgram in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Julia K GoodrichAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
Heesu Ally KimStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Michael W WilsonProgram in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Grace TiaoProgram in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Stephanie P HaoProgram in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Nareh SahakianBroad Genomics, The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Katherine R ChaoProgram in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Mark A WalkerCenter for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Yunfei LyuDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
gnomAD Project Consortium
Heidi L RehmProgram in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0002-6025-0015
Benjamin M NealeStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0003-1513-6077
Michael E TalkowskiStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Mark J DalyStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0002-0949-8752
Harrison BrandProgram in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Konrad J KarczewskiStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Elizabeth G AtkinsonStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0002-6308-776X
Alicia R MartinStanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0003-0241-3522
Broad Institute · USHarvard University · US

Funding

Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI RAYMOND T CHUNG · 1991 to 2026
$35.3M
Scalable tool and comprehensive maps to interpret structural variation across the neuropsychiatric spectrumR01MH115957 · NIMH · BROAD INSTITUTE, INC. · PI TALKOWSKI, MICHAEL E · 2019 to 2025
$5.4M
Integration of polygenic risk and facial morphometrics to decipher the genetic susceptibility of orofacial cleftingR01DE031261 · NIDCR · MASSACHUSETTS GENERAL HOSPITAL · PI Harrison Brand · 2022 to 2026
$3.8M
Generalizing polygenic risk prediction methods across populations for insights into psychiatric diseaseR00MH117229 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI MARTIN, ALICIA · 2020 to 2022
$724k
NIDCR NIH HHS R01 DE031261NIDDK NIH HHS P30 DK043351NIMH NIH HHS R00 MH117229NIMH NIH HHS R01 MH115957
6 · The paper itself

Abstract

Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftover and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.

Identifiers

PMID36747613
PMCPMC9900804
OpenAlexW4317788228

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.