Evidence map›Paper›PMID 39929826›Full record

ArticleNature communications2025

Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility.

Jiao Gong, Huiru Sun, Kaiyuan Wang, Yanhui Zhao, Yechao Huang, Qinsheng Chen, Hui Qiao, Yang Gao, Jialin Zhao, Yunchao Ling and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing 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

10 citing papers in PubMed.

  1. Article
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  3. Review
  4. Article
  5. Review
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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

29 authors.

Jiao Gong *State Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Huiru Sun *State Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Kaiyuan Wang *Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
Yanhui ZhaoState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Yechao HuangState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Qinsheng ChenState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Hui QiaoState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Yang GaoState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Jialin ZhaoState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-1165-8911
Yunchao LingBio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0002-5438-0753
Ruifang CaoBio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Jingze TanState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Qi WangState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Yanyun MaDepartment of Anthropology and Human Genetics, Institute for Six-sector Economy, and MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China.
Jing LiState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Jingchun LuoState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.
Sijia WangCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0001-6961-7867
Jiucun WangState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0003-2765-0620
Guoqing ZhangBio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Shuhua XuState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-1975-1002
Feng QianState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-2312-5936
Fang ZhouSchool of Data Science and Engineering, East China Normal University, Shanghai, China.
Huiru TangState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-7139-2756
Dali LiShanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.ORCID http://orcid.org/0000-0002-0046-8493
Chinese Pangenome Consortium (CPC)
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. Fritz.Sedlazeck@bcm.edu.ORCID http://orcid.org/0000-0001-6040-2691
Li JinState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China. lijin@fudan.edu.cn.ORCID http://orcid.org/0000-0001-9201-2321
Yuting GuanShanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China. ytguan@bio.ecnu.edu.cn.ORCID http://orcid.org/0000-0003-1866-270X
Shaohua FanState Key Laboratory of Genetic Engineering, Lab for Evolutionary Synthesis, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China. shaohua_fan@fudan.edu.cn.ORCID http://orcid.org/0000-0003-0610-9106

Funding

Frequency of variants of unknown significance by ancestry groups in the All of Us Research Program cohortU01HG011758 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI RICHARD A GIBBS, JAMES R. LUPSKI · 2021 to 2026
$13.8M
Therapeutic target discovery in ADSP data via comprehensive whole-genome analysis incorporating ethnic diversity and systems approachesU01AG058589 · NIA · BOSTON UNIVERSITY MEDICAL CAMPUS · PI BOERWINKLE, ERIC A., DE JAGER, PHILIP L · 2018 to 2022
$11.1M
NHGRI NIH HHS U01 HG011758NIA NIH HHS U01 AG058589
6 · The paper itself

Abstract

Genomic structural variants (SVs) are a major source of genetic diversity in humans. Here, through long-read sequencing of 945 Han Chinese genomes, we identify 111,288 SVs, including 24.56% unreported variants, many with predicted functional importance. By integrating human population-level phenotypic and multi-omics data as well as two humanized mouse models, we demonstrate the causal roles of two SVs: one SV that emerges at the common ancestor of modern humans, Neanderthals, and Denisovans in GSDMD for bone mineral density and one modern-human-specific SV in WWP2 impacting height, weight, fat, craniofacial phenotypes and immunity. Our results suggest that the GSDMD SV could serve as a rapid and cost-effective biomarker for assessing the risk of cisplatin-induced acute kidney injury. The functional conservation from human to mouse and widespread signals of positive natural selection suggest that both SVs likely influence local adaptation, phenotypic diversity, and disease susceptibility across diverse human populations.

Indexed as

East Asian PeopleGenetic Predisposition to DiseaseGenome, HumanGenomic Structural VariationAnimalsChinaFemaleHumansMaleMiceNeanderthalsPhenotype

Identifiers

PMID39929826
PMCPMC11811171

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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.