Evidence map›Paper›PMID 41024706›Full record

ArticleNucleic acids research2026

Gene4Denovo2: an updated platform for human de novo mutations discovery and interpretation.

Zhaopo Zhu, Pei Yu, Xinxin Mao, Chenbin Liu, Kuokuo Li, Qiao Zhou, Yijing Wang, Tengfei Luo, Xudong Xiang, Yixiao Zhu and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2026. 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

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

17 authors.

Zhaopo ZhuHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Pei YuHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Xinxin MaoHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Chenbin LiuHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Kuokuo LiDepartment of Obstetrics and Gynecology, Reproductive Medicine Center, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230000, China.ORCID 0000-0001-9422-677X
Qiao ZhouHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Yijing WangHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Tengfei LuoThe Central Laboratory of Birth Defects Prevention and Control & Ningbo Key Laboratory of Genomic Medicine and Birth Defects Prevention, the Affiliated Women and Children's Hospital, Ningbo University, Ningbo, Zhejiang 315000, China.
Xudong XiangHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Yixiao ZhuHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Dai WuHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Xingxing JianHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Bin LiHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Beisha TangKey Laboratory of Hunan Province in Neurodegenerative Disorders, Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.ORCID 0000-0003-2120-1576
Kun XiaThe Key Laboratory of Pediatric Rare Diseases of the Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan 410008, China.ORCID 0000-0001-8090-6002
Guihu ZhaoHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Jinchen LiHunan Key Laboratory of Medical Genetics, School of Life Sciences & Bioinformatics Center, National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.ORCID 0000-0001-5522-806X

Funding

Central South University 2023QYJC010Central South University 2025ZZTS0834Hunan Innovative Province Construction 2021SK1010National Natural Science Foundation of China 82130043National Natural Science Foundation of China 82330035National Natural Science Foundation of China 82361138573National Natural Science Foundation of China 82371552Scientific Research Program of FuRong Laboratory 2023SK2093
6 · The paper itself

Abstract

De novo mutations (DNMs) drive evolution and increase biodiversity, yet concurrently act as a cryptic cause of numerous genetic diseases. Here, we present Gene4Denovo2 (https://genemed.tech/gene4denovo2/), an updated version of the Gene4Denovo, aiming to provide a more comprehensive DNM datasets and their interpretations. The key improvements include the following: (i) We have substantially expanded the number and scope of DNMs, associated samples, and phenotypes. Specifically, Gene4Denovo2 now contains 1 626 050 DNMs from 130 439 individuals across 96 phenotypes. Moreover, clinical information covering nearly 1000 items has been added for 448 096 individuals, including those with DNMs and their unaffected family members. (ii) We have introduced new features to assist in the evaluation of DNMs, including support for ACMG rating and the addition of gene prioritization scores for rapid classification and filtering of candidate genes. (iii) An upgraded analysis interface allowing flexible annotation configuration and a significant expansion in the number of annotatable datasets. Additionally, a new integrated tool enables DNMs calling from family-based sequencing data. In summary, Gene4Denovo2 provides a more extensive collection of DNMs, enhanced annotation capabilities, and upgraded analysis tools, which will facilitate a deeper exploration of the role of DNMs in disease pathogenesis.

Indexed as

Databases, GeneticMutationSoftwareHumansMolecular Sequence AnnotationPhenotype

Identifiers

PMID41024706
PMCPMC12808551

What Socratic holds

Textmetadata
LicenceCC BY-NC
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.