Searching journal content for articles similar to Krumm et al. 22 (8): 1525.

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  1. Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
    • Daniel Schmitz,
    • Adam Ameur,
    • and Åsa Johansson
    Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
    ...moderate and low impact, respectively, and the remaining 6.4% were rated high impact (Fig. 4B). Our results thus suggest that improved gene coverage facilitates detection of functionally relevant variation.We identified 17,446 LoF variants using T2T-CHM13, an increase from GRCh37 and GRCh38 (Table 1...
    OPEN ACCESS ARTICLE
  2. Method: Polishing copy number variant calls on exome sequencing data via deep learning
    • Furkan Özden,
    • Can Alkan,
    • and A. Ercüment Çiçek
    Genome Res. June 2022 32: 1170-1182; Published in Advance June 13, 2022, doi:10.1101/gr.274845.120
    ...@cs.bilkent.edu.trAbstractAccurate and efficient detection of copy number variants (CNVs) is of critical importance owing to their significant association with complex genetic diseases. Although algorithms that use whole- sequencing (WGS) data provide stable results with mostly valid statistical assumptions, copy number detection on whole-exome...
  3. Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    • Hao Zhu,
    • Jiao Zhang,
    • Soumya Rao,
    • Matthew D. Durbin,
    • Ying Li,
    • Ruirui Lang,
    • Jiqiang Liu,
    • Baichuan Xiao,
    • Hailin Shan,
    • Ziqiu Meng,
    • Jinmo Wang,
    • Xiaokai Tang,
    • Zhenni Shi,
    • Liza L. Cox,
    • Shouqin Zhao,
    • Stephanie M. Ware,
    • Tiong Y. Tan,
    • Michelle de Silva,
    • Lyndon Gallacher,
    • Ting Liu,
    • Jie Mi,
    • Changqing Zeng,
    • Hou-Feng Zheng,
    • Qingguo Zhang,
    • Stylianos E. Antonarakis,
    • Timothy C. Cox,
    • and Yong-Biao Zhang
    Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
    ...encompassed by GWAS signals in both cohorts (Supplemental Fig. 1). SHROOM3 was found to harbor the highest number of predicted deleterious coding variants in our cohorts and therefore became the focus of this study.Within the CFM cohort, 15,481 variants were detected across the SHROOM3 locus (including 100 kb...
  4. Method: A machine-learning approach for accurate detection of copy number variants from exome sequencing
    • Vijay Kumar Pounraja,
    • Gopal Jayakar,
    • Matthew Jensen,
    • Neil Kelkar,
    • and Santhosh Girirajan
    Genome Res. July 2019 29: 1134-1143; Published in Advance June 6, 2019, doi:10.1101/gr.245928.118
    ...RK, Mardis ER. 2013. The next-generation sequencing revolution and its impact on genomics. Cell 155: 27–38. doi:10.1016/j.cell.2013.09.006 ↵Krumm N, Sudmant P, Ko A. 2012. Copy number variation detection and genotyping from exome sequence data. Genome Res 22: 1525–1532. doi:10.1101/gr.138115...
  5. Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
    • Nathan Hammond,
    • Linda Liao,
    • Pun Wai Tong,
    • Zena Ng,
    • Thuy-Mi P. Nguyen,
    • Chandler Ho,
    • Yao Yang,
    • and Stuart A. Scott
    Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
    ...JR, Luo M, Conlin LK. 2020. A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data. Genome Med 12: 14. doi:10.1186/s13073-020-0712-0 ↵Rehm HL. 2017. Evolving health care through personal genomics. Nat Rev Genet 18: 259–267. doi:10.1038/nrg.2016...
  6. Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
    • Li Song,
    • Gali Bai,
    • X. Shirley Liu,
    • Bo Li,
    • and Heng Li
    Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
    ...to the reference sequences. This might decrease the allele prediction accuracy and the power to detect variations. In addition, The quality score filter and the abundance fraction filter might suppress a true allele if the other haplotype has copy number gains. Future works like graph representations of the KIR...
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  7. Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
    • Marzia Rossato,
    • Luca Marcolungo,
    • Luca De Antoni,
    • Giulia Lopatriello,
    • Elisa Bellucci,
    • Gaia Cortinovis,
    • Giulia Frascarelli,
    • Laura Nanni,
    • Elena Bitocchi,
    • Valerio Di Vittori,
    • Leonardo Vincenzi,
    • Filippo Lucchini,
    • Kirstin E. Bett,
    • Larissa Ramsay,
    • David James Konkin,
    • Massimo Delledonne,
    • and Roberto Papa
    Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
    ...-mediated repeat depletion on different samples and library typesFinally, we assessed the performance of CRISPR-Cas9-mediated repeat depletion on different lentil genotypes, multiplexing levels, and library types (Supplemental Tables S3, S4). Similar variations in the coverage of repetitive/single-copy...
    OPEN ACCESS ARTICLE
  8. Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
    • Fei Qin,
    • Guoshuai Cai,
    • Christopher I. Amos,
    • and Feifei Xiao
    Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
    ...and CNA detection performance of FLCNA, benchmarking it against existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. Application of FLCNA to a scDNA-seq data set of breast cancer revealed different genomic variation patterns in neoadjuvant...
  9. Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    • Jonas A. Gustafson,
    • Sophia B. Gibson,
    • Nikhita Damaraju,
    • Miranda P.G. Zalusky,
    • Kendra Hoekzema,
    • David Twesigomwe,
    • Lei Yang,
    • Anthony A. Snead,
    • Phillip A. Richmond,
    • Wouter De Coster,
    • Nathan D. Olson,
    • Andrea Guarracino,
    • Qiuhui Li,
    • Angela L. Miller,
    • Joy Goffena,
    • Zachary B. Anderson,
    • Sophie H.R. Storz,
    • Sydney A. Ward,
    • Maisha Sinha,
    • Claudia Gonzaga-Jauregui,
    • Wayne E. Clarke,
    • Anna O. Basile,
    • André Corvelo,
    • Catherine Reeves,
    • Adrienne Helland,
    • Rajeeva Lochan Musunuri,
    • Mahler Revsine,
    • Karynne E. Patterson,
    • Cate R. Paschal,
    • Christina Zakarian,
    • Sara Goodwin,
    • Tanner D. Jensen,
    • Esther Robb,
    • The 1000 Genomes ONT Sequencing Consortium,
    • University of Washington Center for Rare Disease Research (UW-CRDR),
    • Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
    • William Richard McCombie,
    • Fritz J. Sedlazeck,
    • Justin M. Zook,
    • Stephen B. Montgomery,
    • Erik Garrison,
    • Mikhail Kolmogorov,
    • Michael C. Schatz,
    • Richard N. McLaughlin, Jr.,
    • Harriet Dashnow,
    • Michael C. Zody,
    • Matt Loose,
    • Miten Jain,
    • Evan E. Eichler,
    • and Danny E. Miller
    Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
    ...et al. 2019; Zhao et al. 2021). These challenges extend into clinical testing where commonly used approaches, such as exome sequencing, have low sensitivity for SV detection, meaning individuals with disease-causing SVs may remain undiagnosed (Hiatt et al. 2021; Miller et al. 2021; Cohen et al. 2022...
    OPEN ACCESS ARTICLE
  10. Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
    • Xinghua Li,
    • Judith E. Mank,
    • and Liping Ban
    Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
    ...evolutionary distances. As expected, we detect strong collinearity between grasshoppers but few syntenic blocks across orders on the X Chromosome. However, with more gaps allowed (which is less meaningful), we could identify significant enrichment of gene synteny on the X Chromosome (Fig. 2B).Variation...
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