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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...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
..., USA; 2NVIDIA Corporation, Santa Clara, California 95051, USA Corresponding author: wwang7@mdanderson.orgAbstractAccurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were overcome by consensus mutation calling...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...Coriell reference samples to evaluate the performance of high-throughput sequencing (HTS) technologies in accurately detecting genetic variants. The samples were ordered from the Coriell Institute for Medical Research, which provides well-characterized reference materials with publicly available genetic...
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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
...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...
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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
.... ↵Magi A, Tattini L, Cifola I, D'Aurizio R, Benelli M, Mangano E, Battaglia C, Bonora E, Kurg A, Seri M, et al. 2013. EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol 14: R120. doi:10.1186/gb-2013-14-10-r120 ↵Mallory XF, Edrisi M, Navin N, Nakhleh L. 2020. Methods...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
.... 2022; Glinos et al. 2022; Kolmogorov et al. 2023; Kovaka et al. 2024; Stefansson et al. 2024). In addition to its transformative impact on basic sciences, long-read sequencing is emerging as a critical tool in clinical diagnostics. Long-read's ability to accurately detect SVs and other complex variants...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
.... Corresponding authors: smontgom@stanford.edu, mschatz@cs.jhu.edu, wheelerm@stanford.edu, ajbattle@jhu.eduAbstractRare structural variants (SVs)—insertions, deletions, and complex rearrangements—can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed...
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Method: Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
- Ou Wang,
- Robert Chin,
- Xiaofang Cheng,
- Michelle Ka Yan Wu,
- Qing Mao,
- Jingbo Tang,
- Yuhui Sun,
- Ellis Anderson,
- Han K. Lam,
- Dan Chen,
- Yujun Zhou,
- Linying Wang,
- Fei Fan,
- Yan Zou,
- Yinlong Xie,
- Rebecca Yu Zhang,
- Snezana Drmanac,
- Darlene Nguyen,
- Chongjun Xu,
- Christian Villarosa,
- Scott Gablenz,
- Nina Barua,
- Staci Nguyen,
- Wenlan Tian,
- Jia Sophie Liu,
- Jingwan Wang,
- Xiao Liu,
- Xiaojuan Qi,
- Ao Chen,
- He Wang,
- Yuliang Dong,
- Wenwei Zhang,
- Andrei Alexeev,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- Xun Xu,
- Radoje Drmanac,
- and Brock A. Peters
Genome Res. May 2019 29: 798-808; Published in Advance April 2, 2019, doi:10.1101/gr.245126.118
...processes were used (Table 2, no filter). To further improve the variant calling performance in stLFR libraries, we used a machine learning algorithm trained against additional stLFR libraries made from GIAB samples GM12878, GM24385, GM24149, GM24143, and GM24631 (Supplemental Table S3; Methods). This led...
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Resource: Dindel: Accurate indel calls from short-read data
- Cornelis A. Albers,
- Gerton Lunter,
- Daniel G. MacArthur,
- Gilean McVean,
- Willem H. Ouwehand,
- and Richard Durbin
Genome Res. June 2011 21: 961-973; Published in Advance October 27, 2010, doi:10.1101/gr.112326.110
...; 4Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom Abstract Small insertions and deletions (indels) are a common and functionally important type of sequence polymorphism. Most of the focus of studies of sequence variation is on single nucleotide variants (SNVs...
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Method: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
- Yi Wang,
- James Lu,
- Jin Yu,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. May 2013 23: 833-842; Published in Advance January 7, 2013, doi:10.1101/gr.146084.112
...the operational heterogeneity common to large-scale sequencing projects with several thousand BAMs such as the 1000G and projects like GO Exome Sequencing Project (ESP) (http:// evs.gs.washington.edu/EVS/), we developed BBMM, which accurately estimates GLs for putative variant sites by modeling intra...

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