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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
...-defined genomic regions to better inform overall performance, which ultimately determined that HiFi sequencing is accurate and robust. The accuracy of germline small variant detection in non-difficult genomic regions across reference materials was >99.9% for both SNVs and indels, and small variant detection...
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Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
- Antonio Nappi,
- Liubov Shilova,
- Theofanis Karaletsos,
- Na Cai,
- and Francesco Paolo Casale
Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
...Corresponding author: francescopaolo.casale@helmholtz-munich.deAbstractGene-level rare variant association tests (RVATs) are essential for uncovering disease mechanisms and identifying therapeutic targets. Advances in sequence-based machine learning have generated diverse variant pathogenicity scores, creating...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...approaches. In particular, germline adaptive immune system genes, like immunoglobulin (IG) and T cell receptor (TR) genes, are particularly hard to genotype using classic reference-based methods owing to their highly repetitive and homologous nature. In this paper, we present ImmunoTyper2, a new...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...nonambulatory. Several of these features overlap Primrose Syndrome. We have classified this variant as likely pathogenic and the case-level designation is Likely Diagnostic (Table 2).View larger version: In this window In a new window Figure 1. A de novo, 4 Mb paracentric inversion in proband 1, affecting ZBTB...
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Research: A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates
- Alexandra M. Stendahl,
- Rashesh Sanghvi,
- Samuel Peterson,
- Karina Ray,
- Ana C. Lima,
- Raheleh Rahbari,
- and Donald F. Conrad
Genome Res. December 2023 33: 2053-2059; Published in Advance November 20, 2023, doi:10.1101/gr.277977.123
..., Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, et al. 2015. Germline mutations in predisposition genes in pediatric cancer. N Engl J Med 373: 2336–2346. doi:10.1056/NEJMoa1508054 A naturally occurring variant of MBD4 causes maternal germline hypermutation...
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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...to the likelihood ratio estimation equating to strong evidence against pathogenicity, the excellent agreement of our results for variants in the low/no FL reduction category with published splicing data provide confidence that this minigene-derived information may be used to assign an ACMG/AMP benign code...
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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
...were classified as likely pathogenic variants.We utilized LOFTEE to identify HC LoF variants. We consider LoFs to result in a truncated nonfunctional protein unless they trigger nonsense-mediated mRNA decay (NMD). To determine whether LoFs escape NMD, we employed NMDetective with a cutoff of 0...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
.../AMP) guidelines to classify genetic variants into five categories: pathogenic, likely pathogenic, benign, likely benign, and variant(s) of uncertain significance (VUS) (Richards et al. 2015). Whereas the first four classifications could be useful in interpreting rare variants that are found in genes that have...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...are limiting. While mapping functional gene/genomic annotations over from humans can theoretically be used for improving variant annotation, it is estimated that ∼13% of human pathogenic ClinVar variants are common in dogs, and thus likely benign (Gao et al. 2023). Systems such as the dog are therefore rife...
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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...and expand regions with potential structural variants to enable more comprehensive detection. FocalSV is evaluated on 10 germline data sets and two paired normal-tumor cancer data sets, demonstrating superior performance in both precision and efficiency.Single nucleotide variants (SNVs) constitute the most...
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