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Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...-frame indels in TCGA 209 In-frame indels accounted for 7.07% (7,508/106,157) of the TCGA somatic indels and are not 210 expected to trigger NMD. To evaluate the AEV of in-frame indels in driver genes, we focused on 211 oncogenes as in-frame indels accounted for a much higher proportion of somatic indels than...
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Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
...interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset of somatic events in tumors. While the detection of SVs has been markedly improved by the development of long-read sequencing, somatic variant identification...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...high-quality LR scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy number alterations (CNAs), and gene fusions, to reconstruct the tumor clonal heterogeneity. Before somatic variant calling, LongSom reannotates marker gene-based cell types...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...by excluding variants present in the 1000 Genomes Project database with a minor allele frequency ≥0.001.Somatic CNVs were detected in paired tumor and normal samples using FACETS (v0.6.2) (Shen and Seshan 2016), alongside evaluation of tumor purity and ploidy. The analysis was performed with the following...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...Germplasm Enhancement and Specialty Agriculture, Plant Germplasm Research Center, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei 430074, China Corresponding authors: ckang@mail.hzau.edu.cn, hyc660@126.com, 382687178@qq.comAbstractSomatic mutations arise...
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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
...(Supplemental Fig. S3).Accuracy benchmarking for real tumor samplesWe evaluate the performance of MuSE 2 and compare it to other callers using the consensus SNV calls from TCGA (for the WES data) and PCAWG (for the WGS data) as truth sets. The truth sets include 168–2553 somatic SNVs (mean = 1394, median = 932...
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Method: Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice
- Arikuni Uchimura,
- Hirotaka Matsumoto,
- Yasunari Satoh,
- Yohei Minakuchi,
- Sayaka Wakayama,
- Teruhiko Wakayama,
- Mayumi Higuchi,
- Masakazu Hashimoto,
- Ryutaro Fukumura,
- Atsushi Toyoda,
- Yoichi Gondo,
- and Takeshi Yagi
Genome Res. May 2022 32: 945-955; Published in Advance May 9, 2022, doi:10.1101/gr.276363.121
...of Medicine, Isehara, Kanagawa, 259-1193, Japan Corresponding author: uchimura@rerf.or.jpAbstractDe novo mutations accumulate with zygotic cell divisions. However, the occurrence of these mutations and the way they are inherited by somatic cells and germ cells remain unclear. Here, we present a novel method...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity are poorly defined and are virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant...
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Method: A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls
- Modi Safra,
- Lael Werner,
- Ayelet Peres,
- Pazit Polak,
- Naomi Salamon,
- Michael Schvimer,
- Batia Weiss,
- Iris Barshack,
- Dror S. Shouval,
- and Gur Yaari
Genome Res. January 2023 33: 71-79; Published in Advance December 16, 2022, doi:10.1101/gr.276683.122
...A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls Modi Safra1,2,7, Lael Werner3,4,7, Ayelet Peres1,2, Pazit Polak1,2, Naomi Salamon5, Michael Schvimer6, Batia Weiss4,5, Iris Barshack4,6, Dror S. Shouval3,4,8 and Gur Yaari1,2,8 1The...
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Method: RNA-seq as a tool for evaluating human embryo competence
- Abigail F. Groff,
- Nina Resetkova,
- Francesca DiDomenico,
- Denny Sakkas,
- Alan Penzias,
- John L. Rinn,
- and Kevin Eggan
Genome Res. October 2019 29: 1705-1718; Published in Advance September 23, 2019, doi:10.1101/gr.252981.119
...to potential developmental outcomes. Indeed, transcriptional trends ascertained without regard to embryo quality may differ from those obtained from the same cell type in embryos that pass clinical evaluation. For example, poorly formed or apoptosing trophectoderm (TE) would be expected to express different...
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