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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
..., Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568–576. doi:10.1101/gr.129684.111 ↵Köster J, Rahmann S. 2012. Snakemake: a scalable bioinformatics workflow engine. Bioinformatics 28: 2520...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...vials for DNA/ RNA extraction were all acute myeloid leukemia, a liquid tumor, that are not expected to have extensive spatial heterogeneity. The MAF files were prepared by GDC by applying MuTect2 (Cibulskis et al. 2013), VarScan2 (Koboldt et al. 2012), and Pindel (Ye et al. 2009) to the paired WES...
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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
.../btq351 ↵Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568–576. doi:10.1101/gr.129684.111 ↵Koboldt DC, Steinberg KM, Larson DE, Wilson...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...der Auwera et al. 2013) for variant calling. For each of the 6 cells examined, MuTect and VarScan 2 were invoked such that the cell currently under consideration served as the somatic/tumor input, and the union set of 3 cells of the respective other cell type served as the normal/bulk input. The same...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...can alter tissue dynamics and lead to cancer initiation. Although large-scale sequencing projects have illuminated processes that influence somatic mutation and subsequent tumor evolution, the mutational dynamics operating in the very early stages of cancer development are currently not well...
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Research: Frequent somatic gene conversion as a mechanism for loss of heterozygosity in tumor suppressor genes
- Kazuki K. Takahashi and
- Hideki Innan
Genome Res. June 2022 32: 1017-1025; Published in Advance May 26, 2022, doi:10.1101/gr.276617.122
...Lellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568–576. doi:10.1101/gr.129684.111 ↵Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S...
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Resource: GenomeVIP: a cloud platform for genomic variant discovery and interpretation
- R. Jay Mashl,
- Adam D. Scott,
- Kuan-lin Huang,
- Matthew A. Wyczalkowski,
- Christopher J. Yoon,
- Beifang Niu,
- Erin DeNardo,
- Venkata D. Yellapantula,
- Robert E. Handsaker,
- Ken Chen,
- Daniel C. Koboldt,
- Kai Ye,
- David Fenyö,
- Benjamin J. Raphael,
- Michael C. Wendl,
- and Li Ding
Genome Res. August 2017 27: 1450-1459; Published in Advance May 18, 2017, doi:10.1101/gr.211656.116
...D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568–576. Koboldt DC, LarsonDE,Wilson RK. 2013. Using VarScan 2 for germline variant calling and somatic mutation...
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Research: Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma
- David H. Gutmann,
- Michael D. McLellan,
- Ibrahim Hussain,
- John W. Wallis,
- Lucinda L. Fulton,
- Robert S. Fulton,
- Vincent Magrini,
- Ryan Demeter,
- Todd Wylie,
- Cyriac Kandoth,
- Jeffrey R. Leonard,
- Abhijit Guha,
- Christopher A. Miller,
- Li Ding,
- and Elaine R. Mardis
Genome Res. March 2013 23: 431-439; Published in Advance December 5, 2012, doi:10.1101/gr.142604.112
...Deimling A, Mautner VF. 2001. Loss of NF1 alleles distinguish sporadic fromNF1-associated pilocytic astrocytomas. J Neuropathol Exp Neurol 60: 917–920. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: Somatic mutation and copy number...
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Method: Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq
- Pete H. Taylor,
- Amanda Cinquin,
- and Olivier Cinquin
Genome Res. November 2016 26: 1600-1611; Published in Advance October 19, 2016, doi:10.1101/gr.200501.115
.... To quantitatively assay the advantage afforded by SIP-HAVAseq over rare-variant-calling software, we compared the output of Mutinack to the output of two popular programs, VarScan 2 (Koboldt et al. 2012) and MuTect (Cibulskis et al. 2013), which have been shown to be top-performing tools (Wang et al. 2013). When...
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Resource: Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster
- Federico A. Santoni,
- Periklis Makrythanasis,
- Sergey Nikolaev,
- Michel Guipponi,
- Daniel Robyr,
- Armand Bottani,
- and Stylianos E. Antonarakis
Genome Res. February 2014 24: 349-355; Published in Advance January 3, 2014, doi:10.1101/gr.163832.113
...deficiency: Absence of positive effect. J Inherit Metab Dis (Suppl 2) 31: S329–S332. Knocking on the clinic door. [Editorial]. 2012. Nat Biotechnol 30: 1009. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: Somatic mutation and copy number...

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