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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
...tested at a single mutation locus, whereas the SNP-based approach is more statistically powered by testing allele counts at multiple SNP loci. RNA-seq has been known to be useful for detecting low VAF mutations missed by DNA-based analysis (Xu 2018). Despite this empirical knowledge, it is currently...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
..., so too have methods for target enrichment using these platforms. Targeted long-read sequencing methods are powerful tools for studying genomic regions not readily accessible via short-read approaches. Targeted long reads provide enrichment for ROIs while maintaining variant positions within fragments...
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Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
...-to-replication for each cell in our imaging data can be used to determine whether the number of cell cycles, or alternatively, the elapsed time, is a better predictor of the number of somatic mutations, and further, to constrain likely mechanisms of mutagenesis in these cells. Our sample size provided insufficient power...
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Research: One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin
- Alexej Abyzov,
- Livia Tomasini,
- Bo Zhou,
- Nikolaos Vasmatzis,
- Gianfilippo Coppola,
- Mariangela Amenduni,
- Reenal Pattni,
- Michael Wilson,
- Mark Gerstein,
- Sherman Weissman,
- Alexander E. Urban,
- and Flora M. Vaccarino
Genome Res. April 2017 27: 512-523; Published in Advance February 24, 2017, doi:10.1101/gr.215517.116
...(Martincorena et al. 2015) and by using familial trios rather than conducting cell-to-tissue comparison (Lodato et al. 2015), powering us to find mosaic variants at high frequency. We propose this design as an approach worth considering for future genomic mosaicism studies. Somatic mosaicism in fibroblasts...
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Research: An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease
- Farhoud Faraji,
- Ying Hu,
- Gang Wu,
- Natalie E. Goldberger,
- Renard C. Walker,
- Jinghui Zhang,
- and Kent W. Hunter
Genome Res. February 2014 24: 227-240; Published in Advance December 9, 2013, doi:10.1101/gr.166223.113
...isogenic individuals within each subline of the RI panel. This strategy results in a better estimation of genetic effects and increases power to detect genotype–phenotype associations compared with standard genetic mapping strategies, in which every individual animal is genetically unique. The AKXD RI...
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Resource: The million mutation project: A new approach to genetics in Caenorhabditis elegans
- Owen Thompson,
- Mark Edgley,
- Pnina Strasbourger,
- Stephane Flibotte,
- Brent Ewing,
- Ryan Adair,
- Vinci Au,
- Iasha Chaudhry,
- Lisa Fernando,
- Harald Hutter,
- Armelle Kieffer,
- Joanne Lau,
- Norris Lee,
- Angela Miller,
- Greta Raymant,
- Bin Shen,
- Jay Shendure,
- Jon Taylor,
- Emily H. Turner,
- LaDeana W. Hillier,
- Donald G. Moerman,
- and Robert H. Waterston
Genome Res. October 2013 23: 1749-1762; Published in Advance June 25, 2013, doi:10.1101/gr.157651.113
...the strains are available through the Caenorhabditis Genetics Center and all the sequence changes have been deposited in WormBase and are available through an interactive website. [Supplemental material is available for this article.] A powerful approach to understanding the function of a has been to alter...
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Research: Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
- Yotam Drier,
- Michael S. Lawrence,
- Scott L. Carter,
- Chip Stewart,
- Stacey B. Gabriel,
- Eric S. Lander,
- Matthew Meyerson,
- Rameen Beroukhim,
- and Gad Getz
Genome Res. February 2013 23: 228-235; Published in Advance November 2, 2012, doi:10.1101/gr.141382.112
.... 2004. Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: Correlation with mutation spectra in vivo. J Mol Biol 337: 585–596. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser...
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Research: Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors
- Christiane M. Robbins,
- Waibov A. Tembe,
- Angela Baker,
- Shripad Sinari,
- Tracy Y. Moses,
- Stephen Beckstrom-Sternberg,
- James Beckstrom-Sternberg,
- Michael Barrett,
- James Long,
- Arul Chinnaiyan,
- James Lowey,
- Edward Suh,
- John V. Pearson,
- David W. Craig,
- David B. Agus,
- Kenneth J. Pienta,
- and John D. Carpten
Genome Res. January 2011 21: 47-55; Published in Advance December 8, 2010, doi:10.1101/gr.107961.110
...tumors. Our study relied on high-resolution aCGH, which uncovered focal copy number events. We also used novel state-of-the-art approaches for targeted mutational analysis facilitated by NGS technologies. These NGS technologies provide a very sensitive and powerful method for detecting mutations even...
REVIEW: Postsequence genetics of Caenorhabditis elegans.
- R H Plasterk
Genome Res. March 1996 6: 169-175; doi:10.1101/gr.6.3.169
...then be investigated, for example, by tar- geted gene inactivation (see above). The Power of Tags The immense power of sequence tags deserves explicit attention. For example, differential dis- play of mRNA or cDNA becomes child's play, as a single read will identify the gene of interest. Ana- lyzing candidates from...
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LETTER: Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline
- Laurent Duret,
- Jean Cohen,
- Claire Jubin,
- Philippe Dessen,
- Jean-François Goût,
- Sylvain Mousset,
- Jean-Marc Aury,
- Olivier Jaillon,
- Benjamin Noël,
- Olivier Arnaiz,
- Mireille Bétermier,
- Patrick Wincker,
- Eric Meyer,
- and Linda Sperling
Genome Res. April 2008 18: 585-596; Published in Advance February 6, 2008, doi:10.1101/gr.074534.107
...Ciliates are the only unicellular eukaryotes known to separate germinal and somatic functions. Diploid but silent micronuclei transmit the genetic information to the next sexual generation. Polyploid macronuclei express the genetic information from a streamlined version of the genome but are replaced...

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