bioRxiv Channel: Somatic Mosaicism across the Human Tissues Network (SMaHT)
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This feed contains articles for bioRxiv Channel "Somatic Mosaicism across the Human Tissues Network (SMaHT)"
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https://biorxiv.org
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A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex
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https://biorxiv.org/cgi/content/short/2024.12.18.629274v1?rss=1"
Zhou, W.Mumm, C.Gan, Y.Switzenberg, J. A.Wang, J.De Oliveira, P.Kathuria, K.Losh, S. J.McDonald, T. L.Bessell, B.Van Deynze, K.McConnell, M. J.Boyle, A. P.Mills, R. E.2024-12-21doi:10.1101/2024.12.18.629274Cold Spring Harbor Laboratory Press2024-12-21
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Image-based DNA Sequencing Encoding for Detecting Low-Mosaicism Somatic Mobile Element Insertions
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https://biorxiv.org/cgi/content/short/2024.11.07.619809v1?rss=1"
Tan, M.Lin, Z.Chen, Z.Park, J.He, Z.Zhou, H.Lee, E. A.Gao, Z.Zhu, X.2024-11-08doi:10.1101/2024.11.07.619809Cold Spring Harbor Laboratory Press2024-11-08
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Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing
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https://biorxiv.org/cgi/content/short/2024.11.06.622310v1?rss=1"
Swanson, E. G.Mao, Y.Mallory, B. J.Vollger, M. R.Ranchalis, J.Bohaczuk, S. C.Parmalee, N. L.Bennett, J. T.Stergachis, A. B.2024-11-06doi:10.1101/2024.11.06.622310Cold Spring Harbor Laboratory Press2024-11-06
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Characterization of Cancer Evolution Landscape Based on Accurate Detection of Somatic Mutations in Single Tumor Cells
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https://biorxiv.org/cgi/content/short/2023.10.09.561356v1?rss=1"
Niu, M.Zhang, Y.Luo, J.Sinson, J. C.Thompson, A. M.Zong, C.2023-10-09doi:10.1101/2023.10.09.561356Cold Spring Harbor Laboratory Press2023-10-09
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Multi-platform framework for mapping somatic retrotransposition in human tissues
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https://biorxiv.org/cgi/content/short/2025.10.07.680917v1?rss=1"
Wang, S.Bae, M.Wang, J.Zhao, B.Nguyen, K.Mallett, S.Switzenberg, J. A.Losh, S. J.Sexton, C. E.Miao, B.Dong, S.Zeng, X.Wang, Z.McDonald, T. L.Mumm, C.Gadde, R. K.Tariq, A. M.Chen, Z.Feng, W. C.Burn, A.Park, J.Chu, C.Shen, H.Wang, T.Urban, A. E.Zhu, X.Li, H.Burns, K. H.Chun, H.-J. E.Park, P. J.SMaHT MEI Working Group,Boyle, A. P.Mills, R. E.Zhou, W.Lee, E. A.2025-10-07doi:10.1101/2025.10.07.680917Cold Spring Harbor Laboratory Press2025-10-07
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Comprehensive benchmarking of somatic mutation detection by the SMaHT Network
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https://biorxiv.org/cgi/content/short/2025.10.09.678885v1?rss=1"
The Somatic Mosaicism across Human Tissues Network (SMaHT),Abyzov, A.2025-10-10doi:10.1101/2025.10.09.678885Cold Spring Harbor Laboratory Press2025-10-10
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A telomere-to-telomere map of somatic mutation burden and functional impact in cancer
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https://biorxiv.org/cgi/content/short/2025.10.10.681725v1?rss=1"
Sohn, M.-H.Dubocanin, D.Vollger, M. R.Kwon, Y.Minkina, A.Munson, K. M.Hart, S. F.Ranchalis, J. E.Parmalee, N. L.Sedeno-Cortes, A. E.Ou, J.Au, N. Y.Bohaczuk, S.Carroll, B.Frazar, C. D.Harvey, W. T.Hoekzema, K.Huang, M.-F.Jacques, C. N.Jensen, D. M.Kolar, J. T.Lee, R.Lin, J.Loy, K.Mack, T.Mao, Y.Pham, M. M.Ryke, E.Smith, J. D.Sutherlin, L.Swanson, E. G.Weiss, J. M.SMaHT Assembly Working Group,Carvalho, C.Coorens, T. H.Harris, K.Wei, C.-L.Eichler, E. E.Altemose, N.Bennett, J. T.Stergachis, A. B.2025-10-13doi:10.1101/2025.10.10.681725Cold Spring Harbor Laboratory Press2025-10-13
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A comprehensive view of somatic mosaicism by single-cell DNA analysis
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https://biorxiv.org/cgi/content/short/2025.10.31.685648v1?rss=1"
Luquette, L. J.Coorens, T. H. H.Natu, A.Suvakov, M.Caplin, A.Jun, M. S.Mo, A.Pelt, J.Anderson, L.Berselli, M.Bhamidipati, S.Blanchard, T.Brew, J.Chun, H.-J. E.Chun, H.Dehankar, M. K.Feng, W. C.Furatero, R.Grochowski, C. M.Ho, E.Jang, Y.Kottapalli, K.Leonard, M. K.Lim, N. S.Lindsay, T.Nicholson, S.Raimondi, I.Runnels, A.Scharlee, C.Shin, J.Veit, A. D.VonDran, M.Wang, Y.Yuan, D. J.Zhao, Y.Bell, T. J.Ardlie, K.Doddapaneni, H.Fulton, R.Germer, S.Landau, D.Oh, J. W.Park, P. J.Vaccarino, F. M.Walsh, C. A.Abyzov2025-11-03doi:10.1101/2025.10.31.685648Cold Spring Harbor Laboratory Press2025-11-03
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Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data
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https://biorxiv.org/cgi/content/short/2025.10.13.681545v1?rss=1"
2% VAF SNVs, sensitivity and precision approached [~]80% at [≥]300x, with little gain from additional sequencing. This work provides a comprehensive framework for reliable detection of low-VAF mutations in non-cancer tissues and a valuable resource for the community.
]]>Ha, Y.-J. J.Maziec, D.Markowski, J.Georges, S. J.Parmalee, N. L.Berselli, M.Coorens, T. H.Dong, S.Gardiner, S.Kalra, D.Li, D.Miao, B.Musunuri, R.Xue, L.Yu, Z.Walker, K.Anderson, L.Au, N. Y.Cibulskis, C.Doddapaneni, H.Grochowski, C. M.Jensen, D. M.Lindsay, T.Loy, K.Narayan, A.Narzisi, G.Ou, J.Pham, M. M.Runnels, A. M.Stergachis, A. B.Sutherlin, L. M.Wang, T.Jin, H.Feng, W. C.Zhang, Y.Veit, A. D.Kim, C. T.Chun, H.-J. E.Ardlie, K.Fulton, R. S.Germer, S.Gibbs, R. A.Marth, G. T.Bennett, J. T.Park, P. J.2025-10-14doi:10.1101/2025.10.13.681545Cold Spring Harbor Laboratory Press2025-10-14
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Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions
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https://biorxiv.org/cgi/content/short/2025.09.18.677206v1?rss=1"
Zhang, Y.English, A. C.Paulin, L. F.Grochowski, C. M.Maheshwari, S.Mack, T.Berselli, M.Veit, A. D.Fu, Y.SMAHT SV working group,Park, P. J.Sedlazeck, F. J.2025-09-20doi:10.1101/2025.09.18.677206Cold Spring Harbor Laboratory Press2025-09-20
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A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
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https://biorxiv.org/cgi/content/short/2025.09.29.679336v1?rss=1"
6M single-nucleotide variants, 1.8M small insertions/deletions, 49K structural variations, and 10K mobile element insertions across autosomes, X, and mitochondrial chromosomes. We validated the variants using ultra-deep simulated reads and developed a binomial-based model to estimate coverage requirements for variant detection. Evaluating multiple callers showed CHM13 alignment improves structural variant detection and offers advantages in difficult-to-map regions compared to GRCh38. Systematic characterization showed regions with low detection rate are enriched in centromeres, satellite sequences, tandem repeats, and falsely duplicated genes. This accurate, versatile resource enables systematic evaluation of somatic variant detection technologies.
]]>Kong, N.Tang, Z.Ruttenberg, A.Macias-Velasco, J. F.Li, Z.Zhang, W.Miao, B.Xin, Z.Fu, Q.Park, H.Zhuo, X.Mehinovic, E.Belter, E.Garza, J. E.Dong, S.Casey, E.Johnson, B. K.Majewski, M. F.Palmer, T.Cheng, Y.Lindsay, T.Schedl, T.Li, D.Shen, H.SMaHT Network Assembly/Pangenome Working Group,Fulton, R.Wang, T.Jin, S. C.2025-10-01doi:10.1101/2025.09.29.679336Cold Spring Harbor Laboratory Press2025-10-01
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Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq
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https://biorxiv.org/cgi/content/short/2025.12.05.692678v1?rss=1"
Zhang, Y.Chao, H.Niu, M.Grochowski, C. M.Kottapalli, K.Bhamidipati, S. V.muzny, d. m.Gibbs, R. A.Zong, C.Doddapaneni, H. V.2025-12-06doi:10.64898/2025.12.05.692678Cold Spring Harbor Laboratory Press2025-12-06
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MosaicSim: A Novel Mosaic Variant Simulator Reveals Diminishing Returns of Ultra-High Coverage for Mosaic Variant Detection
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https://biorxiv.org/cgi/content/short/2025.12.03.692191v1?rss=1"
Stricker, E.Jaryani, F.Izydorczyk, M.Poon, C.-L.Sanio, P.Alexander, A.Deb, S.Sedlazeck, F.Rogers, J.Atkinson, E. G.2025-12-07doi:10.64898/2025.12.03.692191Cold Spring Harbor Laboratory Press2025-12-07
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Single cell whole genome and transcriptome sequencing links somatic mutations to cell identity and ancestry
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https://biorxiv.org/cgi/content/short/2025.10.28.685157v1?rss=1"
Natu, A.Dehankar, M. K.Pattni, R.Suvakov, M.Olisov, D.Tomasini, L.Jang, Y.Huang, Y.Benito-Garragori, E.Hasenfeld, P.Korbel, J.Urban, A. E.Abyzov, A.Vaccarino, F. M.2025-10-29doi:10.1101/2025.10.28.685157Cold Spring Harbor Laboratory Press2025-10-29
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ToxiTaRGET: a multi-omics resource for toxicant-responsive molecular targets
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https://biorxiv.org/cgi/content/short/2025.07.28.667228v1?rss=1"
Kumar, R.Fu, T.Kuntala, P. K.Fu, S.Li, D.Bartolomei, M. S.Walker, C. L.Wang, T.Zhang, B. A.2025-08-02doi:10.1101/2025.07.28.667228Cold Spring Harbor Laboratory Press2025-08-02
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Long-read MitoScope reveals tissue-resolved somatic mitochondrial variation and landscape of nuclear-embedded mitochondrial sequences
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https://biorxiv.org/cgi/content/short/2026.04.13.718259v1?rss=1"
2-fold more NUMTs than short-read surveys--with evidence of nonrandom trinucleotide contexts at breakpoints. These findings expose pervasive, tissue-resolved somatic mtDNA and NUMT instability with direct relevance for variant interpretation, aging, and human disease.
]]>Zakarian, C.Smith, J. D.Wong, C. H.Frazar, C. D.Ryke, E.McGee, S. R.Richardson, M.Weiss, J. M.Munson, K. M.Hoekzema, K.Mack, T.Kwon, Y.Ou, J.Neph, S. J.Sohn, M.-H.Minkina, A.Bennett, J. T.Stergachis, A. B.Eichler, E. E.Wei, C.-L.2026-04-15doi:10.64898/2026.04.13.718259Cold Spring Harbor Laboratory Press2026-04-15
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Leveraging Human Pangenome for Improved Somatic Variant Detection
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https://biorxiv.org/cgi/content/short/2026.01.04.697580v1?rss=1"
Fu, Q.Xin, Z.Miao, B.Zhang, W.Kong, N.Tang, Z.Ruttenberg, A.Albracht, D.Belter, E. A.Garza, J. E.Tomlinson, C.Mehinovic, E.Shen, J.Zhuo, X.Dong, S.Johnson, B. K.Majewski, M. F.Palmer, T.Jang, H. J.Cheng, Y.Li, Z.Lawson, H. A.Lindsay, T.Li, D.Fulton, R.Shen, H.Jin, S. C.SMaHT Network Assembly/Pangenome Working Group,Macias-Velasco, J. F.Wang, T.2026-01-04doi:10.64898/2026.01.04.697580Cold Spring Harbor Laboratory Press2026-01-04
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Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions
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https://biorxiv.org/cgi/content/short/2026.02.20.707061v1?rss=1"
Mack, T. M.Lin, J.Ren, L.Sohn, M.-H.Minkina, A.Kwon, Y.Yoo, D.Sui, Y.Munson, K. M.Hoekzema, K.Mastrorosa, F. K.Sorensen, M.Ayllon, M.Sun, K. A.Koundiya, N.Ou, J.Noyes, M. D.Sedeno-Cortes, A.Leonardson, A.Jacques, C. N.Oliviera, C.Frazar, C. D.Zakarian, C.Jensen, D. M.Swanson, E. G.Ryke, E.Kolar, J. T.Ranchalis, J.Sutherlin, L.Vollger, M. R.Loy, K.Pham, M. M.Huang, M.-F.Au, N. Y.Nielsen, P. M.McGee, S. R.Neph, S.Bohaczuk, S.Shaffer, T.Freeman, V.Mao, Y.Cohen Stillman, B.Richardson, M.Smith, J. D.Weiss, J. M.2026-02-20doi:10.64898/2026.02.20.707061Cold Spring Harbor Laboratory Press2026-02-20
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Protamine lacunae preserve the paternal chromatin landscape in sperm
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https://biorxiv.org/cgi/content/short/2025.10.03.680364v1?rss=1"
Tullius, T. W.Heuer, R. A.Bohaczuk, S. C.Mallory, B.Dubocanin, D.Ranchalis, J.Ayaz, A.Mason, C.Seli, E.Phillippy, A. M.Stergachis, A.Lesch, B. J.2025-10-05doi:10.1101/2025.10.03.680364Cold Spring Harbor Laboratory Press2025-10-05
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Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes
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https://biorxiv.org/cgi/content/short/2025.12.12.692823v1?rss=1"
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]]>Zhang, Y.Viswanadham, V.Andreopoulos, M.Glodzik, D.Liu, R.Luquette, L.Jo, S.-Y.Narayan, A.Niu, M.Anderson, L.Brew, J.Chao, H.Cibulskis, C.Dong, G.Evani, U.Feng, W.Gronska-Peski, M.Helland, A.Hilal, N.Jabara, N.Jin, H.Li, N.Manam, M.Mallett, S.Runnels, A.Scharlee, C.Smith, C.The SMaHT Duplex Sequencing Working Group,Shao, D.Walsh, C.Adalsteinsson, V.Germer, S.Gibbs, R.Choudhury, S.Doddapaneni, H.Evrony, G.Zong, C.Coorens, T.2025-12-15doi:10.64898/2025.12.12.692823Cold Spring Harbor Laboratory Press2025-12-15
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As48, a First-in-Class Dual-Function TREM2 Modulator: Receptor Activation and Shedding Inhibition
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https://biorxiv.org/cgi/content/short/2025.08.23.671919v1?rss=1"
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]]>Cho, S.El gaamouch, F.Upadhyay, S.Nada, H.Kuncewicz, K.Gabr, M.2025-08-28doi:10.1101/2025.08.23.671919Cold Spring Harbor Laboratory Press2025-08-28