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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
..., and the acquisition of drug resistance. However, available -wide methods have a limited ability to resolve rare somatic variants and the relationships between these variants. Here, we present lineage sequencing, a new sequencing approach that enables somatic event reconstruction by providing quality somatic mutation...
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Research: Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes
- Geoffrey J. Maher,
- Hannah K. Ralph,
- Zhihao Ding,
- Nils Koelling,
- Hana Mlcochova,
- Eleni Giannoulatou,
- Pawan Dhami,
- Dirk S. Paul,
- Stefan H. Stricker,
- Stephan Beck,
- Gilean McVean,
- Andrew O.M. Wilkie,
- and Anne Goriely
Genome Res. December 2018 28: 1779-1790; Published in Advance October 24, 2018, doi:10.1101/gr.239186.118
.... 2013; Holstege et al. 2014; Swanton 2015). This latter phenomenon has been documented in apparently healthy somatic tissues that display stem cell replacement (e.g., skin, colon, small intestine, and blood), where low levels (∼1%–10%) of clonal mutations are prevalent and their incidence and frequency...
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Research: Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer
- Lars A. Forsberg,
- Chiara Rasi,
- Gyula Pekar,
- Hanna Davies,
- Arkadiusz Piotrowski,
- Devin Absher,
- Hamid Reza Razzaghian,
- Aleksandra Ambicka,
- Krzysztof Halaszka,
- Marcin Przewoźnik,
- Anna Kruczak,
- Geeta Mandava,
- Saichand Pasupulati,
- Julia Hacker,
- K. Reddy Prakash,
- Ravi Chandra Dasari,
- Joey Lau,
- Nelly Penagos-Tafurt,
- Helena M. Olofsson,
- Gunilla Hallberg,
- Piotr Skotnicki,
- Jerzy Mituś,
- Jaroslaw Skokowski,
- Michal Jankowski,
- Ewa Śrutek,
- Wojciech Zegarski,
- Eva Tiensuu Janson,
- Janusz Ryś,
- Tibor Tot,
- and Jan P. Dumanski
Genome Res. October 2015 25: 1521-1535; doi:10.1101/gr.187823.114
...) were studied. Comparative analysis between UM(s), PT(s), and blood/skin from the same patient as a control is the core of the study design. We identified 108 patients with at least one aberrant UM, representing 38.3% of cases. Gains in gene copy number were the principal type of mutations...
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Research: Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells
- Monika S. Kowalczyk,
- Itay Tirosh,
- Dirk Heckl,
- Tata Nageswara Rao,
- Atray Dixit,
- Brian J. Haas,
- Rebekka K. Schneider,
- Amy J. Wagers,
- Benjamin L. Ebert,
- and Aviv Regev
Genome Res. December 2015 25: 1860-1872; Published in Advance October 1, 2015, doi:10.1101/gr.192237.115
...heterogeneity within the HSCs and how it may change with age in the steady-state unperturbed hematopoiesis. Given that HSCs are functionally heterogeneous as revealed through transplantation studies (Dykstra et al. 2007; Challen et al. 2010; Muller-Sieburg et al. 2012), wehypothesized that this retrospective...

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