Insertion/deletion and microsatellite alteration profiles in induced pluripotent stem cells
We here demonstrate that microsatellite (MS) alterations are elevated in both mouse and human induced pluripotent stem cells (iPSCs), but importantly we have now identified a type of human iPSC in which these alterations are considerably reduced. We aimed in our present analyses to profile the InDel...
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Published in | Stem cell reports Vol. 16; no. 10; pp. 2503 - 2519 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
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Elsevier Inc
12.10.2021
Elsevier |
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Abstract | We here demonstrate that microsatellite (MS) alterations are elevated in both mouse and human induced pluripotent stem cells (iPSCs), but importantly we have now identified a type of human iPSC in which these alterations are considerably reduced. We aimed in our present analyses to profile the InDels in iPSC/ntESC genomes, especially in MS regions. To detect somatic de novo mutations in particular, we generated 13 independent reprogramed stem cell lines (11 iPSC and 2 ntESC lines) from an identical parent somatic cell fraction of a C57BL/6 mouse. By using this cell set with an identical genetic background, we could comprehensively detect clone-specific alterations and, importantly, experimentally validate them. The effectiveness of employing sister clones for detecting somatic de novo mutations was thereby demonstrated. We then successfully applied this approach to human iPSCs. Our results require further careful genomic analysis but make an important inroad into solving the issue of genome abnormalities in iPSCs.
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•InDels and microsatellite alterations are elevated in iPSCs•These alterations are reduced in human iPSCs derived from cord blood erythroblasts•Employing sister clones is an effective way to detect somatic de novo mutations
In this article, Abe and colleagues conclusively demonstrate that InDels and microsatellite alterations are elevated in reprogrammed pluripotent stem cells, both mouse and human, by employing sister clones and conducting large-scale validation experiments. Furthermore, they show that these alterations are considerably reduced in human iPSCs derived from cord blood erythroblasts. |
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AbstractList | We here demonstrate that microsatellite (MS) alterations are elevated in both mouse and human induced pluripotent stem cells (iPSCs), but importantly we have now identified a type of human iPSC in which these alterations are considerably reduced. We aimed in our present analyses to profile the InDels in iPSC/ntESC genomes, especially in MS regions. To detect somatic
de novo
mutations in particular, we generated 13 independent reprogramed stem cell lines (11 iPSC and 2 ntESC lines) from an identical parent somatic cell fraction of a C57BL/6 mouse. By using this cell set with an identical genetic background, we could comprehensively detect clone-specific alterations and, importantly, experimentally validate them. The effectiveness of employing sister clones for detecting somatic
de novo
mutations was thereby demonstrated. We then successfully applied this approach to human iPSCs. Our results require further careful genomic analysis but make an important inroad into solving the issue of genome abnormalities in iPSCs.
•
InDels and microsatellite alterations are elevated in iPSCs
•
These alterations are reduced in human iPSCs derived from cord blood erythroblasts
•
Employing sister clones is an effective way to detect somatic
de novo
mutations
In this article, Abe and colleagues conclusively demonstrate that InDels and microsatellite alterations are elevated in reprogrammed pluripotent stem cells, both mouse and human, by employing sister clones and conducting large-scale validation experiments. Furthermore, they show that these alterations are considerably reduced in human iPSCs derived from cord blood erythroblasts. We here demonstrate that microsatellite (MS) alterations are elevated in both mouse and human induced pluripotent stem cells (iPSCs), but importantly we have now identified a type of human iPSC in which these alterations are considerably reduced. We aimed in our present analyses to profile the InDels in iPSC/ntESC genomes, especially in MS regions. To detect somatic de novo mutations in particular, we generated 13 independent reprogramed stem cell lines (11 iPSC and 2 ntESC lines) from an identical parent somatic cell fraction of a C57BL/6 mouse. By using this cell set with an identical genetic background, we could comprehensively detect clone-specific alterations and, importantly, experimentally validate them. The effectiveness of employing sister clones for detecting somatic de novo mutations was thereby demonstrated. We then successfully applied this approach to human iPSCs. Our results require further careful genomic analysis but make an important inroad into solving the issue of genome abnormalities in iPSCs. We here demonstrate that microsatellite (MS) alterations are elevated in both mouse and human induced pluripotent stem cells (iPSCs), but importantly we have now identified a type of human iPSC in which these alterations are considerably reduced. We aimed in our present analyses to profile the InDels in iPSC/ntESC genomes, especially in MS regions. To detect somatic de novo mutations in particular, we generated 13 independent reprogramed stem cell lines (11 iPSC and 2 ntESC lines) from an identical parent somatic cell fraction of a C57BL/6 mouse. By using this cell set with an identical genetic background, we could comprehensively detect clone-specific alterations and, importantly, experimentally validate them. The effectiveness of employing sister clones for detecting somatic de novo mutations was thereby demonstrated. We then successfully applied this approach to human iPSCs. Our results require further careful genomic analysis but make an important inroad into solving the issue of genome abnormalities in iPSCs. [Display omitted] •InDels and microsatellite alterations are elevated in iPSCs•These alterations are reduced in human iPSCs derived from cord blood erythroblasts•Employing sister clones is an effective way to detect somatic de novo mutations In this article, Abe and colleagues conclusively demonstrate that InDels and microsatellite alterations are elevated in reprogrammed pluripotent stem cells, both mouse and human, by employing sister clones and conducting large-scale validation experiments. Furthermore, they show that these alterations are considerably reduced in human iPSCs derived from cord blood erythroblasts. |
Author | Abe, Masumi Kamimura, Satoshi Fujita, Mayumi Nakamura, Miki Suga, Tomo Imadome, Kaori Hoki, Yuko Sunayama, Misato Araki, Ryoko |
Author_xml | – sequence: 1 givenname: Satoshi surname: Kamimura fullname: Kamimura, Satoshi organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 2 givenname: Tomo surname: Suga fullname: Suga, Tomo organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 3 givenname: Yuko surname: Hoki fullname: Hoki, Yuko organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 4 givenname: Misato surname: Sunayama fullname: Sunayama, Misato organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 5 givenname: Kaori surname: Imadome fullname: Imadome, Kaori organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 6 givenname: Mayumi surname: Fujita fullname: Fujita, Mayumi organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 7 givenname: Miki surname: Nakamura fullname: Nakamura, Miki organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 8 givenname: Ryoko surname: Araki fullname: Araki, Ryoko email: araki.ryoko@qst.go.jp organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan – sequence: 9 givenname: Masumi surname: Abe fullname: Abe, Masumi email: abe.masumi@qst.go.jp organization: Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan |
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Keywords | hotspots of microsatellite alteration mouse iPSCs genome reprogramming whole-genome sequencing microsatellite alterations cord blood erythroblasts InDels human iPSCs mouse ntESCs sister clones set |
Language | English |
License | This is an open access article under the CC BY-NC-ND license. Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
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References | Nguyen, Markouli, Geens, Barbé, Sermon, Spits (bib17) 2014; 20 Rasmussen, Holst, Tümer, Johnsen, Zhou, Stummann, Hyttel, Clausen (bib20) 2014; 3 Kloosterman, Francioli, Hormozdiari, Marschall, Hehir-Kwa, Abdellaoui, Lameijer, Moed, Koval, Renkens (bib14) 2015; 25 Ninomiya, Hirose (bib18) 2020; 6 Okita, Matsumura, Sato, Okada, Morizane, Okamoto, Hong, Nakagawa, Tanabe, Tezuka (bib19) 2011; 8 Rouhani, Nik-Zainal, Wuster, Li, Conte, Koike-Yusa, Kumasaka, Vallier, Yusa, Bradley (bib21) 2016; 12 Young, Larson, Sun, George, Ding, Miller, Lin, Pawlik, Chen, Fan (bib26) 2012; 10 Araki, Uda, Hoki, Sunayama, Nakamura, Ando, Sugiura, Ideno, Shimada, Nifuji (bib4) 2013; 494 Bhutani, Nazor, Williams, Tran, Dai, Dzakula, Cho, Pang, Rao, Cao (bib6) 2016; 7 Di Prospero, Fischbeck (bib8) 2005; 6 Wang, Baek, Eling (bib24) 2013; 85 Araki, Mizutani, Hoki, Sunayama, Wakayama, Nagatomo, Kasama, Nakamura, Wakayama, Abe (bib3) 2017; 35 Jakubosky, Smith, D'Antonio, Jan Bonder, Young Greenwald, D'Antonio-Chronowska, Matsui, Stegle, Montgomery, DeBoever (bib11) 2020; 11 Assie, Letouze, Fassnacht, Jouinot, Luscap, Barreau, Omeiri, Rodriguez, Perlemoine, Rene-Corail (bib5) 2014; 46 Mandai, Watanabe, Kurimoto, Hirami, Morinaga, Daimon, Fujihara, Akimaru, Sakai, Shibata (bib16) 2017; 376 Takahashi, Yamanaka (bib23) 2006; 126 Cheng, Hansen, Zhao, Du, Zou, Donovan, Chou, Zhou, Li, Dowey (bib7) 2012; 10 Gore, Li, Fung, Young, Agarwal, Antosiewicz-Bourget, Canto, Giorgetti, Israel, Kiskinis (bib10) 2011; 471 Liang, Zhang (bib15) 2013; 13 Abdel-Fatah, Albarakati, Bowell, Agarwal, Moseley, Hawkes, Ball, Chan, Ellis, Madhusudan (bib1) 2013; 142 Willems, Zielinski, Yuan, Gordon, Gymrek, Erlich (bib25) 2017; 14 Araki, Hoki, Suga, Obara, Sunayama, Imadome, Fujita, Kamimura, Nakamura, Wakayama (bib2) 2020; 11 Kemmerich, Dingler, Rada, Neuberger (bib13) 2012; 40 Sugiura, Kasama, Araki, Hoki, Sunayama, Uda, Nakamura, Ando, Abe (bib22) 2014; 2 Ewing, Houlahan, Hu, Ellrott, Caloian, Yamaguchi, Bare, P'ng, Waggott, Sabelnykova (bib9) 2015; 12 Ji, Ng, Sharma, Neculai, Hussein, Sam, Trinh, Church, McPherson, Nagy (bib12) 2012; 30 Young (10.1016/j.stemcr.2021.08.017_bib26) 2012; 10 Araki (10.1016/j.stemcr.2021.08.017_bib3) 2017; 35 Mandai (10.1016/j.stemcr.2021.08.017_bib16) 2017; 376 Wang (10.1016/j.stemcr.2021.08.017_bib24) 2013; 85 Jakubosky (10.1016/j.stemcr.2021.08.017_bib11) 2020; 11 Abdel-Fatah (10.1016/j.stemcr.2021.08.017_bib1) 2013; 142 Rasmussen (10.1016/j.stemcr.2021.08.017_bib20) 2014; 3 Cheng (10.1016/j.stemcr.2021.08.017_bib7) 2012; 10 Sugiura (10.1016/j.stemcr.2021.08.017_bib22) 2014; 2 Araki (10.1016/j.stemcr.2021.08.017_bib4) 2013; 494 Assie (10.1016/j.stemcr.2021.08.017_bib5) 2014; 46 Kloosterman (10.1016/j.stemcr.2021.08.017_bib14) 2015; 25 Ewing (10.1016/j.stemcr.2021.08.017_bib9) 2015; 12 Di Prospero (10.1016/j.stemcr.2021.08.017_bib8) 2005; 6 Araki (10.1016/j.stemcr.2021.08.017_bib2) 2020; 11 Takahashi (10.1016/j.stemcr.2021.08.017_bib23) 2006; 126 Bhutani (10.1016/j.stemcr.2021.08.017_bib6) 2016; 7 Kemmerich (10.1016/j.stemcr.2021.08.017_bib13) 2012; 40 Ji (10.1016/j.stemcr.2021.08.017_bib12) 2012; 30 Okita (10.1016/j.stemcr.2021.08.017_bib19) 2011; 8 Willems (10.1016/j.stemcr.2021.08.017_bib25) 2017; 14 Rouhani (10.1016/j.stemcr.2021.08.017_bib21) 2016; 12 Ninomiya (10.1016/j.stemcr.2021.08.017_bib18) 2020; 6 Liang (10.1016/j.stemcr.2021.08.017_bib15) 2013; 13 Gore (10.1016/j.stemcr.2021.08.017_bib10) 2011; 471 Nguyen (10.1016/j.stemcr.2021.08.017_bib17) 2014; 20 |
References_xml | – volume: 471 start-page: 63 year: 2011 end-page: 67 ident: bib10 article-title: Somatic coding mutations in human induced pluripotent stem cells publication-title: Nature contributor: fullname: Kiskinis – volume: 12 start-page: 623 year: 2015 end-page: 630 ident: bib9 article-title: Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection publication-title: Nat. Methods contributor: fullname: Sabelnykova – volume: 30 start-page: 435 year: 2012 end-page: 440 ident: bib12 article-title: Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells publication-title: Stem Cells contributor: fullname: Nagy – volume: 14 start-page: 590 year: 2017 end-page: 592 ident: bib25 article-title: Genome-wide profiling of heritable and de novo STR variations publication-title: Nat. Methods contributor: fullname: Erlich – volume: 11 start-page: 2928 year: 2020 ident: bib11 article-title: Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats publication-title: Nat. Commun. contributor: fullname: DeBoever – volume: 25 start-page: 792 year: 2015 end-page: 801 ident: bib14 article-title: Characteristics of de novo structural changes in the human genome publication-title: Genome Res. contributor: fullname: Renkens – volume: 13 start-page: 149 year: 2013 end-page: 159 ident: bib15 article-title: Genetic and epigenetic variations in iPSCs: potential causes and implications for application publication-title: Cell Stem Cell contributor: fullname: Zhang – volume: 20 start-page: 981 year: 2014 end-page: 989 ident: bib17 article-title: Human embryonic stem cells show low-grade microsatellite instability publication-title: Mol. Hum. Reprod. contributor: fullname: Spits – volume: 10 start-page: 337 year: 2012 end-page: 344 ident: bib7 article-title: Low incidence of DNA sequence variation in human induced pluripotent stem cells generated by nonintegrating plasmid expression publication-title: Cell Stem Cell contributor: fullname: Dowey – volume: 85 start-page: 597 year: 2013 end-page: 606 ident: bib24 article-title: The diverse roles of nonsteroidal anti-inflammatory drug activated gene (NAG-1/GDF15) in cancer publication-title: Biochem. Pharmacol. contributor: fullname: Eling – volume: 6 start-page: 756 year: 2005 end-page: 765 ident: bib8 article-title: Therapeutics development for triplet repeat expansion diseases publication-title: Nat. Rev. Genet. contributor: fullname: Fischbeck – volume: 2 start-page: 52 year: 2014 end-page: 63 ident: bib22 article-title: Induced pluripotent stem cell generation-associated point mutations arise during the initial stages of the conversion of these cells publication-title: Stem Cell Reports contributor: fullname: Abe – volume: 3 start-page: 404 year: 2014 end-page: 413 ident: bib20 article-title: Transient p53 suppression increases reprogramming of human fibroblasts without affecting apoptosis and DNA damage publication-title: Stem Cell Reports contributor: fullname: Clausen – volume: 142 start-page: 515 year: 2013 end-page: 527 ident: bib1 article-title: Single-strand selective monofunctional uracil-DNA glycosylase (SMUG1) deficiency is linked to aggressive breast cancer and predicts response to adjuvant therapy publication-title: Breast Cancer Res. Treat. contributor: fullname: Madhusudan – volume: 11 start-page: 197 year: 2020 ident: bib2 article-title: Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency publication-title: Nat. Commun. contributor: fullname: Wakayama – volume: 7 start-page: 10536 year: 2016 ident: bib6 article-title: Whole-genome mutational burden analysis of three pluripotency induction methods publication-title: Nat. Commun. contributor: fullname: Cao – volume: 494 start-page: 100 year: 2013 end-page: 104 ident: bib4 article-title: Negligible immunogenicity of terminally differentiated cells derived from induced pluripotent or embryonic stem cells publication-title: Nature contributor: fullname: Nifuji – volume: 12 start-page: e1005932 year: 2016 ident: bib21 article-title: Mutational history of a human cell lineage from somatic to induced pluripotent stem cells publication-title: PLoS Genet. contributor: fullname: Bradley – volume: 46 start-page: 607 year: 2014 end-page: 612 ident: bib5 article-title: Integrated genomic characterization of adrenocortical carcinoma publication-title: Nat. Genet. contributor: fullname: Rene-Corail – volume: 40 start-page: 6016 year: 2012 end-page: 6025 ident: bib13 article-title: Germline ablation of SMUG1 DNA glycosylase causes loss of 5-hydroxymethyluracil- and UNG-backup uracil-excision activities and increases cancer predisposition of Ung–/–Msh2–/– mice publication-title: Nucleic Acids Res. contributor: fullname: Neuberger – volume: 10 start-page: 570 year: 2012 end-page: 582 ident: bib26 article-title: Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells publication-title: Cell Stem Cell contributor: fullname: Fan – volume: 376 start-page: 1038 year: 2017 end-page: 1046 ident: bib16 article-title: Autologous induced stem-cell-derived retinal cells for macular degeneration publication-title: N. Engl. J. Med. contributor: fullname: Shibata – volume: 8 start-page: 409 year: 2011 end-page: 412 ident: bib19 article-title: A more efficient method to generate integration-free human iPS cells publication-title: Nat. Methods contributor: fullname: Tezuka – volume: 126 start-page: 663 year: 2006 end-page: 676 ident: bib23 article-title: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors publication-title: Cell contributor: fullname: Yamanaka – volume: 35 start-page: 1189 year: 2017 end-page: 1196 ident: bib3 article-title: The number of point mutations in induced pluripotent stem cells and nuclear transfer embryonic stem cells depends on the method and somatic cell type used for their generation publication-title: Stem Cells contributor: fullname: Abe – volume: 6 start-page: 6 year: 2020 ident: bib18 article-title: Short tandem repeat-enriched architectural RNAs in nuclear bodies: functions and associated diseases publication-title: Noncoding RNA contributor: fullname: Hirose – volume: 471 start-page: 63 year: 2011 ident: 10.1016/j.stemcr.2021.08.017_bib10 article-title: Somatic coding mutations in human induced pluripotent stem cells publication-title: Nature doi: 10.1038/nature09805 contributor: fullname: Gore – volume: 11 start-page: 197 year: 2020 ident: 10.1016/j.stemcr.2021.08.017_bib2 article-title: Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency publication-title: Nat. Commun. doi: 10.1038/s41467-019-13830-x contributor: fullname: Araki – volume: 40 start-page: 6016 year: 2012 ident: 10.1016/j.stemcr.2021.08.017_bib13 article-title: Germline ablation of SMUG1 DNA glycosylase causes loss of 5-hydroxymethyluracil- and UNG-backup uracil-excision activities and increases cancer predisposition of Ung–/–Msh2–/– mice publication-title: Nucleic Acids Res. doi: 10.1093/nar/gks259 contributor: fullname: Kemmerich – volume: 13 start-page: 149 year: 2013 ident: 10.1016/j.stemcr.2021.08.017_bib15 article-title: Genetic and epigenetic variations in iPSCs: potential causes and implications for application publication-title: Cell Stem Cell doi: 10.1016/j.stem.2013.07.001 contributor: fullname: Liang – volume: 6 start-page: 756 year: 2005 ident: 10.1016/j.stemcr.2021.08.017_bib8 article-title: Therapeutics development for triplet repeat expansion diseases publication-title: Nat. Rev. Genet. doi: 10.1038/nrg1690 contributor: fullname: Di Prospero – volume: 14 start-page: 590 year: 2017 ident: 10.1016/j.stemcr.2021.08.017_bib25 article-title: Genome-wide profiling of heritable and de novo STR variations publication-title: Nat. Methods doi: 10.1038/nmeth.4267 contributor: fullname: Willems – volume: 10 start-page: 337 year: 2012 ident: 10.1016/j.stemcr.2021.08.017_bib7 article-title: Low incidence of DNA sequence variation in human induced pluripotent stem cells generated by nonintegrating plasmid expression publication-title: Cell Stem Cell doi: 10.1016/j.stem.2012.01.005 contributor: fullname: Cheng – volume: 20 start-page: 981 year: 2014 ident: 10.1016/j.stemcr.2021.08.017_bib17 article-title: Human embryonic stem cells show low-grade microsatellite instability publication-title: Mol. Hum. Reprod. doi: 10.1093/molehr/gau059 contributor: fullname: Nguyen – volume: 126 start-page: 663 year: 2006 ident: 10.1016/j.stemcr.2021.08.017_bib23 article-title: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors publication-title: Cell doi: 10.1016/j.cell.2006.07.024 contributor: fullname: Takahashi – volume: 494 start-page: 100 year: 2013 ident: 10.1016/j.stemcr.2021.08.017_bib4 article-title: Negligible immunogenicity of terminally differentiated cells derived from induced pluripotent or embryonic stem cells publication-title: Nature doi: 10.1038/nature11807 contributor: fullname: Araki – volume: 7 start-page: 10536 year: 2016 ident: 10.1016/j.stemcr.2021.08.017_bib6 article-title: Whole-genome mutational burden analysis of three pluripotency induction methods publication-title: Nat. Commun. doi: 10.1038/ncomms10536 contributor: fullname: Bhutani – volume: 11 start-page: 2928 year: 2020 ident: 10.1016/j.stemcr.2021.08.017_bib11 article-title: Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats publication-title: Nat. Commun. doi: 10.1038/s41467-020-16481-5 contributor: fullname: Jakubosky – volume: 85 start-page: 597 year: 2013 ident: 10.1016/j.stemcr.2021.08.017_bib24 article-title: The diverse roles of nonsteroidal anti-inflammatory drug activated gene (NAG-1/GDF15) in cancer publication-title: Biochem. Pharmacol. doi: 10.1016/j.bcp.2012.11.025 contributor: fullname: Wang – volume: 10 start-page: 570 year: 2012 ident: 10.1016/j.stemcr.2021.08.017_bib26 article-title: Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells publication-title: Cell Stem Cell doi: 10.1016/j.stem.2012.03.002 contributor: fullname: Young – volume: 142 start-page: 515 year: 2013 ident: 10.1016/j.stemcr.2021.08.017_bib1 article-title: Single-strand selective monofunctional uracil-DNA glycosylase (SMUG1) deficiency is linked to aggressive breast cancer and predicts response to adjuvant therapy publication-title: Breast Cancer Res. Treat. doi: 10.1007/s10549-013-2769-6 contributor: fullname: Abdel-Fatah – volume: 12 start-page: 623 year: 2015 ident: 10.1016/j.stemcr.2021.08.017_bib9 article-title: Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection publication-title: Nat. Methods doi: 10.1038/nmeth.3407 contributor: fullname: Ewing – volume: 2 start-page: 52 year: 2014 ident: 10.1016/j.stemcr.2021.08.017_bib22 article-title: Induced pluripotent stem cell generation-associated point mutations arise during the initial stages of the conversion of these cells publication-title: Stem Cell Reports doi: 10.1016/j.stemcr.2013.11.006 contributor: fullname: Sugiura – volume: 8 start-page: 409 year: 2011 ident: 10.1016/j.stemcr.2021.08.017_bib19 article-title: A more efficient method to generate integration-free human iPS cells publication-title: Nat. Methods doi: 10.1038/nmeth.1591 contributor: fullname: Okita – volume: 46 start-page: 607 year: 2014 ident: 10.1016/j.stemcr.2021.08.017_bib5 article-title: Integrated genomic characterization of adrenocortical carcinoma publication-title: Nat. Genet. doi: 10.1038/ng.2953 contributor: fullname: Assie – volume: 35 start-page: 1189 year: 2017 ident: 10.1016/j.stemcr.2021.08.017_bib3 article-title: The number of point mutations in induced pluripotent stem cells and nuclear transfer embryonic stem cells depends on the method and somatic cell type used for their generation publication-title: Stem Cells doi: 10.1002/stem.2601 contributor: fullname: Araki – volume: 6 start-page: 6 year: 2020 ident: 10.1016/j.stemcr.2021.08.017_bib18 article-title: Short tandem repeat-enriched architectural RNAs in nuclear bodies: functions and associated diseases publication-title: Noncoding RNA doi: 10.3390/ncrna6010006 contributor: fullname: Ninomiya – volume: 30 start-page: 435 year: 2012 ident: 10.1016/j.stemcr.2021.08.017_bib12 article-title: Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells publication-title: Stem Cells doi: 10.1002/stem.1011 contributor: fullname: Ji – volume: 3 start-page: 404 year: 2014 ident: 10.1016/j.stemcr.2021.08.017_bib20 article-title: Transient p53 suppression increases reprogramming of human fibroblasts without affecting apoptosis and DNA damage publication-title: Stem Cell Reports doi: 10.1016/j.stemcr.2014.07.006 contributor: fullname: Rasmussen – volume: 376 start-page: 1038 year: 2017 ident: 10.1016/j.stemcr.2021.08.017_bib16 article-title: Autologous induced stem-cell-derived retinal cells for macular degeneration publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa1608368 contributor: fullname: Mandai – volume: 25 start-page: 792 year: 2015 ident: 10.1016/j.stemcr.2021.08.017_bib14 article-title: Characteristics of de novo structural changes in the human genome publication-title: Genome Res. doi: 10.1101/gr.185041.114 contributor: fullname: Kloosterman – volume: 12 start-page: e1005932 year: 2016 ident: 10.1016/j.stemcr.2021.08.017_bib21 article-title: Mutational history of a human cell lineage from somatic to induced pluripotent stem cells publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1005932 contributor: fullname: Rouhani |
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Snippet | We here demonstrate that microsatellite (MS) alterations are elevated in both mouse and human induced pluripotent stem cells (iPSCs), but importantly we have... |
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SubjectTerms | Animals Cells, Cultured Cellular Reprogramming Cellular Reprogramming Techniques - methods cord blood erythroblasts Genetic Profile genome reprogramming hotspots of microsatellite alteration human iPSCs Humans INDEL Mutation InDels Induced Pluripotent Stem Cells - metabolism Mice Mice, Inbred C57BL microsatellite alterations Microsatellite Repeats mouse iPSCs mouse ntESCs sister clones set Whole Genome Sequencing |
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Title | Insertion/deletion and microsatellite alteration profiles in induced pluripotent stem cells |
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