Decoding cell lineage from acquired mutations using arbitrary deep sequencing

Because mutations are inevitable, the genome of each cell in a multicellular organism becomes unique and therefore encodes a record of its ancestry. Here we coupled arbitrary single primer PCR with next-generation DNA sequencing to catalog mutations and deconvolve the phylogeny of cultured mouse cells. This study helps pave the way toward construction of retrospective cell-fate maps based on mutations accumulating in genomes of somatic cells.

[1]  D. Housman,et al.  Chromosome-mediated transfer of the murine Na,K-ATPase alpha subunit confers ouabain resistance , 1987, Molecular and cellular biology.

[2]  J. Lingrel,et al.  Structure-function relationships in the sodium-potassium ATPase .alpha. subunit: site-directed mutagenesis of glutamine-111 to arginine and asparagine-122 to aspartic acid generates a ouabain-resistant enzyme , 1988 .

[3]  J. Lingrel,et al.  Structure-function relationships in the Na,K-ATPase alpha subunit: site-directed mutagenesis of glutamine-111 to arginine and asparagine-122 to aspartic acid generates a ouabain-resistant enzyme. , 1988, Biochemistry.

[4]  M. McClelland,et al.  DNA fingerprinting by arbitrarily primed PCR. , 1994, PCR methods and applications.

[5]  L. Cantley,et al.  Ouabain-resistant OR6 cells express the murine alpha 1-subunit of the Na,K-ATPase with a T797-I797 substitution. , 1994, The Journal of biological chemistry.

[6]  T. Prolla,et al.  Involvement of mouse Mlh1 in DNA mismatch repair and meiotic crossing over , 1996, Nature Genetics.

[7]  J. Lingrel,et al.  Extensive random mutagenesis analysis of the Na+/K+-ATPase alpha subunit identifies known and previously unidentified amino acid residues that alter ouabain sensitivity--implications for ouabain binding. , 1997, European journal of biochemistry.

[8]  J. Sulston Caenorhabditis elegans: The Cell Lineage and Beyond (Nobel Lecture) , 2003, Chembiochem : a European journal of chemical biology.

[9]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[10]  J. Nicolas,et al.  Methods in clonal analysis and applications. , 2005, Reproduction, nutrition, development.

[11]  Uriel Feige,et al.  Genomic Variability within an Organism Exposes Its Cell Lineage Tree , 2005, PLoS Comput. Biol..

[12]  Qi Zheng New algorithms for Luria-Delbrück fluctuation analysis. , 2005, Mathematical biosciences.

[13]  W. Gilks,et al.  A novel algorithm and web-based tool for comparing two alternative phylogenetic trees , 2006, Bioinform..

[14]  S. Salipante,et al.  Phylogenetic fate mapping. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[15]  S. Tavaré,et al.  Stem Cell Chronicles: Autobiographies Within Genomes , 2007, Stem Cell Reviews.

[16]  Eran Segal,et al.  Estimating Cell Depth from Somatic Mutations , 2008, PLoS Comput. Biol..

[17]  James M Thompson,et al.  Phylogenetic Fate Mapping: Theoretical and Experimental Studies Applied to the Development of Mouse Fibroblasts , 2008, Genetics.

[18]  Qi Zheng A note on plating efficiency in fluctuation experiments. , 2008, Mathematical biosciences.

[19]  E. Shapiro,et al.  Reconstruction of Cell Lineage Trees in Mice , 2008, PLoS ONE.

[20]  E. Shapiro,et al.  Cell lineage analysis of a mouse tumor. , 2008, Cancer research.

[21]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[22]  Laura C. Greaves,et al.  A Methodological Approach to Tracing Cell Lineage in Human Epithelial Tissues , 2009, Stem cells.

[23]  R. Yung,et al.  Following Mitochondrial Footprints through a Long Mucosal Path to Lung Cancer , 2009, PloS one.

[24]  R. Goldsby,et al.  DNA polymerase ε and δ proofreading suppress discrete mutator and cancer phenotypes in mice , 2009, Proceedings of the National Academy of Sciences.

[25]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[26]  A. Kas,et al.  Phylogenetic analysis of developmental and postnatal mouse cell lineages , 2010, Evolution & development.

[27]  B. Preston,et al.  DNA replication fidelity and cancer. , 2010, Seminars in cancer biology.

[28]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.