Abstract
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.
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Acknowledgements
We thank D. Anderson, J. Salk and L. Loeb for discussion and comments. This work was supported by US National Institutes of Health grants DP1OD003278 and R01DK078340 (to M.S.H.), R01CA111582 and R01CA098243 (to B.D.P.), T32HL007093 (for C.A.C.), F30AG030316 (to S.J.S.) and T32GM007266 (to M.S.H.), and Achievement Rewards for College Scientists Foundation fellowship grants to the University of Washington Medical Scientist Training Program (for S.J.S.).
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C.A.C., B.D.P., L.E.H., S.J.S. and M.S.H. designed the experiments. C.A.C., S.J.S. and L.E.H. carried out the experiments. C.A.C., A.K., R.K. and M.S.H. contributed to analyzing the data. M.S.H., with input from other authors, wrote the paper.
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Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–6, Supplementary Tables 1,3,4 (PDF 3453 kb)
Supplementary Table 2
Compilation of identified mutations. (XLS 167 kb)
Supplementary Software
PrimerDesign.pl is a Perl program for evaluation of arbitrary primers; ChromosomePrep.pl is a Perl program to prepare mouse reference sequence for PrimerDesign.pl; and Geno.pl is a Perl program to perform mutational analysis. (ZIP 9 kb)
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Carlson, C., Kas, A., Kirkwood, R. et al. Decoding cell lineage from acquired mutations using arbitrary deep sequencing. Nat Methods 9, 78–80 (2012). https://doi.org/10.1038/nmeth.1781
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DOI: https://doi.org/10.1038/nmeth.1781
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