CV-hiPS-F and CV-hiPS-B were reprogrammed from CV Fibroblasts using 4-factor retroviral vectors. PGP1-iPS cells were reprogrammed by Cellular Dynamics using the same four factors in a lentiviral vector from PGP1F fibroblasts29 (link). dH1F-iPS8, dH1F-iPS9, dH1cF16-iPS1, dH1cF16-iPS4, dH1cF16, and dH1F cells were obtained from previous cultures30 (link) reprogrammed with retroviral vectors containing the same factors31 (link). DF-6-9-9, DF-19-11, iPS4.7, and FS cells were obtained from previously existing cultures; the reprogramming process and characterization of lines has been described previously24 (link). iPS11a, iPS11b, iPS17a, iPS17b, iPS29A, iPS29e, Hib11, Hib17, and Hib29 cells were obtained from previous cultures reprogrammed using retroviral vectors encoding three or four factors32 (link). FiPS3F1 and FiPS4F7 were reprogrammed from HFFxF fibroblasts using similar protocols33 (link)-35 (link). FiPS4F2 and FiPS4F-shpRB4.5 were reprogrammed using the same 4-factor protocol from IMR90 fibroblasts. The mRNA-derived lines (CF-RiPS1.4, CF-RiPS1.9, and CF Fibroblasts) were obtained from previous cultures36 . All hiPS lines were extensively characterized for pluripotency. Fourteen lines were tested for teratoma formation and shown to express all embryonic germ layers in vivo. DNA was extracted from each cell type using Qiagen’s DNeasy kit.
Exome capture was performed with either a library of padlock probes, commercial hybridization capture DNA baits (NimbleGen SeqCap EZ), or RNA baits (Agilent SureSelect), and the resulting libraries were sequenced on an Illumina GA IIx sequencer. Putative mutations were rejected if they were known polymorphisms or contained any minor allele presence in the fibroblast. All candidate mutations were confirmed using capillary Sanger sequencing.
For digital quantification, mutations were PCR-amplified and sequenced using an Illumina GA IIx. These libraries were sequenced to obtain on average one million independent base calls for each location. A binomial test was then used to determine if the observed minor allele frequency could be separated from error and estimate the frequency of each mutation.
Detailed methods are available in theSupplementary Materials .
Exome capture was performed with either a library of padlock probes, commercial hybridization capture DNA baits (NimbleGen SeqCap EZ), or RNA baits (Agilent SureSelect), and the resulting libraries were sequenced on an Illumina GA IIx sequencer. Putative mutations were rejected if they were known polymorphisms or contained any minor allele presence in the fibroblast. All candidate mutations were confirmed using capillary Sanger sequencing.
For digital quantification, mutations were PCR-amplified and sequenced using an Illumina GA IIx. These libraries were sequenced to obtain on average one million independent base calls for each location. A binomial test was then used to determine if the observed minor allele frequency could be separated from error and estimate the frequency of each mutation.
Detailed methods are available in the