Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent™ PGM™

摘要: Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by millions DNA fragments simultaneously. Compared Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis indeed sample basis. In this study, human mitochondria (mtGenome) were sequenced Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), out data assessed, results compared previously generated MiSeqTM (Illumina, Diego, CA). The objectives paper determine feasibility, accuracy, reliability obtained from PGM. 24 multiplexed (in groups six) at least 10 megabase throughput 314 chip. depth pattern was similar among all samples; however across genome varied. For strand bias, average ratio between forward reverse strands each position indicated that two-thirds positions had ratios greater than 0.5. A few sites more extreme bias. Another observation 156 false deletion rate 0.15 in one individuals. There 31-98 (SNP) mtGenome variants observed for analyzed. total 1237 concordant PGM MiSeq. quality scores haplogroup assignment ranged 88.8%-100%. mtDNA analyzed output evaluated. Depth variation bias identified but generally infrequent did not impact variant calls. Multiplexing demonstrated which improve Overall, based orthogonal concordance testing phylogenetic scrutiny, supported accuracy be using platform.