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Document Type |
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Article In Journal |
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Document Title |
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Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent™ PGM™ Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent™ PGM™ |
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Document Language |
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English |
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Abstract |
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ackground
Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeqTM (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM.
Results
24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%.
Conclusions
In this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed. Overall, the results of this study, based on orthogonal concordance testing and phylogenetic scrutiny, supported that whole mtGenome sequence data with high accuracy can be obtained using the PGM platform. |
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ISSN |
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1471-2164 |
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Journal Name |
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BMC genomics |
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Volume |
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16 |
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Issue Number |
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1 |
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Publishing Year |
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1436 AH
2015 AD |
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Article Type |
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Article |
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Added Date |
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Sunday, March 20, 2016 |
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Researchers
| Seung Bum Seo | Seo, Seung Bum | Investigator | | |
| Xiangpei Zeng | Zeng, Xiangpei | Researcher | | |
| Jonathan L King | King, Jonathan L | Researcher | | |
| Bobby L Larue | Larue, Bobby L | Researcher | | |
| Mourad Assidi | Assidi, Mourad | Researcher | | |
| Mohamed Al-Qahtani | Al-Qahtani, Mohamed | Researcher | | |
| Antti Sajantila | Sajantila, Antti | Researcher | | |
| Bruce Budowle | Budowle, Bruce | Researcher | | |
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