High-Quality and High-Throughput Massively Parallel Sequencing of the Human Mitochondrial Genome Using the Illumina MiSeq

• NCJ Number: 248151
• Journal: Forensic Science International Genetics Volume: 12 Dated: September 2014 Pages: 128-135
• Author(s): Jonathan L. King; Bobby L. LaRue; Nicole M. Novroski; Monika Stoljarova; Seung B. Seo; Xiangpei Zeng; David H. Warshauer; Carey P. Davis; Walther Parson; Antti Sajantila; Bruce Budowle
• Date Published: June 2014
• Length: 8 pages
• Grant Number(s): 2012-DN-BX-K033; 2011-MU-MU-K402
• Sponsoring Agency: National Institute of Justice (NIJ)
• Publication Format: Article
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Report (Grant Sponsored)
• Language: English
• Country: Ireland

Annotation

The Nextera XT DNA Sample Preparation Kit and the illumina MiSeq were used to generate quality whole genome mitochondrial haplotypes from 283 individuals in a cost-effective and rapid manner.

Abstract

Results showed that haplotypes can be generated at a high depth of coverage with limited strand bias. The distribution of variants across the mitochondrial genome demonstrated greater variation within the coding region than the non-coding region. The overall increase in haplotype or genetic diversity and random match probability, as well as better haplogroup assignment, shows that shows that the massively parallel sequencing (MPS) of the mtGenome using the Illuina MiSeq system is a viable and reliable methodology. This is the first report of a relatively large number of mtGenomes that has been sequenced in a high throughput fashion using the illumina MiSeq system. The throughput level was high due to the use of Nexter XT DNA Sample Preparation Kit and MPS. Although some strand bias was observed, it generally was limited to areas of low coverage and did not diminish the ability to assign variant calls. In sequencing the entire mtGenome versus only HVI/HVII, the only variant calls significantly improved the discrimination power of haplotypes. An overall improvement in the resolution of haplogroup assignments was observed compared with only the control region to the mtGenome; haplogroup assignment was ambiguous for HVI/HVII segments of those mtGenome sequences that were not represented by control revion polymorphisms in Phylotree. The study sequenced approximately 300 individual mtGenomes by a single individual in 1 month at an average reagent cost of approximately $50 per sample. 2 figures, 4 tables, and 47 references