Investigation of length heteroplasmy in mitochondrial DNA control region by massively parallel sequencing

Chun-Yen Lin, Li-Chin Tsai, Hsing-Mei Hsieh, Chia-Hung Huang, Yu-Jen Yu, Bill Tseng, Adrian Linacre, James Lee

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


Accurate sequencing of the control region of the mitochondrial genome is notoriously difficult due to the presence of polycytosine bases, termed C-tracts. The precise number of bases that constitute a C-tract and the bases beyond the poly cytosines may not be accurately defined when analyzing Sanger sequencing data separated by capillary electrophoresis. Massively parallel sequencing has the potential to resolve such poor definition and provides the opportunity to discover variants due to length heteroplasmy. In this study, the control region of mitochondrial genomes from 20 samples was sequenced using both standard Sanger methods with separation by capillary electrophoresis and also using massively parallel DNA sequencing technology. After comparison of the two sets of generated sequence, with the exception of the C-tracts where length heteroplasmy was observed, all sequences were concordant. Sequences of three segments 16184–16193, 303–315 and 568–573 with C-tracts in HVI, II and III can be clearly defined from the massively parallel sequencing data using the program SEQ Mapper. Multiple sequence variants were observed in the length of C-tracts longer than 7 bases. Our report illustrates the accurate designation of all the length variants leading to heteroplasmy in the control region of the mitochondrial genome that can be determined by SEQ Mapper based on data generated by massively parallel DNA sequencing.

Original languageEnglish
Pages (from-to)127-133
Number of pages7
JournalForensic Science International: Genetics
Publication statusPublished - Sep 2017


  • C-tract
  • Control region
  • Forensic science
  • Length heteroplasmy
  • Massively parallel sequencing
  • Mitochondrial DNA
  • SEQ mapper


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