Next Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy

Taosheng Huang1

1 Division of Human Genetics/Department of Pediatrics, Center for Molecular and Mitochondrial Medicine and Genetics, University of California, Irvine, Irvine, California
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 19.8
DOI:  10.1002/0471142905.hg1908s71
Online Posting Date:  October, 2011
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This protocol describes the methodology to characterize mitochondrial DNA (mtDNA) heteroplasmy by parallel sequencing. Mitochondria play an important role in essential cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondria genomes. Mutant and wild‐type mtDNA may co‐exist as heteroplasmy, and cause human disease. The purpose of this protocol is to simultaneously determine mtDNA sequence and quantify the heteroplasmic level. This protocol includes a two‐fragment mitochondrial genome DNA PCR amplification. The PCR product is then mixed at an equimolar ratio. The samples are then barcoded and sequenced with high‐throughput, next‐generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the level of heteroplasmy. Curr. Protoc. Hum. Genet. 71:19.8.1‐19.8.12 © 2011 by John Wiley & Sons, Inc.

Keywords: mitochondria; next‐generation sequencing; heteroplasmy

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Table of Contents

  • Introduction
  • Basic Protocol 1: PCR Amplification of mtDNA for Illumina‐Paired End Sequencing
  • Basic Protocol 2: Analysis of Sequencing Data to Determine Degree of Heteroplasmy
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: PCR Amplification of mtDNA for Illumina‐Paired End Sequencing

  • DNAse‐ and RNAse‐free, ulltra‐pure water (Gibco, cat. no. 10977‐015, Milli‐Q, or equivalent)
  • 10 µM primers:
    • hmtF1 569 (5′‐AACCAAACCCCAAAGACACC‐3′)
    • hmtR1 9819 (5′‐GCCAATAATGACGTGAAGTCC‐3′)
    • htmF2 9611 (5′‐TCCCACTCCTAAACACATCC‐3′)
    • hmtR2 626 (5′‐TTTATGGGGTGATGTGAGCC‐3′)
  • 100 mM 4dNTP mix (Roche; 25 mM each dNTP; also see appendix 2D)
  • 5 U/µl Takara Taq DNA polymerase (Takara)
  • 10× PCR amplification buffer containing 15 mM MgCl 2 (Roche)
  • Positive control DNA
  • Genomic DNA stored in TE buffer, pH 7.4 (total genomic DNA extracted from peripheral blood using QIAamp DNA extraction kit, QIAGEN)
  • Low‐melting agarose (e.g., Fisher)
  • 10× Tris/borate/EDTA (TBE) buffer
  • 10 mg/ml ethidium bromide
  • 5× gel loading dye (see recipe)
  • 1‐kb DNA ladder
  • Thermal cycler (Perkin Elmer, cat. no. N801‐0150)
  • Gel apparatus and power source
  • Gel documentation system
  • NanoDrop 2000 spectrophotometer (Thermo Scientific; see appendix 3D)
  • Illumina GA sequencer (Illumina, part no. 1005063,‐End_SamplePrep_Guide_1005063_B.pdf

Basic Protocol 2: Analysis of Sequencing Data to Determine Degree of Heteroplasmy

  • Computer with minimum requirements of Windows 7, 64 bit, 8‐GB RAM, 2 CPUs
  • Illumina CASAVA software (ver 1.6.0, Illumina)
  • NextGene software V2.1 (Softgenetics) to align to the genome (≥6‐GB RAM to align to multiple mitochondrial genomes with 1 GB of data file; more is required for the assembly of larger data sets)
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Literature Cited

Literature Cited
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