The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection

Genome Res. 2004 May;14(5):812-9. doi: 10.1101/gr.2228504.


Somatic mitochondrial mutations are common in human cancers, and can be used as a tool for early detection of cancer. We have developed a mitochondrial Custom Reseq microarray as an array-based sequencing platform for rapid and high-throughput analysis of mitochondrial DNA. The MitoChip contains oligonucleotide probes synthesized using standard photolithography and solid-phase synthesis, and is able to sequence >29 kb of double-stranded DNA in a single assay. Both strands of the entire human mitochondrial coding sequence (15,451 bp) are arrayed on the MitoChip; both strands of an additional 12,935 bp (84% of coding DNA) are arrayed in duplicate. We used 300 ng of genomic DNA to amplify the mitochondrial coding sequence in three overlapping long PCR fragments. We then sequenced >2 million base pairs of mitochondrial DNA, and successfully assigned base calls at 96.0% of nucleotide positions. Replicate experiments demonstrated >99.99% reproducibility. In matched fluid samples (urine and pancreatic juice, respectively) obtained from five patients with bladder cancer and four with pancreatic cancer, the MitoChip detected at least one cancer-associated mitochondrial mutation in six (66%) of nine samples. The MitoChip is a high-throughput sequencing tool for the reliable identification of mitochondrial DNA mutations from primary tumors in clinical samples.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Body Fluids / chemistry
  • Body Fluids / metabolism
  • Cell Line, Tumor
  • Computational Biology / methods
  • Computational Biology / organization & administration
  • DNA / genetics
  • DNA Mutational Analysis / methods*
  • DNA, Mitochondrial / genetics
  • DNA, Neoplasm / genetics
  • Genotype
  • Humans
  • Lung Neoplasms / chemistry
  • Lung Neoplasms / genetics
  • Lymphocytes / chemistry
  • Matched-Pair Analysis
  • Mitochondria / genetics*
  • Mitochondria / pathology
  • Mutation / genetics
  • Neoplasms / chemistry
  • Neoplasms / genetics
  • Neoplasms / pathology
  • Oligonucleotide Array Sequence Analysis
  • Pancreatic Juice / chemistry
  • Pancreatic Juice / metabolism
  • Pancreatic Juice / microbiology
  • Reproducibility of Results
  • Urinary Bladder Neoplasms / chemistry
  • Urinary Bladder Neoplasms / genetics


  • DNA, Mitochondrial
  • DNA, Neoplasm
  • DNA