Estimating relative mitochondrial DNA copy number using high throughput sequencing data.

Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao YY, Shyr Y, Guo Y
Genomics. 2017 109 (5-6): 457-462

PMID: 28734953 · DOI:10.1016/j.ygeno.2017.07.002

We hypothesize that the relative mitochondria copy number (MTCN) can be estimated by comparing the abundance of mitochondrial DNA to nuclear DNA reads using high throughput sequencing data. To test this hypothesis, we examined relative MTCN across 13 breast cancer cell lines using the RT-PCR based NovaQUANT Human Mitochondrial to Nuclear DNA Ratio Kit as the gold standard. Six distinct computational approaches were used to estimate the relative MTCN in order to compare to the RT-PCR measurements. The results demonstrate that relative MTCN correlates well with the RT-PCR measurements using exome sequencing data, but not RNA-seq data. Through analysis of copy number variants (CNVs) in The Cancer Genome Atlas, we show that the two nuclear genes used in the NovaQUANT assay to represent the nuclear genome often experience CNVs in tumor cells, questioning the accuracy of this gold-standard method when it is applied to tumor cells.

Copyright © 2017 Elsevier Inc. All rights reserved.

MeSH Terms (16)

Breast Neoplasms Cell Line, Tumor Computational Biology Databases, Genetic Data Mining DNA, Mitochondrial DNA Copy Number Variations Female Genes, Essential High-Throughput Nucleotide Sequencing Humans Mitochondria Real-Time Polymerase Chain Reaction Sequence Analysis, DNA Sequence Analysis, RNA Whole Exome Sequencing

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