Contamination and Sample Mix-up Can Best Explain Some Patterns of MtDNA Instabilities in Buccal Cells and Oral Squamous Cell Carcinoma

Overview

Journal BMC Cancer

Publisher Biomed Central

Specialty Oncology

Date 2009 Apr 18

PMID 19371404

Citations 21

Authors

Hans-Jurgen Bandelt

Antonio Salas

Affiliations

Soon will be listed here.

Abstract

The study of somatic DNA instabilities constitutes a debatable topic because different causes can lead to seeming DNA alteration patterns between different cells or tissues from the same individual. Carcinogenesis or the action of a particular toxic could generate such patterns, and this is in fact the leitmotif of a number of studies on mitochondrial DNA (mtDNA) instability. Patterns of seeming instabilities could also arise from technical errors at any stage of the analysis (DNA extraction, amplification, mutation screening/sequencing, and documentation). Specifically, inadvertent DNA contamination or sample mixing would yield mosaic variation that could be erroneously interpreted as real mutation differences (instabilities) between tissues from the same individual. From the very beginning, mtDNA studies comparing cancerous to non-cancerous tissues have suffered from such mosaic results. We demonstrate here that the phylogenetic linkage of whole arrays of mtDNA mutations provides strong evidence of artificial recombination in previous studies on buccal cells and oral squamous cell carcinoma.

Citing Articles

Profiling of Mitochondrial DNA Heteroplasmy in a Prospective Oral Squamous Cell Carcinoma Study.

Fendt L, Fazzini F, Weissensteiner H, Bruckmoser E, Schonherr S, Schafer G Cancers (Basel). 2020; 12(7).

PMID: 32708892 PMC: 7409097. DOI: 10.3390/cancers12071933.

A New Paradigm for Tissue Diagnostics: Tools and Techniques to Standardize Tissue Collection, Transport, and Fixation.

Bauer D, Otter M, Chafin D Curr Pathobiol Rep. 2018; 6(2):135-143.

PMID: 29780664 PMC: 5956061. DOI: 10.1007/s40139-018-0170-1.

Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions.

Ballenghien M, Faivre N, Galtier N BMC Biol. 2017; 15(1):25.

PMID: 28356154 PMC: 5370491. DOI: 10.1186/s12915-017-0366-6.

The complete mitogenome of a 500-year-old Inca child mummy.

Gomez-Carballa A, Catelli L, Pardo-Seco J, Martinon-Torres F, Roewer L, Vullo C Sci Rep. 2015; 5:16462.

PMID: 26561991 PMC: 4642457. DOI: 10.1038/srep16462.

Mitochondrial DNA mutations in single human blood cells.

Yao Y, Kajigaya S, Young N Mutat Res. 2015; 779:68-77.

PMID: 26149767 PMC: 6466630. DOI: 10.1016/j.mrfmmm.2015.06.009.

References

Yoon J, Smith L, Feng Z, Tang M, Lee C, Pfeifer G . Methylated CpG dinucleotides are the preferential targets for G-to-T transversion mutations induced by benzo[a]pyrene diol epoxide in mammalian cells: similarities with the p53 mutation spectrum in smoking-associated lung cancers. Cancer Res. 2001; 61(19):7110-7. View

Bandelt H, Quintana-Murci L, Salas A, Macaulay V . The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet. 2002; 71(5):1150-60. PMC: 385090. DOI: 10.1086/344397. View

Denissenko M, Pao A, Tang M, Pfeifer G . Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in P53. Science. 1996; 274(5286):430-2. DOI: 10.1126/science.274.5286.430. View

Salas A, Bandelt H, Macaulay V, Richards M . Phylogeographic investigations: the role of trees in forensic genetics. Forensic Sci Int. 2006; 168(1):1-13. DOI: 10.1016/j.forsciint.2006.05.037. View

Gilbert M, Bandelt H, Hofreiter M, Barnes I . Assessing ancient DNA studies. Trends Ecol Evol. 2006; 20(10):541-4. DOI: 10.1016/j.tree.2005.07.005. View

Salas A, Carracedo A, Macaulay V, Richards M, Bandelt H . A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun. 2005; 335(3):891-9. DOI: 10.1016/j.bbrc.2005.07.161. View

Suzuki M, Toyooka S, Miyajima K, Iizasa T, Fujisawa T, Bekele N . Alterations in the mitochondrial displacement loop in lung cancers. Clin Cancer Res. 2003; 9(15):5636-41. View

Bandelt H, Salas A, Bravi C . What is a 'novel' mtDNA mutation--and does 'novelty' really matter?. J Hum Genet. 2006; 51(12):1073-1082. DOI: 10.1007/s10038-006-0066-5. View

Kong Q, Salas A, Sun C, Fuku N, Tanaka M, Zhong L . Distilling artificial recombinants from large sets of complete mtDNA genomes. PLoS One. 2008; 3(8):e3016. PMC: 2515346. DOI: 10.1371/journal.pone.0003016. View

10.

Kivisild T, Shen P, Wall D, Do B, Sung R, Davis K . The role of selection in the evolution of human mitochondrial genomes. Genetics. 2005; 172(1):373-87. PMC: 1456165. DOI: 10.1534/genetics.105.043901. View

11.

Bandelt H, Yao Y, Salas A . The search of 'novel' mtDNA mutations in hypertrophic cardiomyopathy: MITOMAPping as a risk factor. Int J Cardiol. 2007; 126(3):439-42. DOI: 10.1016/j.ijcard.2007.02.049. View

12.

Yao Y, Bravi C, Bandelt H . A call for mtDNA data quality control in forensic science. Forensic Sci Int. 2004; 141(1):1-6. DOI: 10.1016/j.forsciint.2003.12.004. View

13.

Bandelt H, Olivieri A, Bravi C, Yao Y, Torroni A, Salas A . 'Distorted' mitochondrial DNA sequences in schizophrenic patients. Eur J Hum Genet. 2007; 15(4):400-2. DOI: 10.1038/sj.ejhg.5201781. View

14.

Bandelt H, Salas A, Bravi C . Problems in FBI mtDNA database. Science. 2004; 305(5689):1402-4. DOI: 10.1126/science.305.5689.1402b. View

15.

Trejaut J, Kivisild T, Loo J, Lee C, He C, Hsu C . Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol. 2005; 3(8):e247. PMC: 1166350. DOI: 10.1371/journal.pbio.0030247. View

16.

Roostalu U, Kutuev I, Loogvali E, Metspalu E, Tambets K, Reidla M . Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Mol Biol Evol. 2006; 24(2):436-48. DOI: 10.1093/molbev/msl173. View

17.

Bandelt H, Lahermo P, Richards M, Macaulay V . Detecting errors in mtDNA data by phylogenetic analysis. Int J Legal Med. 2001; 115(2):64-9. DOI: 10.1007/s004140100228. View

18.

Wong L, Liang M, Kwon H, Park J, Bai R, Tan D . Comprehensive scanning of the entire mitochondrial genome for mutations. Clin Chem. 2002; 48(11):1901-12. View

19.

Tan D, Chang J, Liu L, Bai R, Wang Y, Yeh K . Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer. BMC Cancer. 2006; 6:93. PMC: 1459869. DOI: 10.1186/1471-2407-6-93. View

20.

Alonso A, Alves C, Suarez-Mier M, Albarran C, Pereira L, Fernandez de Simon L . Mitochondrial DNA haplotyping revealed the presence of mixed up benign and neoplastic tissue sections from two individuals on the same prostatic biopsy slide. J Clin Pathol. 2004; 58(1):83-6. PMC: 1770540. DOI: 10.1136/jcp.2004.017673. View