HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human Papillomavirus 18

Journal of Virology

Volumn 89, Issue 8, 2015, Pages 4051-4057

  Cantalupo, Paul G ^a   Katz, Joshua P ^a   Pipas, James M ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE 6 PHOSPHATE DEHYDROGENASE; NUCLEIC ACID;

ARTICLE; CELL JUNCTION; CHROMOSOME 8; G6PD GENE; GENE EXPRESSION; GENE FREQUENCY; GENOTYPE; HPV18 GENE; HUMAN; HUMAN PAPILLOMAVIRUS TYPE 18; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; UTERINE CERVIX CANCER; VIRUS GENE; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS STRAIN; CHEMISTRY; DNA CONTAMINATION; GENETIC DATABASE; GENETICS; HELA CELL LINE; HUMAN GENOME; MOLECULAR GENETICS; NEOPLASM; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; VIRUS DNA CELL DNA INTERACTION;

HUMAN PAPILLOMAVIRUS - 18;

BASE SEQUENCE; DATABASES, GENETIC; DNA CONTAMINATION; GENOME, HUMAN; GLUCOSEPHOSPHATE DEHYDROGENASE; HELA CELLS; HUMAN PAPILLOMAVIRUS 18; HUMANS; MOLECULAR SEQUENCE DATA; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; VIRUS INTEGRATION;

EID: 84925400655     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.03365-14     Document Type: Article

References (29)

1. Gey GO, Coffman WD, Kubicek MT. 1952. Tissue culture studies of the proliferative capacity of cervical carcinoma and normal epithelium. Cancer Res 12:264-265.
2. Gartler SM. 1968. Apparent Hela cell contamination of human heteroploid cell lines. Nature 217:750-751. http://dx.doi.org/10.1038/217750a0.
3. Nelson-Rees WA, Daniels DW, Flandermeyer RR. 1981. Crosscontamination of cells in culture. Science 212:446-452. http://dx.doi.org/10.1126/science.6451928.
4. Lucey BP, Nelson-Rees WA, Hutchins GM. 2009. Henrietta Lacks, HeLa cells, and cell culture contamination. Arch Pathol Lab Med 133:1463-1467. http://dx.doi.org/10.1043/1543-2165-133.9.1463.
5. Nardone RM. 2007. Eradication of cross-contaminated cell lines: a call for action. Cell Biol Toxicol 23:367-372. http://dx.doi.org/10.1007/s10565-007-9019-9.
6. Masters JR. 2002. HeLa cells 50 years on: the good, the bad and the ugly. Nat Rev Cancer 2:315-319. http://dx.doi.org/10.1038/nrc775.
7. Jäger W, Horiguchi Y, Shah J, Hayashi T, Awrey S, Gust KM, Hadaschik BA, Matsui Y, Anderson S, Bell RH, Ettinger S, So AI, Gleave ME, Lee IL, Dinney CP, Tachibana M, McConkey DJ, Black PC. 2013. Hiding in plain view: genetic profiling reveals decades old cross contamination of bladder cancer cell line KU7 with HeLa. J Urol 190:1404-1409. http://dx.doi.org/10.1016/j.juro.2013.03.009.
8. MacLeod RA, Dirks WG, Matsuo Y, Kaufmann M, Milch H, Drexler HG. 1999. Widespread intraspecies cross-contamination of human tumor cell lines arising at source. Int J Cancer 83:555-563.
9. Chatterjee R. 2007. Cell biology. Cases of mistaken identity. Science 315: 928-931. http://dx.doi.org/10.1126/science.315.5814.928.
10. Schwarz E, Freese UK, Gissmann L, Mayer W, Roggenbuck B, Stremlau A, zur Hausen H. 1985. Structure and transcription of human papillomavirus sequences in cervical carcinoma cells. Nature 314:111-114. http://dx.doi.org/10.1038/314111a0.
11. Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, Qiu R, Lee C, Shendure J. 2013. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature 500:207-211. http://dx.doi.org/10.1038/nature12064.
12. Thierry F. 2009. Transcriptional regulation of the papillomavirus oncogenes by cellular and viral transcription factors in cervical carcinoma. Virology 384:375-379. http://dx.doi.org/10.1016/j.virol.2008.11.014.
13. Meissner JD. 1999. Nucleotide sequences and further characterization of human papillomavirus DNA present in the CaSki, SiHa and HeLa cervical carcinoma cell lines. J Gen Virol 80:1725-1733.
14. Crow JM. 2012. HPV: the global burden. Nature 488:S2-S3. http://dx.doi.org/10.1038/488S2a.
15. Johansson C, Schwartz S. 2013. Regulation of human papillomavirus gene expression by splicing and polyadenylation. Nat Rev Microbiol 11: 239-251. http://dx.doi.org/10.1038/nrmicro2984.
16. Cheng JY, Sheu LF, Meng CL, Lee WH, Lin JC. 1995. Detection of human papillomavirus DNA in colorectal carcinomas by polymerase chain reaction. Gut 37:87-90. http://dx.doi.org/10.1136/gut.37.1.87.
17. Gornick MC, Castellsague X, Sanchez G, Giordano TJ, Vinco M, Greenson JK, Capella G, Raskin L, Rennert G, Gruber SB, Moreno V. 2010. Human papillomavirus is not associated with colorectal cancer in a large international study. Cancer Causes Control 21:737-743. http://dx.doi.org/10.1007/s10552-010-9502-0.
18. Salepci T, Yazici H, Dane F, Topuz E, Dalay N, Onat H, Aykan F, Seker M, Aydiner A. 2009. Detection of human papillomavirus DNA by polymerase chain reaction and southern blot hybridization in colorectal cancer patients. J BUON 14:495-499.
19. Tang KW, Alaei-Mahabadi B, Samuelsson T, Lindh M, Larsson E. 2013. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun 4:2513. http://dx.doi.org/10.1038/ncomms 3513.
20. Salyakina D, Tsinoremas NF. 2013. Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data. Hum Genomics 7:23. http://dx.doi.org/10.1186/1479-7364-7-23.
21. Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863-864. http://dx.doi.org/10.1093/bioinformatics/btr026.
22. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-359. http://dx.doi.org/10.1038/nmeth.1923.
23. Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178-192. http://dx.doi.org/10.1093/bib/bbs017.
24. Katz JP, Pipas JM. 2014. SummonChimera infers integrated viral genomes with nucleotide precision from NGS data. BMC Bioinform 15:348. http://dx.doi.org/10.1186/s12859-014-0348-4.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
26. Wang X, Meyers C, Wang HK, Chow LT, Zheng ZM. 2011. Construction of a full transcription map of human papillomavirus type 18 during productive viral infection. J Virol 85:8080-8092. http://dx.doi.org/10.1128/JVI.00670-11.
27. Yoshida A, Watanabe S, Gartler SM. 1971. Identification of HeLa cell glucose 6-phosphate dehydrogenase. Biochem Genet 5:533-539. http://dx.doi.org/10.1007/BF00485671.
28. Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stutz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM. 2013. The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) 3:1213-1224. http://dx.doi.org/10.1534/g3.113.005777.
29. Borozan I, Wilson S, Blanchette P, Laflamme P, Watt SN, Krzyzanowski PM, Sircoulomb F, Rottapel R, Branton PE, Ferretti V. 2012. CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes. BMC Bioinform 13:206. http://dx.doi.org/10.1186/1471-2105-13-206.