SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Didion, John P ^a,b   Buus, Ryan J ^a,b   Naghashfar, Zohreh ^c   Threadgill, David W ^d,e   Morse, Herbert C ^c   de Villena, Fernando Pardo Manuel ^a,b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^d TEXAS A AND M UNIVERSITY   (United States)

^e TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ANALYTICAL ERROR; ANEUPLOIDY; ANIMAL CELL; ARTICLE; CELL LINE; CELL LINE AUTHENTICATION BY SNP PROFILING; CHROMOSOME NUMBER; CONCENTRATION (PARAMETERS); CONTAMINATION; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; GENETIC VARIABILITY; INBRED STRAIN; MATHEMATICAL COMPUTING; MOUSE; MOUSE STRAIN; NONHUMAN; REFERENCE DATABASE; SINGLE NUCLEOTIDE POLYMORPHISM; TAXONOMY; VALIDATION PROCESS; WILD TYPE; ANIMAL; COPY NUMBER VARIATION; CROSS BREEDING; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOTYPE; INBRED MOUSE STRAIN;

MICROSATELLITE DNA;

ANEUPLOIDY; ANIMALS; CELL LINE; CROSSES, GENETIC; DNA COPY NUMBER VARIATIONS; GENE EXPRESSION PROFILING; GENOTYPE; LINKAGE DISEQUILIBRIUM; MICE; MICE, INBRED STRAINS; MICROSATELLITE REPEATS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84908068927     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-847     Document Type: Article

References (34)

1. Nature Identity crisis. Nature 2009, 457:935-936. Nature.
2. American Type Culture Collection Standards Development Organization Workgroup ASN-0002 Cell line misidentification: the beginning of the end. Nat Rev Cancer 2010, 10:441-448. 10.1038/nrc2852, 20448633, American Type Culture Collection Standards Development Organization Workgroup ASN-0002.
3. Podolak E. Ending Cell Line Contamination by Cutting off Researchers, Biotechniques Online News (2010).
4. Capes-Davis A, Theodosopoulos G, Atkin I, Drexler HG, Kohara A, MacLeod RAF, Masters JR, Nakamura Y, Reid YA, Reddel RR, Freshney RI. Check your cultures! A list of cross-contaminated or misidentified cell lines. Int J Cancer 2010, 127:1-8. 10.1002/ijc.25242, 20143388.
5. Yoshino K, Saijo K, Noro C, Nakamura Y. Development of a simple method to determine the mouse strain from which cultured cell lines originated. Interdisciplinary Bio Central 2010, 2:1-9.
6. Masters JR, Thomson JA, Daly-Burns B, Reid YA, Dirks WG, Packer P, Toji LH, Ohno T, Tanabe H, Arlett CF. Short tandem repeat profiling provides an international reference standard for human cell lines. Proc Natl Acad Sci U S A 2001, 98:8012-8017. 10.1073/pnas.121616198, 35459, 11416159.
7. Almeida JL, Hill CR, Cole KD. Mouse cell line authentication. Cytotechnology 2014, 66:133-147. 10.1007/s10616-013-9545-7, 3886540, 23430347.
8. Castro F, Dirks WG, Fähnrich S, Hotz-Wagenblatt A, Pawlita M, Schmitt M. High-Throughput SNP-Based Authentication of Human Cell Lines 2012, n/a-n/a. A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations.
9. Phillips JL, Hayward SW, Wang Y, Vasselli J, Pavlovich C, Padilla-Nash H, Pezullo JR, Ghadimi BM, Grossfeld GD, Rivera A, Linehan WM, Cunha GR, Ried T. The consequences of chromosomal aneuploidy on gene expression profiles in a cell line model for prostate carcinogenesis. Cancer Res 2001, 61:8143-8149.
10. Rebuzzini P, Neri T, Zuccotti M, Redi CA, Garagna S. Chromosome number variation in three mouse embryonic stem cell lines during culture. Mamm Genome 2008, 58:17-23.
11. Peterson SE, Westra JW, Rehen SK, Young H, Bushman DM, Paczkowski CM, Yung YC, Lynch CL, Tran HT, Nickey KS, Wang Y-C, Laurent LC, Loring JF, Carpenter MK, Chun J. Normal human pluripotent stem cell lines exhibit pervasive mosaic aneuploidy. PLoS ONE 2011, 6:e23018. 10.1371/journal.pone.0023018, 3156708, 21857983.
12. Petkov PM, Cassell MA, Sargent EE, Donnelly CJ, Robinson P, Crew V, Asquith S, Haar RV, Wiles MV. Development of a SNP genotyping panel for genetic monitoring of the laboratory mouse. Genomics 2004, 83:902-911. 10.1016/j.ygeno.2003.11.007, 15081119.
13. Demichelis F, Greulich H, Macoska JA, Beroukhim R, Sellers WR, Garraway L, Rubin MA. SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res 2008, 36:2446-2456. 10.1093/nar/gkn089, 2367734, 18304946.
14. Pakstis AJ, Speed WC, Fang R, Hyland FCL, Furtado MR, Kidd JR, Kidd KK. SNPs for a universal individual identification panel. Hum Genet 2010, 127:315-324. 10.1007/s00439-009-0771-1, 19937056.
15. Gibbs JR, Singleton A. Application of genome-wide single nucleotide polymorphism typing: simple association and beyond. PLoS Genet 2006, 2:e150. 10.1371/journal.pgen.0020150, 1592240, 17029559.
16. Collaborative Cross Consortium The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 2012, 190:389-401. 3276630, 22345608, Collaborative Cross Consortium.
17. Rogala AR, Morgan AP, Christensen AM, Gooch TJ, Bell TA, Miller DR, Godfrey VL, Pardo-Manuel de Villena F. The collaborative cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis. Mamm Genome 2014, 25:95-108. 10.1007/s00335-013-9499-2, 3960486, 24487921.
18. Didion JP, Yang H, Sheppard K, Fu C-P, McMillan L, Pardo-Manuel de Villena F, Churchill GA. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genomics 2012, 13:34. 10.1186/1471-2164-13-34, 3305361, 22260749.
19. The information about Ba/F3 (RCB0805). [http://www.brc.riken.jp/lab/cell/english/rcb0805_announce.shtml].
20. Shimada T, Aplin KP, Suzuki H. Mus lepidoides (Muridae, Rodentia) of central Burma is a distinct species of potentially great evolutionary and biogeographic significance. Zool Sci 2010, 27:449-459. 10.2108/zsj.27.449, 20443693.
21. Didion JP, Pardo-Manuel de Villena F. Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse. Mamm Genome 2013, 24:1-20. 10.1007/s00335-012-9441-z, 4034049, 23223940.
22. Yang W, Tempelman RJ. A bayesian antedependence model for whole genome prediction. Genetics 2012, 190:1491-501. 10.1534/genetics.111.131540, 3316658, 22135352.
23. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 2006, 16:1136-1148. 10.1101/gr.5402306, 1557768, 16899659.
24. Sun W, Wright FA, Tang Z, Nordgard SH, Loo PV, Yu T, Kristensen VN, Perou CM. Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res 2009, 37:5365-5377. 10.1093/nar/gkp493, 2935461, 19581427.
25. Fahey JR, Katoh H, Malcolm R, Perez AV. The case for genetic monitoring of mice and rats used in biomedical research. Mamm Genome 2013, 24:89-94. 10.1007/s00335-012-9444-9, 3627018, 23314661.
26. Manukjan G, Tauscher M, Ripperger T, Schwarzer A, Schlegelberger B, Steinemann D. Induced G1 phase arrest of fast-dividing cells improves the quality of genomic profiles generated by array-CGH. Biotechniques 2012, 53:245-248.
27. van Heesch S, Mokry M, Boskova V, Junker W, Mehon R, Toonen P, de Bruijn E, Shull JD, Aitman TJ, Cuppen E, Guryev V. Systematic biases in DNA copy number originate from isolation procedures. Genome Biol 2013, 14:R33. 10.1186/gb-2013-14-4-r33, 4054094, 23618369.
28. Fu C-P, Welsh CE, Pardo-Manuel de Villena F, McMillan L. Inferring ancestry in admixed populations using microarray probe intensities. BCB '12 2012, 105-112. New York, New York, USA: ACM Press.
29. Sugawara A, Goto K, Sotomaru Y, Sofuni T, Ito T. Current status of chromosomal abnormalities in mouse embryonic stem cell lines used in Japan. Comp Med 2006, 56:31-34.
30. Masters JR. Cell-line authentication: end the scandal of false cell lines. Nature 2012, 492:186-186.
31. Kidd KK, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SLB, Karoma NJ, Kungulilo S, Kim J-J, Lu R-B, Odunsi A, Okonofua F, Parnas J, Schulz LO, Zhukova OV, Kidd JR. Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 2006, 164:20-32. 10.1016/j.forsciint.2005.11.017, 16360294.
32. Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Höglund M, Borg T, Ringnér M. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 2008, 9:409. 10.1186/1471-2105-9-409, 2572624, 18831757.
33. Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res 2008, 36:e126. 10.1093/nar/gkn556, 2577347, 18784189.
34. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007, 17:1665-1674. 10.1101/gr.6861907, 2045149, 17921354.