In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Nickles, Dorothee ^a   Madireddy, Lohith ^a   Yang, Shan ^b   Khankhanian, Pouya ^a   Lincoln, Steve ^b   Hauser, Stephen L ^a   Oksenberg, Jorge R ^a   Baranzini, Sergio E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Complete Genomics Inc ^*  (United States)

Author keywords

EBV transformation; Genetics; Lymphoblastoid cell line; Next generation sequencing

Indexed keywords

DNA; VIRUS DNA;

ANIMAL CELL; ARTICLE; CHROMOSOME REARRANGEMENT; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA POLYMORPHISM; EPSTEIN BARR VIRUS; FEMALE; FRAMESHIFT MUTATION; GENE DELETION; GENE INSERTION; GENE LOCUS; GENE SEQUENCE; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; HUMAN CELL; HUMAN GENOME; INDEL MUTATION; KARYOTYPE; LYMPHOBLASTOID CELL LINE; MALE; METAPHASE; MISSENSE MUTATION; NONHUMAN; NONSENSE MUTATION; SINGLE NUCLEOTIDE POLYMORPHISM; STOP CODON; VIRUS TRANSFORMATION;

CELL LINE; CELL TRANSFORMATION, VIRAL; DNA; GENOME, VIRAL; HERPESVIRUS 4, HUMAN; HUMANS;

HUMAN HERPESVIRUS 4;

EID: 84866150097     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-477     Document Type: Article

References (54)

1. Pattle SB, Farrell PJ. The role of Epstein-Barr virus in cancer. Expert Opin Biol Ther 2006, 6:1193-1205. 10.1517/14712598.6.11.1193, 17049016.
2. Thorley-Lawson DA, Allday MJ. The curious case of the tumour virus: 50 years of Burkitt's lymphoma. Nat Rev Microbiol 2008, 6:913-924. 10.1038/nrmicro2015, 19008891.
3. Kuppers R. The biology of Hodgkin's lymphoma. Nat Rev Cancer 2009, 9:15-27. 10.1038/nrc2542, 19078975.
4. Young LS, Rickinson AB. Epstein-Barr virus: 40 years on. Nat Rev Cancer 2004, 4:757-768. 10.1038/nrc1452, 15510157.
5. Sie L, Loong S, Tan EK. Utility of lymphoblastoid cell lines. J Neurosci Res 2009, 87:1953-1959. 10.1002/jnr.22000, 19224581.
6. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 2008, 4:e1000287. 10.1371/journal.pgen.1000287, 2583954, 19043577.
7. Simon-Sanchez J, Scholz S, Fung HC, Matarin M, Hernandez D, Gibbs JR, Britton A, de Vrieze FW, Peckham E, Gwinn-Hardy K, et al. Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals. Hum Mol Genet 2007, 16:1-14. 10.1093/hmg/ddm004, 17116639.
8. Ramagopalan SV, Heger A, Berlanga AJ, Maugeri NJ, Lincoln MR, Burrell A, Handunnetthi L, Handel AE, Disanto G, Orton SM, et al. A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res 2010, 20:1352-1360. 10.1101/gr.107920.110, 2945184, 20736230.
9. Bullaughey K, Chavarria CI, Coop G, Gilad Y. Expression quantitative trait loci detected in cell lines are often present in primary tissues. Hum Mol Genet 2009, 18:4296-4303. 10.1093/hmg/ddp382, 2766291, 19671653.
10. Hannula K, Lipsanen-Nyman M, Scherer SW, Holmberg C, Hoglund P, Kere J. Maternal and paternal chromosomes 7 show differential methylation of many genes in lymphoblast DNA. Genomics 2001, 73:1-9. 10.1006/geno.2001.6502, 11352560.
11. Grafodatskaya D, Choufani S, Ferreira JC, Butcher DT, Lou Y, Zhao C, Scherer SW, Weksberg R. EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines. Genomics 2010, 95:73-83. 10.1016/j.ygeno.2009.12.001, 20005943.
12. Caliskan M, Cusanovich DA, Ober C, Gilad Y. The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet 2011, 20:1643-1652. 10.1093/hmg/ddr041, 3063990, 21289059.
13. Mazzei F, Guarrera S, Allione A, Simonelli V, Narciso L, Barone F, Minoprio A, Ricceri F, Funaro A, D'Errico M, et al. 8-Oxoguanine DNA-glycosylase repair activity and expression: a comparison between cryopreserved isolated lymphocytes and EBV-derived lymphoblastoid cell lines. Mutat Res 2011, 718:62-67. 10.1016/j.mrgentox.2010.10.004, 20971211.
14. Thorley-Lawson DA. Epstein-Barr virus: exploiting the immune system. Nat Rev Immunol 2001, 1:75-82. 10.1038/35095584, 11905817.
15. Gruhne B, Kamranvar SA, Masucci MG, Sompallae R. EBV and genomic instability-a new look at the role of the virus in the pathogenesis of Burkitt's lymphoma. Semin Cancer Biol 2009, 19:394-400. 10.1016/j.semcancer.2009.07.005, 19619655.
16. Morissette G, Flamand L. Herpesviruses and chromosomal integration. J Virol 2010, 84:12100-12109. 10.1128/JVI.01169-10, 2976420, 20844040.
17. Jox A, Rohen C, Belge G, Bartnitzke S, Pawlita M, Diehl V, Bullerdiek J, Wolf J. Integration of Epstein-Barr virus in Burkitt's lymphoma cells leads to a region of enhanced chromosome instability. Ann Oncol 1997, 8(Suppl 2):131-135. 10.1093/annonc/8.suppl_2.S131, 9209656.
18. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
19. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 2010, 328:636-639. 10.1126/science.1186802, 3037280, 20220176.
20. Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet 2010, 19:4313-4318. 10.1093/hmg/ddq352, 2957323, 20719861.
21. Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA, et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med 2010, 362:1181-1191. 10.1056/NEJMoa0908094, 20220177.
22. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008, 40:722-729. 10.1038/ng.128, 2705838, 18438408.
23. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008, 456:66-72. 10.1038/nature07485, 2603574, 18987736.
24. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2009, 461:809-813. 10.1038/nature08489, 19812674.
25. Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, Yue P, Zhang Y, Pant KP, Bhatt D, et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 2010, 465:473-477. 10.1038/nature09004, 20505728.
26. Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol 2010, 11:R82. 10.1186/gb-2010-11-8-r82, 2945784, 20696054.
27. Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, et al. Initial genome sequencing and analysis of multiple myeloma. Nature 2011, 471:467-472. 10.1038/nature09837, 21430775.
28. Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 2010, 464:1351-1356. 10.1038/nature08990, 2862593, 20428171.
29. Puente XS, Pinyol M, Quesada V, Conde L, Ordonez GR, Villamor N, Escaramis G, Jares P, Bea S, Gonzalez-Diaz M, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011, 475:101-105. 10.1038/nature10113, 3322590, 21642962.
30. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011, 476(7360):298-303. 10.1038/nature10351, 3210554, 21796119.
31. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, et al. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet 2011, 7:e1002280. 10.1371/journal.pgen.1002280, 3174201, 21935354.
32. Tao Y, Ruan J, Yeh SH, Lu X, Wang Y, Zhai W, Cai J, Ling S, Gong Q, Chong Z, et al. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc Natl Acad Sci U S A 2011, 108:12042-12047. 10.1073/pnas.1108715108, 3141952, 21730188.
33. Londin ER, Keller MA, D'Andrea MR, Delgrosso K, Ertel A, Surrey S, Fortina P. Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor. BMC Genomics 2011, 12:464. 10.1186/1471-2164-12-464, 3203102, 21943378.
34. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 2010, 327:78-81. 10.1126/science.1181498, 19892942.
35. Takakuwa T, Luo WJ, Ham MF, Wada N, Aozasa K. Identification of Epstein-Barr virus integrated sites in lymphoblastoid cell line (IB4). Virus Res 2005, 108:133-138. 10.1016/j.virusres.2004.08.021, 15681063.
36. Ohshima K, Suzumiya J, Kanda M, Kato A, Kikuchi M. Integrated and episomal forms of Epstein-Barr virus (EBV) in EBV associated disease. Cancer Lett 1998, 122:43-50. 10.1016/S0304-3835(97)00368-6, 9464490.
37. Lestou VS, De Braekeleer M, Strehl S, Ott G, Gadner H, Ambros PF. Non-random integration of Epstein-Barr virus in lymphoblastoid cell lines. Genes Chromosomes Cancer 1993, 8:38-48. 10.1002/gcc.2870080108, 7691158.
38. Gao J, Luo X, Tang K, Li X, Li G. Epstein-Barr virus integrates frequently into chromosome 4q, 2q, 1q and 7q of Burkitt's lymphoma cell line (Raji). J Virol Methods 2006, 136:193-199. 10.1016/j.jviromet.2006.05.013, 16806502.
39. Takakuwa T, Luo WJ, Ham MF, Sakane-Ishikawa F, Wada N, Aozasa K. Integration of Epstein-Barr virus into chromosome 6q15 of Burkitt lymphoma cell line (Raji) induces loss of BACH2 expression. Am J Pathol 2004, 164:967-974. 10.1016/S0002-9440(10)63184-7, 1614712, 14982850.
40. Luo WJ, Takakuwa T, Ham MF, Wada N, Liu A, Fujita S, Sakane-Ishikawa E, Aozasa K. Epstein-Barr virus is integrated between REL and BCL-11A in American Burkitt lymphoma cell line (NAB-2). Lab Invest 2004, 84:1193-1199. 10.1038/labinvest.3700152, 15241441.
41. Jeon JP, Shim SM, Nam HY, Baik SY, Kim JW, Han BG. Copy number increase of 1p36.33 and mitochondrial genome amplification in Epstein-Barr virus-transformed lymphoblastoid cell lines. Cancer Genet Cytogenet 2007, 173:122-130. 10.1016/j.cancergencyto.2006.10.010, 17321327.
42. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol 2011, 29:24-26. 10.1038/nbt.1754, 3346182, 21221095.
43. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29:308-311. 10.1093/nar/29.1.308, 29783, 11125122.
44. Schmid E, Roos H, Sauter W, Rickinger A, Jaehnert I, Eckardt-Schupp F. Chromosome analysis of the differential radiosensitivity of an Epstein-Barr virus (EBV)-transformed B cell line and B and T lymphocytes from the same blood donor. Int J Radiat Biol 2010, 86:47-55. 10.3109/09553000903264523, 20070215.
45. Herbeck JT, Gottlieb GS, Wong K, Detels R, Phair JP, Rinaldo CR, Jacobson LP, Margolick JB, Mullins JI. Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies. PLoS One 2009, 4:e6915. 10.1371/journal.pone.0006915, 2731852, 19730697.
46. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. Global variation in copy number in the human genome. Nature 2006, 444:444-454. 10.1038/nature05329, 2669898, 17122850.
47. Danjoh I, Saijo K, Hiroyama T, Nakamura Y. The sonoda-tajima cell collection: a human genetics research resource with emphasis on South american indigenous populations. Genome Biol Evol 2011, 3:272-283. 10.1093/gbe/evr014, 3070430, 21383383.
48. Ling PD, Huls HM. Isolation and immortalization of lymphocytes. Curr Protoc Mol Biol 2005, Chapter 28:Unit 28:22.
49. cgatools 1.3.0 package http://cgatools.sourceforge.net/, cgatools 1.3.0 package.
50. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645. 10.1101/gr.092759.109, 2752132, 19541911.
51. Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005, 21:3439-3440. 10.1093/bioinformatics/bti525, 16082012.
52. Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007, 23:257-258. 10.1093/bioinformatics/btl567, 17098774.
53. bwa http://bio-bwa.sourceforge.net/, bwa.
54. samtools http://samtools.sourceforge.net/), samtools.