Differences between the genomes of lymphoblastoid cell lines and blood-derived samples

References

• Choy E, Yelensky R, Bonakdar S, et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet. 2008;4(11):e1000287.
   Web of Science ®Google Scholar
• Sie L, Loong S, Tan EK. Utility of lymphoblastoid cell lines. J Neurosci Res. 2009;87(9):1953–1959.
   PubMed Web of Science ®Google Scholar
• Simon-Sanchez J, Scholz S, Fung H-C, 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):1–14.
   PubMed Web of Science ®Google Scholar
• Zook JM, Chapman B, Wang J, et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014;32(3):246–251.
   PubMed Web of Science ®Google Scholar
• Zook JM, Catoe D, McDaniel J, et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci data. 2016;3:160025.
   PubMed Web of Science ®Google Scholar
• Diroma MA, Calabrese C, Simone D, et al. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics. 2014;15(Suppl 3):S2.
   PubMedGoogle Scholar
• Chakrabarty S, D’Souza RR, Kabekkodu SP, Gopinath PM, Rossignol R, Satyamoorthy K. Upregulation of TFAM and mitochondria copy number in human lymphoblastoid cells. Mitochondrion. 2014;15(1):52–58.
   Google Scholar
• Shirley MD, Baugher JD, Stevens EL, et al. Chromosomal variation in lymphoblastoid cell lines. Hum Mutat. 2012;33(7):1075–1086.
   Web of Science ®Google Scholar
• 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(2):122–130.
   Google Scholar
• Nickles D, Madireddy L, Yang S, et al. In depth comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing. BMC Genomics. 2012;13:477.
   PubMed Web of Science ®Google Scholar
• Londin ER, Keller MA, D’Andrea MR, et al. Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor. BMC Genomics. 2011;12:464.
   PubMed Web of Science ®Google Scholar
• Oh JH, Kim YJ, Moon S, et al. Genotype instability during long-term subculture of lymphoblastoid cell lines. J Hum Genet. 2013;58(1):16–20.
   Web of Science ®Google Scholar
• Çalişkan M, Cusanovich DA, Ober C, Gilad Y. The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet. 2011;20(8):1643–1652.
   PubMed Web of Science ®Google Scholar
• Aberg K, Khachane AN, Rudolf G, et al. Methylome-wide comparison of human genomic DNA extracted from whole blood and from EBV-transformed lymphocyte cell lines. Eur J Hum Genet. 2012;20(9):953–955.
   PubMed Web of Science ®Google Scholar
• Carnevali P, Baccash J, Halpern AL, et al. Computational techniques for human genome resequencing using mated gapped reads. J Comput Biol. 2011;19(3):279–292.
   Web of Science ®Google Scholar
• Glusman G, Severson A, Dhankani V, et al. Identification of copy number variants in whole-genome data using reference coverage profiles. Front Genet. 2015;6:45.
   Web of Science ®Google Scholar
• Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006;22(9):1036–1046.
   PubMed Web of Science ®Google Scholar
• Hiratani I, Ryba T, Itoh M, et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008;6(10):2220–2236.
   Web of Science ®Google Scholar
• Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM. Genome-scale analysis of replication timing: from bench to bioinformatics. Nat Protoc. 2011;6(6):870–895.
   Web of Science ®Google Scholar
• Gaziev AI, Shaikhaev GO. Nuclear mitochondrial pseudogenes. Mol Biol. 2010;44(3):358–368.
   Web of Science ®Google Scholar
• Kim MA, Johannsmann R, Grzeschik KH. Giemsa staining of the sites replicating DNA early in human lymphocyte chromosomes. Cytogenet Cell Genet. 1975;15(6):363–371.
   Google Scholar
• Schwaiger M, Schübeler D. A question of timing: Emerging links between transcription and replication. Curr Opin Genet Dev. 2006;16(2):177–183.
   Web of Science ®Google Scholar
• Makova KD, Hardison RC. The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet. 2015;16(4):213–223.
   Web of Science ®Google Scholar
• Koren A, Polak P, Nemesh J, et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet. 2012;91(6):1033–1040.
   PubMed Web of Science ®Google Scholar
• Aymard F, Bugler B, Schmidt CK, et al. Transcriptionally active chromatin recruits homologous recombination at DNA double strand breaks. Nat Struct Mol Biol. 2015;21(4):366–374.
   Web of Science ®Google Scholar
• Martin CL, Kirkpatrick BE, Ledbetter DH. Copy number variants, aneuploidies, and human disease. Clin Perinatol. 2015;42(2):227–242.
   PubMed Web of Science ®Google Scholar
• McCarroll SA. Extending genome-wide association studies to copy-number variation. Hum Mol Genet. 2008;17(R2):135–142.
   Google Scholar