{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001000693"],"sample_count":["2"],"description":["EGA dataset EGAD00001000693"],"repository":["EGA"],"title":["Whole genome sequencing of an individual's genomic DNA and that of its lymphoblastoid cell line."],"pubmed_abstract":["<h4>Background</h4>A detailed analysis of whole genomes can be now achieved with next generation sequencing. Epstein Barr Virus (EBV) transformation is a widely used strategy in clinical research to obtain an unlimited source of a subject's DNA. Although the mechanism of transformation and immortalization by EBV is relatively well known at the transcriptional and proteomic level, the genetic consequences of EBV transformation are less well understood. A detailed analysis of the genetic alterations introduced by EBV transformation is highly relevant, as it will inform on the usefulness and limitations of this approach.<h4>Results</h4>We used whole genome sequencing to assess the genomic signature of a low-passage lymphoblastoid cell line (LCL). Specifically, we sequenced the full genome (40X) of an individual using DNA purified from fresh whole blood as well as DNA from his LCL. A total of 217.33 Gb of sequence were generated from the cell line and 238.95 Gb from the normal genomic DNA. We determined with high confidence that 99.2% of the genomes were identical, with no reproducible changes in structural variation (chromosomal rearrangements and copy number variations) or insertion/deletion polymorphisms (indels).<h4>Conclusions</h4>Our results suggest that, at this level of resolution, the LCL is genetically indistinguishable from its genomic counterpart and therefore their use in clinical research is not likely to introduce a significant bias."],"pubmed_title":["In depth comparison of an individual's DNA and its lymphoblastoid cell line using whole genome sequencing."],"pubmed_authors":["Nickles Dorothee D, Madireddy Lohith L, Yang Shan S, Khankhanian Pouya P, Lincoln Steve S, Hauser Stephen L SL, Oksenberg Jorge R JR, Baranzini Sergio E SE"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["genetic, Animal Virus, Viruses, Genomes, Virus, familial, Animal Viruses, inherited genetic, Animal, whole genome, Zoophaginae, constitutitional genetic, hereditary, Genomes."],"pubmed_title_synonyms":["thymus nucleic acid, Whole Genome, DNS, (Deoxyribonucleotide)n, DNAn+1, Complete Genome Sequencing, Genome Sequencing, Double Stranded, Deoxyribonucleic acid, Double-Stranded, Sequencing, Deoxyribonucleic acids, (Deoxyribonucleotide)n+m, Complete., Complete Genome, Deoxyribonucleic Acid, lymphoblastoid cell, Whole, ds DNA, Desoxyribonukleinsaeure, Double-Stranded DNA, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, DNAn, ds-DNA, desoxyribose nucleic acid"],"pubmed_abstract_synonyms":["Human Study Subject, Identical, Scientific Bias, Nucleotide Sequencing, Unlimited Hand Positioning, STUDY SUBJECT, determination, Massively-Parallel, Feature, Blood, Resolution Property, Suggestion, Significant, Fresh Specimen, 238, Epstein-Barr virus, Highly, E-B Virus, Story, Cellular Transformation, limitations, copy_number, Falkland Islands, High-Throughput RNA Sequencing, Chromosomal Rearrangements, Statistical Significance, Acquisition, Likely, Epidemiologic Biase, Line, Generation, Details, Ecological, Transforming, Burkitt Lymphoma Virus, domain, study limitations, Mononucleosis Viruses, Obtained, Deep Sequencing, Transcriptional, Protein Motif, average, Ecological Biases, FLK, FALKLAND ISLANDS (ISLAS MALVINAS), Clinical Studies, thymus nucleic acid, me75, Copy Number Reported, Burkitt, Genomes, Determination, Illumina Sequencing, statistically significant, D17Mit170, T1, Gene Transcription, genetic, Mechanism Device, European Directorate for the Quality of Medicines and HealthCare Transformation, High Throughput RNA Sequencing, Statistical Biases, Familiar, COPYNUM, Ecological Bias, Usefulness, Double-Stranded DNA, Systematic, deoxyribonucleic acids, DNAn, Epidemiologic Biases, Protein Domain, Protein Feature, High-Throughput RNA, Infectious Mononucleosis Viruses, Determined, Scientific, Array Feature, statistics and numerical data, Epidemiologic, familial, assessment, Genome Sequencing, High-Throughput DNA Sequencing, StudySubject, Double-Stranded, Resolution of Pathologic Process, Ecological Fallacies, Tl3, Tl2, copy number, results, Significance, Herpesvirus, (Deoxyribonucleotide)n+m, Outcome Measurement Errors, Epstein-Barr Virus, Ion Torrent Sequencing, Signed, Experimental, Complete Genome, EDQM-HC Transformation Terminology, significant, Massively-Parallel Sequencing, High Confidence, Epstein Barr Virus, Obtain, Next-Generation, numerical data, Ion Torrent, Structural Chromosome Aberration, Truncation Bias, Assessed, desoxyribose nucleic acid, Region, Domain, Deviation, Mononucleosis Virus, Lines, Epstein-Barr virus EBV, statistical significance, Image Feature, FK, VARIATION, Bias, Epstein Barr virus, Detailed, Relevance, Transformed, Islas Malvinas, Clinical Research, subject/trial subject, Passageway, whole genome, Immortalized, Outcome Measurement, Features, Genomic, High Throughput Sequencing, Experimental Bias, Outcome Measurement Error, Falkland Islands (Malvinas), lymphoblastoid cell, Imaging Feature, PBMCs, Infectious Mononucleosis Virus, Subject, ds DNA, Herpesvirus 4 (gamma), Assess, inherited genetic, Chromosomal Rearrangement, Lymphoma Virus, DNA, Structural Chromosomal Abnormality, FALKLAND ISLANDS (MALVINAS), Pathology Resolution, Fresh, transcription, Study Subject, High Throughput DNA Sequencing, DNS, (Deoxyribonucleotide)n, Ecological Fallacy, FRESH, Truncation, Systematic Bias, High-Throughput DNA, Determine, Outcome Measurement., Illumina, Next-Generation Sequencing, Deoxyribonucleic acids, gDNA, Human, clinical study, Degree, Structural, Deoxyribonucleic Acid, utilization, Investigative Subject, Deep, Passage, Core Genome, PBMC, Variant, Low, Immortalization, Massively Parallel Sequencing, Unlimited, Useful, Level, Higher, High confidence, Fallacies, study, Transcription, RNA Expression, Complete, Routine Signature, Ion Proton Sequencing, Unlimited Manual Dexterity, Whole Genome, Pathologic Process Resolution, Suggest, Mechanism, Accessory Genome, Aggregation, Complete Genome Sequencing, Double Stranded, Genetic Transcription, Deoxyribonucleic acid, Pyrosequencing, Human Subject, Structural Chromosome Anomalies, EBV, Structure, Sequencing, Solution, Study, Burkitt Herpesvirus, Purification, HHV-4, Acquire, transformation, Statistically Significant, Whole, Resolve, study participant, Physiologic Resolution, genome, High-Throughput, RNA Sequencing, Human herpesvirus type 4, (Deoxyribonucleotide)m, Characteristics, Known, constitutitional genetic, Study Participant, Variation, Rearrangement, Biase, TRA, Transformation, Fallacy, Probably, use, cou, whole blood, DNAn+1, Burkitt's Lymphoma Virus, Cell Lines, Infectious, Truncation Biases, Resolved, Pangenome, Clinical Study, Cell, Human herpesvirus 4, CLINICAL STUDY, data transformations, Lr, Characteristic, Channel, Purified, DNA Sequencing, chemical analysis, sequence, Errors, background, ds-DNA, Approach, Relevant, E-B Viruses, Detail, Next Generation Sequencing, signatureText, Resolution, Manual Dexterity Unlimited, Copy Number, Burkitts Lymphoma Virus, Purify, Assessment, Peripheral Blood, Unlimited Walking Ability, FALKLAND ISLANDS, INS, Biases, Likeliness, primary structure of sequence macromolecule, introduction, E B Virus, Human Herpesvirus 4, Data Transformation, High, Reticuloendothelial System, Floor, Protein Region, LAB_SEQ_METHOD, Generated, Pan-genome, High-Throughput Sequencing, Error, DEL, Aggregation Bias, Statistical Bias, human subject, Desoxyribonukleinsaeure, Bra, High Throughput Nucleotide Sequencing, assay, Cell Transformation, Signature, Total, Statistical, Strategy, Ion Proton, hereditary, Genome, High-Throughput Nucleotide, Motif"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-UCSF-05-11-2013-23:32:06:281-123 - samples","description":"The genetic consequences of cellular transformation by Epstein-Barr-Virus were assessed by comparing whole genome sequences of the original genome (before transformation) and the genome after transformation.","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAD00001000693","cross_references":{"TAXONOMY":["9606"],"pubmed":["22974163"],"EGA":["EGAC00001000065","EGAS00001000323"]}}