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GM12003 LCL from B-Lymphocyte

Description:

CEPH/UTAH PEDIGREE 1420
INTERNATIONAL HAPMAP PROJECT - CEPH (PLATE I) [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
INTERNATIONAL HAPMAP PROJECT - CEPH [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
NA CUSTOM SERVICE PLATE 01

Affected:

No Data

Sex:

Male

Age:

No Data

  • Overview
  • Characterizations
  • Phenotypic Data
  • Publications
  • External Links
  • Culture Protocols

Overview

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Repository NIGMS Human Genetic Cell Repository
Subcollection CEPH
Repository Linkage Families
Pharmacogenetics
PIGI Consented Sample
Biopsy Source Peripheral vein
Cell Type B-Lymphocyte
Tissue Type Blood
Transformant Epstein-Barr Virus
Sample Source LCL from B-Lymphocyte
Race White
Ethnicity UTAH/MORMON
Country of Origin USA
Family Member 9
Relation to Proband paternal grandfather
Confirmation Clinical summary/Case history
Species Homo sapiens
Common Name Human
Remarks Paternal Grandfather. This cell line may be monoclonal as indicated by the very high proportion of IgL kappa (99%) compared to total lgL expression determined by cDNA microarray (see PMID: 14583597)

Characterizations

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IDENTIFICATION OF SPECIES OF ORIGIN Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis
 
Gene CYP2D6
Chromosomal Location 22q13.1
Allelic Variant 1 V11M; R296C;S486T; DEBRISOQUINE, ULTRARAPID METABOLISM OF
Identified Mutation VAL11MET,ARG296CYS,SER486THR
 
Gene CYP2D6
Chromosomal Location 22q13.1
Allelic Variant 2 124030.0001; DEBRISOQUINE, POOR METABOLISM OF
Identified Mutation IVSDS3, G>A, +1; This allelic variant is also known as CYP2D6*4 or CYP2D6(B). In 20 individuals with poor metabolism of debrisoquine (608902), Gough et al. (Nature 347: 773-776, 1990) identified a G-to-A transition at the first nucleotide of exon 4 in the CYP2D6 gene, resulting in a shift of the splice site and introduction of a premature termination codon. The mutant protein had no residual activity. Gough et al. (1990) presented preliminary data suggesting a reduction in the proportion of poor metabolizers among patients with lung or bladder cancer.

Phenotypic Data

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Remarks Paternal Grandfather. This cell line may be monoclonal as indicated by the very high proportion of IgL kappa (99%) compared to total lgL expression determined by cDNA microarray (see PMID: 14583597)

Publications

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Lee SB, Shin JY, Kwon NJ, Kim C, Seo JS., ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation. PLoS One17: 2022
PubMed ID: 35901010
 
Botton MR, Yang Y, Scott ER, Desnick RJ, Scott SA, Phased Haplotype Resolution of the Genes11: 2020
PubMed ID: 33198140
 
Dong Z, Chau MHK, Zhang Y, Yang Z, Shi M, Wah YM, Kwok YK, Leung TY, Morton CC, Choy KW, Low-pass genome sequencing-based detection of absence of heterozygosity: validation in clinical cytogenetics Genetics in medicine : official journal of the American College of Medical Genetics23:1225-1233 2020
PubMed ID: 33772221
 
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE, Haplotype-resolved diverse human genomes and integrated analysis of structural variation Science (New York, NY)372:1225-1233 2020
PubMed ID: 33632895
 
Fløyel T, Meyerovich K, Prause MC, Kaur S, Frørup C, Mortensen HB, Nielsen LB, Pociot F, Cardozo AK, Størling J, SKAP2, a Candidate Gene for Type 1 Diabetes, Regulates ß-Cell Apoptosis and Glycaemic Control in Newly Diagnosed Patients Diabetes372:1225-1233 2020
PubMed ID: 33203694
 
Gaedigk A, Turner A, Everts RE, Scott SA, Aggarwal P, Broeckel U, McMillin GA, Melis R, Boone EC, Pratt VM, Kalman LV, Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles A GeT-RM Collaborative Project The Journal of molecular diagnostics : JMD372:1225-1233 2019
PubMed ID: 31401124
 
Lee SB, Wheeler MM, Thummel KE, Nickerson DA, Calling star alleles with Stargazer in 28 pharmacogenes with whole genome sequences Clinical pharmacology and therapeutics372:1225-1233 2019
PubMed ID: 31206625
 
Sangkuhl K, Whirl-Carrillo M, Whaley RM, Woon M, Lavertu A, Altman RB, Carter L, Verma A, Ritchie MD, Klein TE, Pharmacogenomics Clinical Annotation Tool (PharmCAT) Clinical pharmacology and therapeutics372:1225-1233 2019
PubMed ID: 31306493
 
Twesigomwe D, Wright GEB, Drögemöller BI, da Rocha J, Lombard Z, Hazelhurst S, A systematic comparison of pharmacogene star allele calling bioinformatics algorithms: a focus on NPJ genomic medicine5:30 2019
PubMed ID: 32789024
 
Ali AT, Boehme L, Carbajosa G, Seitan VC, Small KS, Hodgkinson A, Nuclear genetic regulation of the human mitochondrial transcriptome eLife8:30 2018
PubMed ID: 30775970
 
Dias C, Elzein S, Sladek R, Goodyer CG, Sex-specific effects of a microsatellite polymorphism on human growth hormone receptor gene expression Molecular and cellular endocrinology492:110442 2018
PubMed ID: 31063794
 
Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Pantano L, Bitarello BD, Izquierdo D, Noguera I, Olalde I, Delprat A, Blancher A, Lalueza-Fox C, Esko T, O'Reilly PF, Andrés AM, Ferretti L, Puig M, Cáceres M, Evolutionary and functional impact of common polymorphic inversions in the human genome Nature communications10:4222 2018
PubMed ID: 31530810
 
Grimm FA, House JS, Wilson MR, Sirenko O, Iwata Y, Wright FA, Ball N, Rusyn I, Multi-dimensional in vitro bioactivity profiling for grouping of glycol ethers Regulatory toxicology and pharmacology : RTP101:91-102 2018
PubMed ID: 30471335
 
Swart M, Stansberry WM, Pratt VM, Medeiros EB, Kiel PJ, Shen F, Schneider BP, Skaar TC, Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology The Journal of molecular diagnostics : JMD21:491-502 2018
PubMed ID: 30794985
 
Numanagic I, Malikic S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, Sahinalp SC, Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes Nature communications9:828 2017
PubMed ID: 29483503
 
Pratt VM, Everts RE, Aggarwal P, Beyer BN, Broeckel U, Epstein-Baak R, Hujsak P, Kornreich R, Liao J, Lorier R, Scott SA, Smith CH, Toji LH, Turner A, Kalman LV., Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project.18(1):109-23 2016
PubMed ID: 26621101
 
Londin ER, Keller MA, Maista C, Smith G, Mamounas LA, Zhang R, Madore SJ, Gwinn K, Corriveau RA. , CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins. Plos One5(10):e13443 2010
PubMed ID: 20976178
 
Moreno-Estrada A, Aparicio-Prat E, Sikora M, Engelken J, Ramírez-Soriano A, Calafell F, Bosch E, African signatures of recent positive selection in human FOXI1 BMC evolutionary biology10:267 2010
PubMed ID: 20809947
 
Xue Y, Zhang X, Huang N, Daly A, Gillson CJ, Macarthur DG, Yngvadottir B, Nica AC, Woodwark C, Chen Y, Conrad DF, Ayub Q, Mehdi SQ, Li P, Tyler-Smith C, Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation Genetics183:1065-77 2009
PubMed ID: 19737746
 
Riethman H, Human subtelomeric copy number variations Cytogenetic and genome research123:244-52 2008
PubMed ID: 19287161
 
Podder M, Ruan J, Tripp W, Chu E, Tebbutt J, Robust SNP genotyping by multiplex PCR and arrayed primer extension BMC medical genomics1:5 2007
PubMed ID: 18237385
 
de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, Ke X, Monsuur AJ, Whittaker P, Delgado M, Morrison J, Richardson A, Walsh EC, Gao X, Galver L, Hart J, Hafler DA, Pericak-Vance M, Todd JA, Daly MJ, Trowsdale J, Wijmenga C, Vyse TJ, Beck S, Murray SS, Carrington M, Gregory S, Deloukas P, Rioux JD, A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC Nature Genetics38(10):1166-1172 2006
PubMed ID: 16998491
 
Ji H, Kumm J, Zhang M, Farnam K, Salari K, Faham M, Ford JM, Davis RW, Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma Cancer research66:7910-9 2006
PubMed ID: 16912164
 
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME, Global variation in copy number in the human genome Nature444:444-54 2006
PubMed ID: 17122850
 
Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P; International HapMap Consortium, A haplotype map of the human genome. Nature437(7063):1299-320 2005
PubMed ID: 16255080
 
Ferraren DO, Liu C, Badner JA, Corona W, Rezvani A, Monje VD, Gershon ES, Bonner TI, Detera-Wadleigh SD, Linkage disequilibrium analysis in the LOC93081-KDELC1-BIVM region on 13q in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet133(1):12-7 2005
PubMed ID: 15635705
 
Miretti MM, Walsh EC, Ke X, Delgado M, Griffiths M, Hunt S, Morrison J, Whittaker P, Lander ES, Cardon LR, Bentley DR, Rioux JD, Beck S, Deloukas P, A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms. Am J Hum Genet76(4):634-46 2005
PubMed ID: 15747258
 
Sabeti PC, Walsh E, Schaffner SF, Varilly P, Fry B, Hutcheson HB, Cullen M, Mikkelsen TS, Roy J, Patterson N, Cooper R, Reich D, Altshuler D, O'Brien S, Lander ES, The case for selection at CCR5-Delta32 PLoS biology3:e378 2005
PubMed ID: 16248677
 
Walsh EC, Sabeti P, Hutcheson HB, Fry B, Schaffner SF, de Bakker PI, Varilly P, Palma AA, Roy J, Cooper R, Winkler C, Zeng Y, de The G, Lander ES, O'brien S, Altshuler D, Searching for signals of evolutionary selection in 168 genes related to immune function Human genetics119:92-102 2005
PubMed ID: 16362345
 
Yakub I, Lillibridge KM, Moran A, Gonzalez OY, Belmont J, Gibbs RA, Tweardy DJ, Single nucleotide polymorphisms in genes for 2'-5'-oligoadenylate synthetase and RNase L inpatients hospitalized with West Nile virus infection The Journal of infectious diseases192:1741-8 2005
PubMed ID: 16235172
 
Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN, Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet74(6):1111-20 2004
PubMed ID: 15114531
 
Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh PS, Jones KW, Fodor SP, Mei R, Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods1(2):109-11 2004
PubMed ID: 15782172
 
Pastinen T, Sladek R, Gurd S, Sammak A, Ge B, Lepage P, Lavergne K, Villeneuve A, Gaudin T, Brandstrom H, Beck A, Verner A, Kingsley J, Harmsen E, Labuda D, Morgan K, Vohl MC, Naumova AK, Sinnett D, Hudson TJ, A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics16(2):184-93 2004
PubMed ID: 14583597

External Links

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dbSNP dbSNP ID: 464
Gene Cards CYP2C19
Gene Ontology GO:0004497 monooxygenase activity
GO:0005783 endoplasmic reticulum
GO:0005792 microsome
GO:0006118 electron transport
GO:0016020 membrane
GO:0018676 (S)-limonene 7-monooxygenase activity
GO:0019825 oxygen binding
GEO GEO Accession No: GSM159536
GEO Accession No: GSM188801
GEO Accession No: GSM188983
GEO Accession No: GSM238583
GEO Accession No: GSM238584
GEO Accession No: GSM238585
GEO Accession No: GSM245610
GEO Accession No: GSM420737
GEO Accession No: GSM424339
GEO Accession No: GSM48655
GEO Accession No: GSM486779
GEO Accession No: GSM486780
GEO Accession No: GSM651097
GEO Accession No: GSM651098
GEO Accession No: GSM659983
GEO Accession No: GSM660191
GEO Accession No: GSM660395
GEO Accession No: GSM83467
GEO Accession No: GSM83468
GEO Accession No: GSM83469
GEO Accession No: GSM83648
GEO Accession No: GSM83649
GEO Accession No: GSM83650
GEO Accession No: GSM848631
GEO Accession No: GSM905860
GEO Accession No: GSM905955
GEO Accession No: GSM906050
NCBI Gene Gene ID:1557
NCBI GTR 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
OMIM 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19

Culture Protocols

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Split Ratio 1:5
Temperature 37 C
Percent CO2 5%
Medium Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent
Serum 15% fetal bovine serum Not Inactivated
Substrate None specified
Subcultivation Method dilution - add fresh medium
Supplement -
Pricing
International/Commercial/For-profit:
$373.00USD
U.S. Academic/Non-profit/Government:
$216.00USD
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