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GM11839 LCL from B-Lymphocyte

Description:

CEPH/UTAH PEDIGREE 1349
INTERNATIONAL HAPMAP PROJECT - CEPH (PLATE I) [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 9; CYP2C9
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 13
Relation to Proband maternal grandfather
Confirmation Clinical summary/Case history
Species Homo sapiens
Common Name Human
Remarks Maternal Grandfather; donor subject is heterozygous for an A>C change at nucleotide 1061 (1061A>C) in exon 7 of the CYP2C9 gene (CYP2C9*3) which results in a substitution of leucine for isoleucine at codon 359 [Ile359Leu (I359L)]

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
 

Phenotypic Data

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Remarks Maternal Grandfather; donor subject is heterozygous for an A>C change at nucleotide 1061 (1061A>C) in exon 7 of the CYP2C9 gene (CYP2C9*3) which results in a substitution of leucine for isoleucine at codon 359 [Ile359Leu (I359L)]

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
 
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: 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: 2020
PubMed ID: 33203694
 
Uppugunduri CRS, Huezo-Diaz Curtis P, Nava T, Rezgui MA, Mlakar V, Mlakar SJ, Waespe N, Théoret Y, Gumy-Pause F, Bernard F, Chalandon Y, Boelens JJ, Bredius RGM, Dalle JH, Nath C, Corbacioglu S, Peters C, Bader P, Shaw P, Bittencourt H, Krajinovic M, Ansari M, Association study of candidate DNA-repair gene variants and acute graft versus host disease in pediatric patients receiving allogeneic hematopoietic stem-cell transplantation The pharmacogenomics journal22:9-18 2020
PubMed ID: 34711928
 
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 : JMD22:9-18 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 therapeutics22:9-18 2019
PubMed ID: 31206625
 
Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, Whirl-Carrillo M, Weck KE, Recommendations for Clinical Warfarin Sensitivity Genotyping Allele Selection: A Report of the Association for Molecular Pathology and College of American Pathologists The Journal of molecular diagnostics : JMD22:9-18 2019
PubMed ID: 32380173
 
Suzuki O, Dong OM, Howard RM, Wiltshire T, Characterizing the pharmacogenome using molecular inversion probes for targeted next-generation sequencing Pharmacogenomics20:1005-1020 2019
PubMed ID: 31559919
 
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
 
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
 
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
 
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., Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project.18(1):109-23 2016
PubMed ID: 26621101
 
Deng L, Tang X, Hao X, Chen W, Lin J, Yu Y, Zhang D, Zeng C, Genetic flux between h1 and h2 haplotypes of the 17q2131 inversion in European population Genomics, proteomics & bioinformatics / Beijing Genomics Institute9:113-8 2010
PubMed ID: 21802048
 
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
 
Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, White TJ, Nielsen R, Clark AG, Bustamante CD, Assessing the evolutionary impact of amino acid mutations in the human genome PLoS genetics4:e1000083 2007
PubMed ID: 18516229
 
Crawford DC, Nord AS, Badzioch MD, Ranchalis J, McKinstry LA, Ahearn M, Bertucci C, Shephard C, Wong M, Rieder MJ, Schellenberg GD, Nickerson DA, Heagerty PJ, Wijsman EM, Jarvik GP, A common VLDLR polymorphism interacts with APOE genotype in the prediction of carotid artery disease risk Journal of lipid research49:588-96 2007
PubMed ID: 18056683
 
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
 
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
 
Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG, Natural selection on protein-coding genes in the human genome Nature437:1153-7 2005
PubMed ID: 16237444
 
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
 
Ting C, Ye Y, Thomas H, Ruczinski I, Pevsner J, Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan Am J Hum Genet7:25 2005
PubMed ID: 16420694
 
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
 
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
 
Norman PJ, Cook MA, Carey BS, Carrington CV, Verity DH, Hameed K, Ramdath DD, Chandanayingyong D, Leppert M, Stephens HA, Vaughan RW, SNP haplotypes and allele frequencies show evidence for disruptive and balancing selection in the human leukocyte receptor complex Immunogenetics56:225-37 2004
PubMed ID: 15185041
 
Randolph AG, Lange C, Silverman EK, Lazarus R, Silverman ES, Raby B, Brown A, Ozonoff A, Richter B, Weiss ST, The IL12B gene is associated with asthma. Am J Hum Genet75(4):709-15 2004
PubMed ID: 15322986
 
Hall MA, Norman PJ, Thiel B, Tiwari H, Peiffer A, Vaughan RW, Prescott S, Leppert M, Schork NJ, Lanchbury JS, Quantitative trait loci on chromosomes 1, 2, 3, 4, 8, 9, 11, 12, and 18 control variation in levels of T and B lymphocyte subpopulations. Am J Hum Genet70(5):1172-82 2002
PubMed ID: 11951176
 
Brzustowicz LM, Gardner JP, Hopp L, Jeanclos E, Ott J, Yang XY, Fekete Z,Aviv A, Linkage analysis using platelet-activating factor Ca2+ response in transformed lymphoblasts. Hypertension29(1 Pt 2):158-64 1997
PubMed ID: 9039096

External Links

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dbSNP dbSNP ID: 252
Gene Cards CYP2C19
CYP2C9
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: GSM159528
GEO Accession No: GSM188792
GEO Accession No: GSM188974
GEO Accession No: GSM238559
GEO Accession No: GSM238560
GEO Accession No: GSM238561
GEO Accession No: GSM245601
GEO Accession No: GSM420663
GEO Accession No: GSM424333
GEO Accession No: GSM48654
GEO Accession No: GSM486763
GEO Accession No: GSM486764
GEO Accession No: GSM659825
GEO Accession No: GSM659984
GEO Accession No: GSM660180
GEO Accession No: GSM83455
GEO Accession No: GSM83456
GEO Accession No: GSM83457
GEO Accession No: GSM83570
GEO Accession No: GSM83571
GEO Accession No: GSM83572
GEO Accession No: GSM848624
GEO Accession No: GSM905852
GEO Accession No: GSM905947
GEO Accession No: GSM906042
NCBI Gene Gene ID:1557
Gene ID:1559
NCBI GTR 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
601130 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 9; CYP2C9
OMIM 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
601130 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 9; CYP2C9

Culture Protocols

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Split Ratio 1:4
Temperature 37 C
Percent CO2 5%
Percent O2 AMBIENT
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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