GM12716
LCL from B-Lymphocyte
Description:
CEPH/UTAH PEDIGREE 1358
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
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Repository
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NIGMS Human Genetic Cell Repository
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| Subcollection |
CEPH
Repository Linkage Families
Pharmacogenetics
PIGI Consented Sample |
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Biopsy Source
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Peripheral vein
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Cell Type
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B-Lymphocyte
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Tissue Type
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Blood
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Transformant
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Epstein-Barr Virus
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Sample Source
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LCL from B-Lymphocyte
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Race
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White
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Ethnicity
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UTAH/MORMON
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Country of Origin
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USA
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Family Member
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11
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Relation to Proband
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paternal grandfather
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Confirmation
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Clinical summary/Case history
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Species
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Homo sapiens
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Common Name
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Human
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Remarks
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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 |
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| Remarks |
Paternal Grandfather; donor subject has a single bp (G-to-A) transition at nucleotide 681 in exon 5 of the CYP2C19 gene (CYP2C19*2) which creates an aberrant splice site. The change altered the reading frame of the mRNA starting with amino acid 215 and produced a premature stop codon 20 amino acids downstream, resulting in a truncated, nonfunctional protein. Because of the aberrant splice site, a 40-bp deletion occurred at the beginning of exon 5 (from bp 643 to bp 682), resulting in deletion of amino acids 215 to 227. The truncated protein had 234 amino acids and would be catalytically inactive because it lacked the heme-binding region. |
| 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 |
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| 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 |
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| Raj P, Song R, Zhu H, Riediger L, Jun DJ, Liang C, Arana C, Zhang B, Gao Y, Wakeland BE, Dozmorov I, Zhou J, Kelly JA, Lauwerys BR, Guthridge JM, Olsen NJ, Nath SK, Pasare C, van Oers N, Gilkeson G, Tsao BP, Gaffney PM, Gregersen PK, James JA, Zuo X, Karp DR, Li QZ, Wakeland EK, Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus Genome biology21:281 2019 |
| PubMed ID: 33213505 |
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| 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 |
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| Garieri M1,2,3, Delaneau O1,2,3, Santoni F1,4, Fish RJ1, Mull D1, Carninci P5, Dermitzakis ET1,2,3, Antonarakis SE1,2,4, Fort A6., The effect of genetic variation on promoter usage and enhancer activity. Nat Commun8(1):1358 2017 |
| PubMed ID: 29116076 |
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| Taudien S, Szafranski K, Felder M, Groth M, Huse K, Raffaelli F, Petzold A, Zhang X, Rosenstiel P, Hampe J, Schreiber S, Platzer M, Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing BMC genomics12:243 2011 |
| PubMed ID: 21592371 |
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| 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 |
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| 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 |
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| 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 |
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| Riethman H, Human subtelomeric copy number variations Cytogenetic and genome research123:244-52 2008 |
| PubMed ID: 19287161 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| Redmon JB, Gettys TW, Sheorain VS, Corbin JD, Taylor IL, Failure of insulin to antagonize cAMP-mediated glycogenolysis in rat ventricular cardiomyocytes The American journal of physiology258:E871-7 1990 |
| PubMed ID: 2159237 |
| Split Ratio |
1:2 |
| Temperature |
37 C |
| Percent CO2 |
5% |
| Percent O2 |
AMBIENT |
| Medium |
Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent |
| Serum |
20% fetal bovine serum Not Inactivated |
| Substrate |
None specified |
| Subcultivation Method |
dilution - add fresh medium |
| Supplement |
- |
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