GM11992
LCL from B-Lymphocyte
Description:
CEPH/UTAH PEDIGREE 1362
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
dbGaP |
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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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13
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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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| 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 |
| 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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| 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 |
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| Chan W, Lee M, Yeo ZX, Ying D, Grimaldi KA, Pickering C, Yang MMS, Sundaram SK, Tzang LCH, Development and validation of next generation sequencing based 35-gene hereditary cancer panel Hereditary cancer in clinical practice18:9 2019 |
| PubMed ID: 32368312 |
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| Mucaki EJ, Shirley BC, Rogan PK, Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing Frontiers in genetics11:109 2019 |
| PubMed ID: 32211018 |
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| 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 |
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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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| Luzum JA, English JD, Ahmad US, Sun JW, Canan BD, Sadee W, Kitzmiller JP, Binkley PF, Association of Genetic Polymorphisms in the Beta-1 Adrenergic Receptor with Recovery of Left Ventricular Ejection Fraction in Patients with Heart Failure Journal of cardiovascular translational research12:280-289 2018 |
| PubMed ID: 30756358 |
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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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| 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 |
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| Håvik B, Le Hellard S, Rietschel M, Lybæk H, Djurovic S, Mattheisen M, Mühleisen TW, Degenhardt F, Priebe L, Maier W, Breuer R, Schulze TG, Agartz I, Melle I, Hansen T, Bramham CR, Nöthen MM, Stevens B, Werge T, Andreassen OA, Cichon S, Steen VM, The complement control-related genes CSMD1 and CSMD2 associate to schizophrenia Biological psychiatry70:35-42 2010 |
| PubMed ID: 21439553 |
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| Kiialainen A, Karlberg O, Ahlford A, Sigurdsson S, Lindblad-Toh K, Syvänen AC, Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery PloS one6:e16486 2010 |
| PubMed ID: 21347407 |
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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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| 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 |
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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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| Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C, Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing Nature biotechnology27:182-9 2008 |
| PubMed ID: 19182786 |
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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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| 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 |
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| 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 |
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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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| Merla G, Howald C, Henrichsen CN, Lyle R, Wyss C, Zabot MT, Antonarakis SE, Reymond A, Submicroscopic deletion in patients with williams-beuren syndrome influences expression levels of the nonhemizygous flanking genes American journal of human genetics79:332-41 2006 |
| PubMed ID: 16826523 |
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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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| Walley DC, Tripp BW, Song YC, Walley KR, Tebbutt SJ, MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data Bioinformatics (Oxford, England)22:1147-9 2006 |
| PubMed ID: 16522668 |
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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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| 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 |
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| 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 |
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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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| 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 |
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| 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 |
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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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| 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 |
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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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| 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 |
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| Smirnov D, Bruzel A, Morley M, Cheung VG, Direct IBD mapping: identical-by-descent mapping without genotyping Genomics83:335-45 2004 |
| PubMed ID: 14706463 |
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| Lovmar L, Fredriksson M, Liljedahl U, Sigurdsson S, Syvanen AC, Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res31(21):e129 2003 |
| PubMed ID: 14576329 |
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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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| 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 |
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| Attwood J, Chiano M, Collins A, Donis-Keller H, Dracopoli N, Fountain J, Falk C, Goudie D, Gusella J, Haines J, et al, CEPH consortium Map of chromosome 9. Genomics19:203-14 1994 |
| PubMed ID: 8188250 |
| 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 |
15% fetal bovine serum Not Inactivated |
| Substrate |
None specified |
| Subcultivation Method |
dilution - add fresh medium |
| Supplement |
- |
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