GM10842
LCL from B-Lymphocyte
Description:
CEPH/UTAH PEDIGREE 1423
INTERNATIONAL HAPMAP PROJECT - CEPH (PLATE II) [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
HUMAN VARIATION PANEL - EUROPEAN WHITE PANEL OF 8
HUMAN VARIATION PANEL - EUROPEAN WHITE PANEL OF 16
HUMAN VARIATION PANEL - EUROPEAN WHITE PANEL OF 24
NA CUSTOM SERVICE PLATE 02
INTERNATIONAL HAPMAP PROJECT - CEPH [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEPTIDE A1; UGT1A1
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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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Family Member
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1
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Relation to Proband
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father
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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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| GENE MAPPING & DOSAGE STUDIES - Y CHROMOSOME |
PCR analysis of DNA from this cell culture gave a positive result with a primer for Yq11, DYS227. |
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| UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEPTIDE A1 |
Genotypes were generated using (1) the FDA cleared Invader UGT1A1 Molecular Assay and (2) sequencing. |
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| Gene |
UGT1A1 |
| Chromosomal Location |
2q37 |
| Allelic Variant 1 |
191740.0011; GILBERT SYNDROME |
| Identified Mutation |
7 TA Repeats; Beutler et al (Proc Nat Acad Sci 95:8170-8174, 1998) described the variant in the promoter of the UGT1A1 gene that is responsible for most cases of Gilbert syndrome as the presence of 7 instead of 6 thymine-adenine (TA) repeats in the promoter region of the gene. This variant has been designated UGT1A1*28 (Mackenzie et al., Pharmacogenetics 7:255-269,1997). |
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| Gene |
UGT1A1 |
| Chromosomal Location |
2q37 |
| Allelic Variant 2 |
191740.0011; GILBERT SYNDROME |
| Identified Mutation |
7 TA Repeats; Beutler et al (Proc Nat Acad Sci 95:8170-8174, 1998) described the variant in the promoter of the UGT1A1 gene that is responsible for most cases of Gilbert syndrome as the presence of 7 instead of 6 thymine-adenine (TA) repeats in the promoter region of the gene. This variant has been designated UGT1A1*28 (Mackenzie et al., Pharmacogenetics 7:255-269,1997). |
| Remarks |
Father; the number of TA repeats in the UGT1A1 gene are 7 and 7 |
| 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 |
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| Wernstedt A, Valtorta E, Armelao F, Togni R, Girlando S, Baudis M, Heinimann K, Messiaen L, Staehli N, Zschocke J, Marra G, Wimmer K, Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL Genes, chromosomes & cancer51:819-31 2012 |
| PubMed ID: 22585707 |
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| Wang X, Abudu A, Son S, Dang Y, Venta PJ, Zheng YH, Analysis of Human APOBEC3H Haplotypes and Anti-Human Immunodeficiency Virus Type-1 Activity Journal of virology85(7):3142-52 2011 |
| PubMed ID: 21270145 |
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| Lambert CA, Connelly CF, Madeoy J, Qiu R, Olson MV, Akey JM, Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history American journal of human genetics86:34-44 2009 |
| PubMed ID: 20085712 |
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| Li L, Fridley B, Kalari K, Jenkins G, Batzler A, Safgren S, Hildebrandt M, Ames M, Schaid D, Wang L, Gemcitabine and Cytosine Arabinoside Cytotoxicity: Association with Lymphoblastoid Cell Expression Cancer research68:7050-7058 2008 |
| PubMed ID: 18757419 |
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| Smirnov DA, Cheung VG, ATM Gene Mutations Result in Both Recessive and Dominant Expression Phenotypes of Genes and MicroRNAs American journal of human genetics83:243-53 2008 |
| PubMed ID: 18674748 |
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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, Ritchie MD, Rieder MJ, Identifying the genotype behind the phenotype: a role model found in VKORC1 and its association with warfarin dosing Pharmacogenomics8:487-96 2007 |
| PubMed ID: 17465713 |
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| rieder, M.J., Reiner, A.P. and Rettie, A.E., Gamma-glutamyl carboxylase (GGCX) tagSNPs have limited utility for predicting warfarin maintenance dose.
J Thrombosis and Haemostasis5(11):2227-2234 2007 |
| PubMed ID: 17764537 |
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| Wong KK, Deleeuw RJ, Dosanjh NS, Kimm LR, Cheng Z, Horsman DE, Macaulay C, Ng RT, Brown CJ, Eichler EE, Lam WL, A comprehensive analysis of common copy-number variations in the human genome American journal of human genetics80:91-104 2006 |
| PubMed ID: 17160897 |
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| Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA, Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet14(1):59-69 2005 |
| PubMed ID: 15525656 |
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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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| Carlson CS, Aldred SF, Lee PK, Tracy RP, Schwartz SM, Rieder M, Liu K, Williams OD, Iribarren C, Lewis EC, Fornage M, Boerwinkle E, Gross M, Jaquish C, Nickerson DA, Myers RM, Siscovick DS, Reiner AP, Polymorphisms within the C-Reactive Protein (CRP) Promoter Region Are Associated with Plasma CRP Levels. Am J Hum Genet77(1):64-77 2005 |
| PubMed ID: 15897982 |
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| Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA, Genomic regions exhibiting positive selection identified from dense genotype data Genome research15:1553-65 2005 |
| PubMed ID: 16251465 |
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| Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR, Whole-genome patterns of common DNA variation in three human populations. Science307(5712):1072-9 2005 |
| PubMed ID: 15718463 |
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| Kouprina N, Pavlicek A, Noskov VN, Solomon G, Otstot J, Isaacs W, Carpten JD, Trent JM, Schleutker J, Barrett JC, Jurka J, Larionov V, Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27 Genome research15:1477-86 2005 |
| PubMed ID: 16251457 |
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| Meza MM, Yu L, Rodriguez YY, Guild M, Thompson D, Gandolfi AJ, Klimecki WT, Developmentally restricted genetic determinants of human arsenic metabolism: association between urinary methylated arsenic and CYT19 polymorphisms in children Environmental health perspectives113:775-81 2005 |
| PubMed ID: 15929903 |
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| Ramsey CD, Lazarus R, Camargo CA, Weiss ST, Celedón JC, Polymorphisms in the interleukin 17F gene (IL17F) and asthma Genes and immunity6:236-41 2005 |
| PubMed ID: 15703761 |
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| Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L, Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol2(10):e286 2004 |
| PubMed ID: 15361935 |
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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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| Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA, Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet74(1):106-20 2004 |
| PubMed ID: 14681826 |
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| Crawford DC, Bhangale T, Li N, Hellenthal G, Rieder MJ, Nickerson DA, Stephens M, Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet36(7):700-6 2004 |
| PubMed ID: 15184900 |
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| Crawford DC, Carlson CS, Rieder MJ, Carrington DP, Yi Q, Smith JD, Eberle MA, Kruglyak L, Nickerson DA, Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet74(4):610-22 2004 |
| PubMed ID: 15015130 |
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| Ding K, Zhou K, Zhang J, Knight J, Zhang X, Shen Y, The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection Molecular biology and evolution22:148-59 2004 |
| PubMed ID: 15371531 |
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| Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D, Cardon LR, Deloukas P, The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet13(6):577-88 2004 |
| PubMed ID: 14734624 |
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| 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 |
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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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| Tantisira K, Klimecki WT, Lazarus R, Palmer LJ, Raby BA, Kwiatkowski DJ, Silverman E, Vercelli D, Martinez FD, Weiss ST, Toll-like receptor 6 gene (TLR6): single-nucleotide polymorphism frequencies and preliminary association with the diagnosis of asthma. Genes Immun5(5):343-6 2004 |
| PubMed ID: 15266299 |
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| Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, Nickerson DA, Additional SNPs and linkage-disequilibrium analyses are necessary for
whole-genome association studies in humans. Nat Genet33(4):518-21 2003 |
| PubMed ID: 12652300 |
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| Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, Morley M, Spielman RS, Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet33(3):422-5 2003 |
| PubMed ID: 12567189 |
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| Rutter JL, Smith AM, Dávila MR, Sigurdson AJ, Giusti RM, Pineda MA, Doody MM, Tucker MA, Greene MH, Zhang J, Struewing JP, Mutational analysis of the BRCA1-interacting genes ZNF350/ZBRK1 and BRIP1/BACH1 among BRCA1 and BRCA2-negative probands from breast-ovarian cancer families and among early-onset breast cancer cases and reference individuals Human mutation22:121-8 2003 |
| PubMed ID: 12872252 |
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| Yu L, Kalla K, Guthrie E, Vidrine A, Klimecki WT, Genetic variation in genes associated with arsenic metabolism: glutathione S-transferase omega 1-1 and purine nucleoside phosphorylase polymorphisms in European and indigenous Americans Environmental health perspectives111:1421-7 2003 |
| PubMed ID: 12928150 |
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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 |
| Split Ratio |
1:3 |
| 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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