GM06991

GM06991 LCL from B-Lymphocyte

Description:

CEPH/UTAH PEDIGREE 1341
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:

Female

Age:

No Data

Overview

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

Relation to Proband

mother

Confirmation

Clinical summary/Case history

Species

Homo sapiens

Common Name

Human

Remarks

Mother

Characterizations

IDENTIFICATION OF SPECIES OF ORIGIN

Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis

GENE MAPPING & DOSAGE STUDIES - Y CHROMOSOME

PCR analysis of DNA from this cell culture gave a negative result with a primer for Yq11, DYS227.

Phenotypic Data

Remarks

Mother

Publications

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

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

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

Livak KJ, Wills QF, Tipping AJ, Datta K, Mittal R, Goldson AJ, Sexton DW, Holmes CC, Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells Methods (San Diego, Calif)59:71-9 2012

PubMed ID: 23079396

Tynan JA, Mahboubi P, Cagasan LL, van den Boom D, Ehrich M, Oeth P, Restriction enzyme-mediated enhanced detection of circulating cell-free fetal DNA in maternal plasma The Journal of molecular diagnostics : JMD13:382-9 2010

PubMed ID: 21704271

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

Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM, Irizarry RA, Broman KW, Feinberg AP, SNP-specific array-based allele-specific expression analysis Genome research18:771-9 2008

PubMed ID: 18369178

Riethman H, Human subtelomeric copy number variations Cytogenetic and genome research123:244-52 2008

PubMed ID: 19287161

Nakamoto K, Kidd JR, Jenison RD, Klaassen CD, Wan YJ, Kidd KK, Zhong XB, Genotyping and haplotyping of CYP2C19 functional alleles on thin-film biosensor chips Pharmacogenetics and genomics17:103-14 2007

PubMed ID: 17301690

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

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

Wang Y, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M, Allele quantification using molecular inversion probes (MIP) Nucleic acids research33:e183 2005

PubMed ID: 16314297

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

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

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

Smilinich NJ, Day CD, Fitzpatrick GV, Caldwell GM, Lossie AC, Cooper PR, Smallwood AC, Joyce JA, Schofield PN, Reik W, Nicholls RD, Weksberg R, Driscoll DJ, Maher ER, Shows TB, Higgins MJ, A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome. Proc Natl Acad Sci U S A96:8064-9 1999

PubMed ID: 10393948

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

Nussbaum RL, Orrison BM, Janne PA, Charnas L, Chinault AC, Physical mapping and genomic structure of the Lowe syndrome gene OCRL1. Hum Genet99(2):145-50 1997

PubMed ID: 9048911

Bengtsson U, Altherr MR, Wasmuth JJ, Winokur ST, High resolution fluorescence in situ hybridization to linearly extended DNA visually maps a tandem repeat associated with facioscapulohumeral muscular dystrophy immediately adjacent to the telomere of 4q. Hum Mol Genet3:1801-5 1994

PubMed ID: 7849703

Goldman D, O'Brien SJ, Lucas-Derse S, Dean M, Linkage mapping of human polymorphic proteins identified by two-dimensional electrophoresis. Genomics11:875-84 1991

PubMed ID: 1686020

Higgins MJ, Turmel C, Noolandi J, Neumann PE, Lalande M, Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map. Proc Natl Acad Sci U S A87:3415-9 1990

PubMed ID: 1970636

Nicholls RD, Knoll JH, Glatt K, Hersh JH, Brewster TD, Graham JM Jr, Wurster-Hill D, Wharton R, Latt SA, Restriction fragment length polymorphisms within proximal 15q and their use in molecular cytogenetics and the Prader-Willi syndrome. Am J Med Genet33:66-77 1989

PubMed ID: 2568752

Simon M, Phillips M, Green H, Stroh H, Glatt K, Burns G, Latt SA, Absence of a single repeat from the coding region of the human involucrin gene leading to RFLP. Am J Hum Genet45:910-6 1989

PubMed ID: 2574003

Bufton L, Bruns GA, Magenis RE, Tomar D, Shaw D, Brook D, Litt M, Four restriction fragment length polymorphisms revealed by probes from a single cosmid map to chromosome 19. Am J Hum Genet38:447-60 1986

PubMed ID: 3010711

Buroker NE, Magenis RE, Weliky K, Bruns G, Litt M, Four restriction fragment length polymorphisms revealed by probes from a single cosmid map to human chromosome 12q. Hum Genet72:86-94 1986

PubMed ID: 3002956