GM17057

GM17057 LCL from B-Lymphocyte

Description:

HUMAN VARIATION PANEL - JAPANESE
CYTOCHROME P450, SUBFAMILY IID, POLYPEPTIDE 6; CYP2D6
UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEPTIDE A1; UGT1A1
SNP500 PANEL

Affected:

No

Sex:

Female

Age:

No Data

Overview

Repository

NIGMS Human Genetic Cell Repository

Subcollection

Human Variation
Pharmacogenetics
GeT-RM Samples

Alternate IDs

GM11589 [HUMAN VARIATION PANEL - JAPANESE]

Biopsy Source

Peripheral vein

Cell Type

B-Lymphocyte

Tissue Type

Blood

Transformant

Epstein-Barr Virus

Sample Source

LCL from B-Lymphocyte

Species

Homo sapiens

Common Name

Human

Remarks

Donor subject is heterozygous for a C>T transition at nucleotide 188 in exon 1 of the CYP2D6 gene (CYP2D6*10) resulting in a pro34-to-ser substitution [Pro34Ser (P34S)]; the number of TA repeats in the UGT1A1 gene are 6 and 6

Characterizations

IDENTIFICATION OF SPECIES OF ORIGIN

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

UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEPTIDE A1

Genotypes were generated using (1) the FDA cleared Invader UGT1A1 Molecular Assay and (2) sequencing.

Pharmacogenomics Panel

For pharmacogenetic variants please click here: GeT-RM PGx Search

Gene

CYP2D6

Chromosomal Location

22q13.1

Allelic Variant 1

124030.0005; DEBRISOQUINE, POOR METABOLISM OF

Identified Mutation

PRO34SER; This allelic variant is also known as CYP2D6*10 or CYP2D6(J) or CYP2D6(Ch1, Ch2). Kagimoto et al. (J Biol Chem 265:17209-17214, 1990) identified a 188C-T transition in exon 1 of the CYP2D6 gene, resulting in a pro34-to-ser (P34S) substitution as a cause of the debrisoquine poor metabolizer phenotype (608902).

Gene

UGT1A1

Chromosomal Location

2q37

Allelic Variant 1

;

Identified Mutation

6 TA Repeats

Gene

UGT1A1

Chromosomal Location

2q37

Allelic Variant 2

;

Identified Mutation

6 TA Repeats

Phenotypic Data

Remarks

Publications

Pratt VM, Turner A, Broeckel U, Dawson DB, Gaedigk A, Lynnes TC, Medeiros EB, Moyer AM, Requesens D, Ventrini F, Kalman LV, Characterization of Reference Materials for CYP2C9, CYP2C19, VKORC1, CYP2C Cluster Variant, GGCX, and Other Pharmacogenetic Alleles with an Association for Molecular Pathology (AMP) Pharmacogenetics Working Group Tier 2 Status - A GeT-RM Collaborative Project The Journal of molecular diagnostics : JMD: 2021

PubMed ID: 34020041

Mun S, Kim S, Lee W, Kang K, Meyer TJ, Han BG, Han K, Kim HS, A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome Experimental & molecular medicine53:615-630 2019

PubMed ID: 33833373

Talal AH, Ding Y, Venuto CS, Chakan LM, McLeod A, Dharia A, Morse GD, Brown LS, Markatou M, Kharasch ED, Toward precision prescribing for methadone: Determinants of methadone deposition PloS one15:e0231467 2019

PubMed ID: 32302325

Bettinotti MP1, Ferriola D2, Duke JL2, Mosbruger TL2, Tairis N2, Jennings L3, Kalman LV4, Monos D5., Characterization of 108 Genomic DNA Reference Materials for 11 Human Leukocyte Antigen Loci: A GeT-RM Collaborative Project. Journal of Molecular Diagnostics18:30111-30119 2018

PubMed ID: 29959025

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

Fairbanks DJ, Fairbanks AD, Ogden TH, Parker GJ, Maughan PJ, NANOGP8: evolution of a human-specific retro-oncogene G3 (Bethesda, Md)2:1447-57 2012

PubMed ID: 23173096

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

Lee CC, McMillin GA, Babic N, Melis R, Yeo KT, Evaluation of a CYP2C19 genotype panel on the GenMark eSensor® platform and the comparison to the Autogenomics Infiniti™ and Luminex CYP2C19 panels Clinica chimica acta; international journal of clinical chemistry412(11-12):133-7 2010

PubMed ID: 21385571

Pratt VM, Zehnbauer B, Wilson JA, Baak R, Babic N, Bettinotti M, Buller A, Butz K, Campbell M, Civalier C, El-Badry A, Farkas DH, Lyon E, Mandal S, McKinney J, Muralidharan K, Noll L, Sander T, Shabbeer J, Smith C, Telatar M, Toji L, Vairavan A, Vance C, Weck KE, Wu AH, Yeo KT, Zeller M, and Kalman L., Characterization of 107 Genomic DNA Reference Materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1 J Mol Diagn12(6):835-46 2010

PubMed ID: 20889555

Long JC, Li J, Healy ME, Human DNA sequences: more variation and less race American journal of physical anthropology139:23-34 2009

PubMed ID: 19226648

Marini NJ, Gin J, Ziegle J, Keho KH, Ginzinger D, Gilbert DA, Rine J, The prevalence of folate-remedial MTHFR enzyme variants in humans Proceedings of the National Academy of Sciences of the United States of America139:23-34 2008

PubMed ID: 18523009

Gonzalez-Covarrubias V, Ghosh D, Lakhman SS, Pendyala L, Blanco JG, A functional genetic polymorphism on human carbonyl reductase 1 (CBR1 V88I) impacts on catalytic activity and NADPH binding affinity Drug metabolism and disposition: the biological fate of chemicals35:973-80 2007

PubMed ID: 17344335

Liu W, Innocenti F, Wu MH, Desai AA, Dolan ME, Cook EH Jr, Ratain MJ, A functional common polymorphism in a Sp1 recognition site of the epidermal growth factor receptor gene promoter. Cancer Res65(1):46-53 2005

PubMed ID: 15665278

Maitland ML, Grimsley C, Kuttab-Boulos H, Witonsky D, Kasza KE, Yang L, Roe BA, Di Rienzo A, Comparative genomics analysis of human sequence variation in the UGT1A gene cluster The pharmacogenomics journal6:52-62 2005

PubMed ID: 16314881

Wang J, Song L, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P, Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms Gene365:11-20 2005

PubMed ID: 16376498

Xu G, Bhatnagar V, Wen G, Hamilton BA, Eraly SA, Nigam SK, Analyses of coding region polymorphisms in apical and basolateral human organic anion transporter (OAT) genes [OAT1 (NKT), OAT2, OAT3, OAT4, URAT (RST)] Kidney international68:1491-9 2005

PubMed ID: 16164626

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