Comparison of Eight Technologies to Determine Genotype at the UGT1A1 (TA)n Repeat Polymorphism: Potential Clinical Consequences of Genotyping Errors?

Tristan M Sissung; Roberto H Barbier; Douglas K Price; Teri M Plona; Kristen M Pike; Stephanie D Mellott; Ryan N Baugher; Gordon R Whiteley; Daniel R Soppet; David Venzon; Arlene Berman; Arun Rajan; Giuseppe Giaccone; Paul Meltzer; William D Figg

doi:10.3390/ijms21030896

Comparison of Eight Technologies to Determine Genotype at the UGT1A1 (TA)_n Repeat Polymorphism: Potential Clinical Consequences of Genotyping Errors?

Int J Mol Sci. 2020 Jan 30;21(3):896. doi: 10.3390/ijms21030896.

Authors

Affiliations

¹ Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
² Molecular Pharmacology Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
³ CLIA Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA.
⁴ Genomics Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA.
⁵ Biostatistics and Data Management, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA.
⁶ Office of Research Nursing in the Office of the Clinical Director, National Cancer Institutes, National Institutes of Health, Bethesda, MD 20892, USA.
⁷ Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
⁸ Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
⁹ Genetics Branch, National Cancer Institute, Bethesda, MD 20814, USA.

Abstract

To ensure accuracy of UGT1A1 (TA)_n (rs3064744) genotyping for use in pharmacogenomics-based irinotecan dosing, we tested the concordance of several commonly used genotyping technologies. Heuristic genotype groupings and principal component analysis demonstrated concordance for Illumina sequencing, fragment analysis, and fluorescent PCR. However, Illumina sequencing and fragment analysis returned a range of fragment sizes, likely arising due to PCR "slippage". Direct sequencing was accurate, but this method led to ambiguous electrophoregrams, hampering interpretation of heterozygotes. Gel sizing, pyrosequencing, and array-based technologies were less concordant. Pharmacoscan genotyping was concordant, but it does not ascertain (TA)₈ genotypes that are common in African populations. Method-based genotyping differences were also observed in the publication record (p < 0.0046), although fragment analysis and direct sequencing were concordant (p = 0.11). Genotyping errors can have significant consequences in a clinical setting. At the present time, we recommend that all genotyping for this allele be conducted with fluorescent PCR (fPCR).

Keywords: UGT1A1; pharmacogenomics.

Publication types

Comparative Study

MeSH terms

Alleles
Genotype
Genotyping Techniques / methods*
Glucuronosyltransferase / genetics*
Humans
Irinotecan
Pharmacogenetics
Polymerase Chain Reaction
Polymorphism, Genetic*

Substances

Irinotecan
UGT1A1 enzyme
Glucuronosyltransferase

Grants and funding

ZIA BC 010627/NH/NIH HHS/United States