Skip to main content
SpringerLink
Log in

Multiplex Genotyping of Allelic Variants of Genes Involved in Metabolizing Antileukemic Drugs

  • Genomics. Transcriptomics
  • Published:
Molecular Biology Aims and scope Submit manuscript

Abstract

A biochip, primer set, and genotyping protocol were developed to simultaneously address 16 single nucleotide polymorphisms in antileukemic drug metabolism genes, including TPMT, ITPA, MTHFR, SLCO1B1, SLC19A1, NR3C1, GRIA1, ASNS, MTRR, and ABCB1. The genotyping procedure included a one-round multiplex polymerase chain reaction (PCR) with simultaneous incorporation of a fluorescent label into the PCR product and subsequent hybridization on a biochip with immobilized probes. The method was used to test 65 DNA samples of leukemia patients. Fluorescence signal intensity ratios in pairs of wildtype and respective mutant sequence probes were analyzed for all polymorphic markers and demonstrated high accuracy of genotyping. The reliability of genotype determination using the biochip was confirmed by direct Sanger sequencing.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

MTX:

methotrexate

AL:

acute leukemia

ALL:

acute lymphoblastic leukemia

PCR:

polymerase chain reaction

ABCB1 :

ATP binding cassette subfamily B member 1 gene

ASNS :

asparagine synthetase (glutamine-hydrolyzing) gene

dNTP:

deoxynucleoside triphosphate

dUTP:

deoxyuridine triphosphate

GRIA1 :

glutamate ionotropic receptor AMPA type subunit 1 gene

ITPA :

inosine triphosphate pyrophosphatase gene

SLCO1B1 :

solute carrier organic anion transporter family member 1B1 gene

MTHFR :

methylenetetrahydrofolate reductase gene

MTRR :

5-methyltetrahydrofolate–homocysteine methyltransferase reductase gene

NR3C1 :

nuclear receptor subfamily 3 group C member 1 gene

SLC19A1 :

solute carrier family 19 member 1 gene

TPMT :

thiopurine S-methyltransferase gene

References

  1. Otterness D., Szumlanski C., Lennard L., et al. 1997. Human thiopurine methyltransferase pharmacogenetics: Gene sequence polymorphisms. Clin. Pharmacol. Ther. 62, 60–73.

    Article  CAS  PubMed  Google Scholar 

  2. Matimba A., Li F., Livshits A., et al. 2014. Thiopurine pharmacogenomics: Association of SNPs with clinical response and functional validation of candidate genes. Pharmacogenomics. 15, 433–447.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kang H.J., Oh Y., Chun S.M., et al. 2008. TotalPlex gene amplification using bulging primers for pharmacogenetic analysis of acute lymphoblastic leukemia. Mol. Cell. Probes. 22, 193–200.

    Article  CAS  PubMed  Google Scholar 

  4. Dulucq S., Laverdière C., Sinnett D., Krajinovic M. 2014. Pharmacogenetic considerations for acute lymphoblastic leukemia therapies. Exp. Opin. Drug Metab. Toxicol. 10, 699–719.

    Article  CAS  Google Scholar 

  5. Adam de Beaumais T., Fakhoury M., et al. 2011. Determinants of mercaptopurine toxicity in paediatric acute lymphoblastic leukemia maintenance therapy. Br. J. Clin. Pharmacol. 71, 575–584.

    Article  Google Scholar 

  6. Marinaki A.M., Ansari A., Duley J.A., et al. 2004. Adverse drug reactions to azathioprine therapy are associated with polymorphism in the gene encoding inosine triphosphate pyrophosphatase (ITPase). Pharmacogenetics. 14, 181–187.

    Article  CAS  PubMed  Google Scholar 

  7. Elaine R. 2008. Mardis The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133–141.

    Article  Google Scholar 

  8. Treviño L.R., Shimasaki N., Yang W., et al. 2009. Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects. J. Clin. Oncol. 35, 5972–5978.

    Article  Google Scholar 

  9. Gervasini G., Vagace J.M. 2012. Impact of genetic polymorphisms on chemotherapy toxicity in childhood acute lymphoblastic leukemia. Front. Genet. 3, 249–260.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Tanfous M.B., Sharif-Askari B., Ceppi F., et al. 2015. Polymorphisms of asparaginase pathway and asparaginase-related complications in children with acute lymphoblastic leukemia. Clin. Cancer Res. 21, 329–334.

    Article  PubMed  Google Scholar 

  11. Jewell C.M., Cidlowski J.A. 2007. Molecular evidence for a link between the n363s glucocorticoid receptor polymorphism and altered gene expression. J. Clin. Endocrinol. Metab. 92, 3268–3277.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Russcher H., Smit P., van den Akker E.L., et al. 2005. Two polymorphisms in the glucocorticoid receptor gene directly affect glucocorticoid-regulated gene expression. J. Clin. Endocrinol. Metab. 90, 5804–5810.

    Article  CAS  PubMed  Google Scholar 

  13. Rubina A.Y., Pan’kov S.V., Dementieva E.I., et al. 2004. Hydrogel drop microchips with immobilized DNA: properties and methods for large-scale production. Anal. Biochem. 325, 92–106.

    Article  CAS  PubMed  Google Scholar 

  14. Fesenko D.O., Zasedatelev A.S., Nasedkina T.V., Kalennik O.V., Barsky V.E. 2012. Biochip development for determining Y-haplogroups that occur in Russian populations. Mol. Biol. (Moscow). 46 (5), 731–734.

    Article  CAS  Google Scholar 

  15. Fesenko D.O., Mityaeva O.N., Nasedkina T.V., Rubtsov P.M., Lysov Yu.P., Zasedatelev A.S. 2010. HLA-DQA1, AB0, and AMEL genotyping of biological material with biochips. Mol. Biol. (Moscow). 44 (3), 401–406.

    Article  CAS  Google Scholar 

  16. Fesenko D.O., Kornienko A.E., Chudinov A.V., Nasedkina T.V. 2011. Preparing of single-stranded DNA in single-stage PCR with low-melt excess primer for hybridization on biochips. Mol. Biol. (Moscow). 45 (2), 237–240.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia

    D. O. Fesenko, M. A. Avdonina, L. G. Gukasyan, S. A. Surzhikov, A. V. Chudinov, A. S. Zasedatelev & T. V. Nasedkina

Authors
  1. D. O. Fesenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. A. Avdonina
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. L. G. Gukasyan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. A. Surzhikov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. V. Chudinov
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. A. S. Zasedatelev
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. T. V. Nasedkina
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to D. O. Fesenko.

Additional information

Original Russian Text © D.O. Fesenko, M.A. Avdonina, L.G. Gukasyan, S.A. Surzhikov, A.V. Chudinov, A.S. Zasedatelev, T.V. Nasedkina, 2018, published in Molekulyarnaya Biologiya, 2018, Vol. 52, No. 2, pp. 238–245.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fesenko, D.O., Avdonina, M.A., Gukasyan, L.G. et al. Multiplex Genotyping of Allelic Variants of Genes Involved in Metabolizing Antileukemic Drugs. Mol Biol 52, 206–211 (2018). https://doi.org/10.1134/S0026893318020036

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026893318020036

Keywords

Search

Navigation