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Pharmacogenomics

Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia

Leukemia volume 25, pages 1001–1006 (2011)Cite this article

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Abstract

Genetic variants, including single-nucleotide polymorphisms (SNPs), are key determiners of interindividual differences in treatment efficacy and toxicity in childhood acute lymphoblastic leukemia (ALL). Although up to 13 chemotherapeutic agents are used in the treatment of this cancer, it remains a model disease for exploring the impact of genetic variation due to well-characterized cytogenetics, drug response pathways and precise monitoring of minimal residual disease. Here, we have selected clinically relevant genes and SNPs through literature screening, and on the basis of associations with key pathways, protein–protein interactions or downstream partners that have a role in drug disposition and treatment efficacy in childhood ALL. This allows exploration of pathways, where one of several genetic variants may lead to similar clinical phenotypes through related molecular mechanisms. We have designed a cost-effective, high-throughput capture assay of ∼25 000 clinically relevant SNPs, and demonstrated that multiple samples can be tagged and pooled before genome capture in targeted enrichment with a sufficient sequencing depth for genotyping. This multiplexed, targeted sequencing method allows exploration of the impact of pharmacogenetics on efficacy and toxicity in childhood ALL treatment, which will be of importance for personalized chemotherapy.

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Acknowledgements

We are grateful to the patients who participated in the study and their referring physicians. We thank Kirsten Kørup Rasmussen for very helpful technical assistance and Jannie Gregers for providing us with previously generated SNP data. We acknowledge The Technical University of Denmark Multi-Assay Core for providing technology consultation and laboratory resources. AW, MDD and LB analyzed, interpreted data and wrote the manuscript. AW performed the sequence analysis. MDD, LB, HL, KS and RG designed the experimental research project setup. LB, MDD, LRH and BFN performed the experimental work and the Affymetrix 6.0 SNP Arrays. RG performed data analysis supervision. MB and NT performed the Illumina sequencing. KA, LG, TSP and NW performed parts of the data analysis. JN provided cell lines. LG, HL, RG, SB and KS provided critical input to the project and manuscript. This study was supported by grants from The Danish Cancer Society (Grant numbers R2-A56-09-S2 and R20-A1156-10-S2), The Danish Childhood Cancer Foundation, The Otto Christensen Foundation, The Villum Kann Rasmussen Foundation, The Ministry of Health (Grant number 2006-12103-250), The Novo Nordisk Foundation, The Danish Research Council for Health and Disease (Grant numbers 271-06-0278, 271-08-0684), The University Hospital Rigshospitalet, Denmark, The Lundbeck Foundation, The research program of the UNIK: Food, Fitness and Pharma for Health and Disease, The Danish Ministry of Science, Technology and Innovation and The Wilhelm Johannsen Centre for Functional Genome Research that is established by the Danish National Research Foundation.

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Author notes

  1. A Wesolowska, M D Dalgaard and L Borst: Joint first authorship.

Authors and Affiliations

  1. Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark,

    A Wesolowska, L Gautier, N Weinhold, K Audouze, S Brunak, T Sicheritz-Ponten & R Gupta

  2. Department of Growth and Reproduction, University Hospital Rigshospitalet, Copenhagen, Denmark

    M D Dalgaard, B F Nielsen & H Leffers

  3. Department of Pediatrics, Pediatric Clinic II, Juliane Marie Centre, University Hospital Rigshospitalet, Copenhagen, Denmark

    L Borst, L R Helt, J Nersting & K Schmiegelow

  4. Department of Cellular and Molecular Medicine, Wilhelm Johannsen Centre for Functional Genome Research, Panum Institute, Copenhagen, Denmark

    M Bak & N Tommerup

  5. Faculty of Medicine, Institute of Gynecology, Obstetrics and Pediatrics, University of Copenhagen, Copenhagen, Denmark

    K Schmiegelow

  6. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,

    S Brunak

  7. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark,

    T Sicheritz-Ponten

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  1. A Wesolowska
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Correspondence to R Gupta.

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Wesolowska, A., Dalgaard, M., Borst, L. et al. Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. Leukemia 25, 1001–1006 (2011). https://doi.org/10.1038/leu.2011.32

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