title: Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia.
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.
authors.affiliation: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: A
authors.initials: A
authors.lastname: Wesolowska
authors.forename: M D
authors.initials: MD
authors.lastname: Dalgaard
authors.forename: L
authors.initials: L
authors.lastname: Borst
authors.forename: L
authors.initials: L
authors.lastname: Gautier
authors.forename: M
authors.initials: M
authors.lastname: Bak
authors.forename: N
authors.initials: N
authors.lastname: Weinhold
authors.forename: B F
authors.initials: BF
authors.lastname: Nielsen
authors.forename: L R
authors.initials: LR
authors.lastname: Helt
authors.forename: K
authors.initials: K
authors.lastname: Audouze
authors.forename: J
authors.initials: J
authors.lastname: Nersting
authors.forename: N
authors.initials: N
authors.lastname: Tommerup
authors.forename: S
authors.initials: S
authors.lastname: Brunak
authors.forename: T
authors.initials: T
authors.lastname: Sicheritz-Ponten
authors.forename: H
authors.initials: H
authors.lastname: Leffers
authors.forename: K
authors.initials: K
authors.lastname: Schmiegelow
authors.forename: R
authors.initials: R
authors.lastname: Gupta
mesh_terms: D000293:Adolescent; D002675:Child, Preschool; D003362:Cost-Benefit Analysis; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D010597:Pharmacogenetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000453:epidemiology / Q000235:genetics*; D016896:Treatment Outcome