title: Automated genotyping of biobank samples by multiplex amplification of insertion/deletion polymorphisms.
abstract: The genomic revolution in oncology will entail mutational analyses of vast numbers of patient-matched tumor and normal tissue samples. This has meant an increased risk of patient sample mix up due to manual handling. Therefore, scalable genotyping and sample identification procedures are essential to pathology biobanks. We have developed an efficient alternative to traditional genotyping methods suited for automated analysis. By targeting 53 prevalent deletions and insertions found in human populations with fluorescent multiplex ligation dependent genome amplification, followed by separation in a capillary sequencer, a peak spectrum is obtained that can be automatically analyzed. 24 tumor-normal patient samples were successfully matched using this method. The potential use of the developed assay for forensic applications is discussed.
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Lucy
authors.initials: L
authors.lastname: Mathot
authors.forename: Elin
authors.initials: E
authors.lastname: Falk-Sörqvist
authors.forename: Lotte
authors.initials: L
authors.lastname: Moens
authors.forename: Marie
authors.initials: M
authors.lastname: Allen
authors.forename: Tobias
authors.initials: T
authors.lastname: Sjöblom
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
mesh_terms: D057205:Automation, Laboratory; D001483:Base Sequence; D003106:Colon / Q000737:chemistry; D015179:Colorectal Neoplasms / Q000235:genetics; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D017931:DNA Primers / Q000235:genetics; D005260:Female; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D015894:Genome, Human; D005838:Genotype; D060005:Genotyping Techniques; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D008969:Molecular Sequence Data; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D014015:Tissue Banks
chemical_list: D017931:DNA Primers; D005404:Fixatives; D005557:Formaldehyde; D004247:DNA