title: Detection and screening of chromosomal rearrangements in uterine leiomyomas by long-distance inverse PCR.
abstract: Genome instability is a hallmark of many tumors and recently, next-generation sequencing methods have enabled analyses of tumor genomes at an unprecedented level. Studying rearrangement-prone chromosomal regions (putative "breakpoint hotspots") in detail, however, necessitates molecular assays that can detect de novo DNA fusions arising from these hotspots. Here we demonstrate the utility of a long-distance inverse PCR-based method for the detection and screening of de novo DNA rearrangements in uterine leiomyomas, one of the most common types of human neoplasm. This assay allows in principle any genomic region suspected of instability to be queried for DNA rearrangements originating there. No prior knowledge of the identity of the fusion partner chromosome is needed. We used this method to screen uterine leiomyomas for rearrangements at genomic locations known to be rearrangement-prone in this tumor type: upstream HMGA2 and within RAD51B. We identified a novel DNA rearrangement upstream of HMGA2 that had gone undetected in an earlier whole-genome sequencing study. In more than 30 additional uterine leiomyoma samples, not analyzed by whole-genome sequencing previously, no rearrangements were observed within the 1,107 bp and 1,996 bp assayed in the RAD51B and HMGA2 rearrangement hotspots. Our findings show that long-distance inverse PCR is a robust, sensitive, and cost-effective method for the detection and screening of DNA rearrangements from solid tumors that should be useful for many diagnostic applications.
authors.affiliation: Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.|Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Barun
authors.initials: B
authors.lastname: Pradhan
authors.affiliation: Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.|Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland.
authors.forename: Nanna
authors.initials: N
authors.lastname: Sarvilinna
authors.affiliation: Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.|Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Matilainen
authors.affiliation: Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.|Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Elli
authors.initials: E
authors.lastname: Aska
authors.affiliation: Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland.
authors.forename: Jari
authors.initials: J
authors.lastname: Sjöberg
authors.affiliation: Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.|Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Liisa
authors.initials: L
authors.lastname: Kauppi
mesh_terms: D001483:Base Sequence; D002869:Chromosome Aberrations; D002881:Chromosomes, Human, Pair 12; D002898:Chromosomes, Human, Pair 8; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D015321:Gene Rearrangement; D025743:HMGA2 Protein / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007889:Leiomyoma / Q000175:diagnosis / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D014594:Uterine Neoplasms / Q000175:diagnosis / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D025743:HMGA2 Protein; C413002:RAD51B protein, human