Automated genotyping of biobank samples by multiplex amplification of insertion/deletion polymorphisms

PLoS One. 2012;7(12):e52750. doi: 10.1371/journal.pone.0052750. Epub 2012 Dec 27.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Automation, Laboratory
  • Base Sequence
  • Colon / chemistry
  • Colorectal Neoplasms / genetics
  • DNA / genetics
  • DNA / isolation & purification
  • DNA Primers / genetics
  • Female
  • Fixatives / chemistry
  • Formaldehyde / chemistry
  • Genome, Human
  • Genotype
  • Genotyping Techniques*
  • Humans
  • INDEL Mutation*
  • Male
  • Molecular Sequence Data
  • Paraffin Embedding
  • Polymerase Chain Reaction
  • Polymorphism, Genetic
  • Sequence Analysis, DNA
  • Tissue Banks*

Substances

  • DNA Primers
  • Fixatives
  • Formaldehyde
  • DNA

Grant support

This work has been supported by grants from the Swedish research council, VINNOVA and the Innovative Medicines Initiative Joint Undertaking under grant agreement n° 115234 (OncoTrack), resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA (European Federation of Pharmaceutical Industries and Associations) companies in kind contribution. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.