A new multiplex for human identification using insertion/deletion polymorphisms

Electrophoresis. 2009 Nov;30(21):3682-90. doi: 10.1002/elps.200900274.


Human identification is usually based on the study of STRs or SNPs depending on the particular characteristics of the investigation. However, other types of genetic variation such as insertion/deletion polymorphisms (indels) have considerable potential in the field of identification, since they can combine the desirable characteristics of both STRs and SNPs. In this study, a set of 38 non-coding bi-allelic autosomal indels reported to be polymorphic in African, European, and Asian populations were selected. We developed a sensitive genotyping assay, which is able to characterize all 38 bi-allelic markers using a single multiplex PCR and detected with standard CE analyzers. Amplicon length was designed to be shorter than 160 bp. Complete profiles were obtained using 0.3 ng of DNA, and full genotyping of degraded samples was possible in cases where standard STR typing had partially failed. A total of 306 individuals from Angola, Mozambique, Portugal, Macau, and Taiwan were studied and population data are presented. All indels were polymorphic in the three population groups studied and the random match probabilities of the set ranged in orders of magnitude from 10(-14) to 10(-15). Therefore, the indel-plex represents a valuable approach in human identification studies, especially in challenging DNA cases, as a more straightforward and efficient alternative to SNP typing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Analysis of Variance
  • Computer Simulation
  • DNA / analysis*
  • Forensic Anthropology / methods*
  • Forensic Genetics / methods*
  • Gene Frequency
  • Humans
  • Linkage Disequilibrium
  • Mutagenesis, Insertional
  • Polymerase Chain Reaction / methods*
  • Polymorphism, Genetic*
  • Sequence Deletion


  • DNA