Development of a genotyping assay for the UK, European, and CODIS core STR loci identifying length and sequence variation in the target loci

David D. Duncan, Kristen M. Boles, John V. Planz, Steven A. Hofstadler, Thomas A. Hall

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

We have developed a highly automated assay covering twenty one markers spanning the UK, European, and CODIS core short tandem repeat (STR) loci. In this assay, sample DNA is amplified with an 8-well PCR panel, and the masses of the PCR products are determined on an electrospray ionization-mass spectrometry platform. The mass measurements are accurate enough to assign a base composition to the PCR products, specifying the number of their constituent dA, dG, dC, and dT residues. The base compositions in turn define the STR genotypes. Sequence variants have been observed in many of the STR loci, and the accuracy of the mass measurements supports their identification with this assay. Parameters in the initial evaluation of the assay included species specificity, sensitivity, reproducibility, accuracy, and concordance. Results indicate that the assay is concordant with existing assays while providing additional information by virtue of the detection of sequence variants of STR alleles.

Original languageEnglish
JournalForensic Science International: Genetics Supplement Series
Volume3
Issue number1
DOIs
StatePublished - 1 Dec 2011

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Microsatellite Repeats
Base Composition
Polymerase Chain Reaction
Species Specificity
Electrospray Ionization Mass Spectrometry
Alleles
Genotype
DNA

Keywords

  • Mass spectrometry
  • SNP
  • STR typing
  • Variant allele

Cite this

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abstract = "We have developed a highly automated assay covering twenty one markers spanning the UK, European, and CODIS core short tandem repeat (STR) loci. In this assay, sample DNA is amplified with an 8-well PCR panel, and the masses of the PCR products are determined on an electrospray ionization-mass spectrometry platform. The mass measurements are accurate enough to assign a base composition to the PCR products, specifying the number of their constituent dA, dG, dC, and dT residues. The base compositions in turn define the STR genotypes. Sequence variants have been observed in many of the STR loci, and the accuracy of the mass measurements supports their identification with this assay. Parameters in the initial evaluation of the assay included species specificity, sensitivity, reproducibility, accuracy, and concordance. Results indicate that the assay is concordant with existing assays while providing additional information by virtue of the detection of sequence variants of STR alleles.",
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Development of a genotyping assay for the UK, European, and CODIS core STR loci identifying length and sequence variation in the target loci. / Duncan, David D.; Boles, Kristen M.; Planz, John V.; Hofstadler, Steven A.; Hall, Thomas A.

In: Forensic Science International: Genetics Supplement Series, Vol. 3, No. 1, 01.12.2011.

Research output: Contribution to journalArticle

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AU - Hofstadler, Steven A.

AU - Hall, Thomas A.

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