Developmental validation of a fully automated genotyping assay capable of detecting length and sequence variation in the CODIS STR loci

David D. Duncan; John V. Planz; Steven A. Hofstadler; Thomas A. Hall

doi:10.1016/j.fsigss.2011.08.126

Developmental validation of a fully automated genotyping assay capable of detecting length and sequence variation in the CODIS STR loci

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

Research output: Contribution to journal › Article › peer-review

Abstract

Sequence variants have been observed in short tandem repeat (STR) loci, but are not detected with conventional electrophoretic analyses. We have validated a high-throughput assay providing base composition analysis of the thirteen CODIS STR loci plus the amelogenin locus. Alleles are amplified with an 8-well panel and the PCR products are directly analyzed on an automated electrospray ionization-mass spectrometry (ESI-MS) platform. The resulting mass determinations are converted to base compositions specifying the number of each of the nucleotides in the PCR amplicons, and STR profiles are derived from the base compositions. Notably, the accuracy of the mass measurements supports detection of sequence variants of STR alleles. Here we describe the developmental validation of the assay and summarize results from analysis of sample panels characterizing allele frequencies, the inheritance of SNP alleles, and the occurrence of germ line mutations in trio sample sets.

Original language	English
Pages (from-to)	e259-e260
Journal	Forensic Science International: Genetics Supplement Series
Volume	3
Issue number	1
DOIs	https://doi.org/10.1016/j.fsigss.2011.08.126
State	Published - Dec 2011

Keywords

Mass spectrometry
SNP
STR typing
Variant allele

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10.1016/j.fsigss.2011.08.126

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title = "Developmental validation of a fully automated genotyping assay capable of detecting length and sequence variation in the CODIS STR loci",

abstract = "Sequence variants have been observed in short tandem repeat (STR) loci, but are not detected with conventional electrophoretic analyses. We have validated a high-throughput assay providing base composition analysis of the thirteen CODIS STR loci plus the amelogenin locus. Alleles are amplified with an 8-well panel and the PCR products are directly analyzed on an automated electrospray ionization-mass spectrometry (ESI-MS) platform. The resulting mass determinations are converted to base compositions specifying the number of each of the nucleotides in the PCR amplicons, and STR profiles are derived from the base compositions. Notably, the accuracy of the mass measurements supports detection of sequence variants of STR alleles. Here we describe the developmental validation of the assay and summarize results from analysis of sample panels characterizing allele frequencies, the inheritance of SNP alleles, and the occurrence of germ line mutations in trio sample sets.",

keywords = "Mass spectrometry, SNP, STR typing, Variant allele",

author = "Duncan, {David D.} and Planz, {John V.} and Hofstadler, {Steven A.} and Hall, {Thomas A.}",

note = "Funding Information: Initial development of this assay was supported by Award No. 2006-DN-BX-K011 and Award No. 2008-DN-BX-K304 from the National Institute of Justice, Office of Justice Programs, United States Department of Justice. The opinions, findings, and conclusions expressed in this paper are those of the authors and do not necessarily reflect those of the Department of Justice. ",

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doi = "10.1016/j.fsigss.2011.08.126",

language = "English",

volume = "3",

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Developmental validation of a fully automated genotyping assay capable of detecting length and sequence variation in the CODIS STR loci. / Duncan, David D.; Planz, John V.; Hofstadler, Steven A. et al.

In: Forensic Science International: Genetics Supplement Series, Vol. 3, No. 1, 12.2011, p. e259-e260.

Research output: Contribution to journal › Article › peer-review

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N1 - Funding Information: Initial development of this assay was supported by Award No. 2006-DN-BX-K011 and Award No. 2008-DN-BX-K304 from the National Institute of Justice, Office of Justice Programs, United States Department of Justice. The opinions, findings, and conclusions expressed in this paper are those of the authors and do not necessarily reflect those of the Department of Justice.

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AB - Sequence variants have been observed in short tandem repeat (STR) loci, but are not detected with conventional electrophoretic analyses. We have validated a high-throughput assay providing base composition analysis of the thirteen CODIS STR loci plus the amelogenin locus. Alleles are amplified with an 8-well panel and the PCR products are directly analyzed on an automated electrospray ionization-mass spectrometry (ESI-MS) platform. The resulting mass determinations are converted to base compositions specifying the number of each of the nucleotides in the PCR amplicons, and STR profiles are derived from the base compositions. Notably, the accuracy of the mass measurements supports detection of sequence variants of STR alleles. Here we describe the developmental validation of the assay and summarize results from analysis of sample panels characterizing allele frequencies, the inheritance of SNP alleles, and the occurrence of germ line mutations in trio sample sets.

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Developmental validation of a fully automated genotyping assay capable of detecting length and sequence variation in the CODIS STR loci

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