title: Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles.
abstract: A population study of Chamorros and Filipinos using short tandem repeat (STR) loci amplified with the AmpFlSTR Profiler Plus PCR amplification kit demonstrated an excess of observed homozygosity at the D8S1179 locus. Use of a different set of D8S1179 primers to type the same samples did not demonstrate an excess of homozygosity and showed discordant genotypes at the D8S1179 locus. A single point mutation, G-to-A transition, 16 nucleotides from the 3' end of the reverse primer, was identified to cause allele dropout when using the AmpFlSTR Profiler Plus primer set. An additional D8S1179 reverse primer specific for the variant was constructed resulting in the recovery of the null allele. The primer was included in the newly developed AmpFlSTR Identifiler PCR amplification kit. No deleterious effects or non-specific peaks were observed in validation experiments evaluating primer concentration, Mg2+ concentration, annealing temperature and population samples.
authors.affiliation: Applied Biosystems, 850 Lincoln Centre Drive, M/S 404-3, Foster City, CA 94404, USA. leibelcs@appliedbiosystems.com
authors.forename: Craig
authors.initials: C
authors.lastname: Leibelt
authors.forename: Bruce
authors.initials: B
authors.lastname: Budowle
authors.forename: Patrick
authors.initials: P
authors.lastname: Collins
authors.forename: Yasser
authors.initials: Y
authors.lastname: Daoudi
authors.forename: Tamyra
authors.initials: T
authors.lastname: Moretti
authors.forename: Gary
authors.initials: G
authors.lastname: Nunn
authors.forename: Dennis
authors.initials: D
authors.lastname: Reeder
authors.forename: Rhonda
authors.initials: R
authors.lastname: Roby
mesh_terms: D000483:Alleles; D001665:Binding Sites; D016172:DNA Fingerprinting / Q000379:methods; D017931:DNA Primers; D005828:Genetics, Population; D005838:Genotype; D006720:Homozygote; D006801:Humans; D015636:Magnesium Chloride; D017354:Point Mutation; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences
chemical_list: D017931:DNA Primers; D015636:Magnesium Chloride