Accurate STR allele designations at the FGA and vWA loci despite primer site polymorphisms.
Polymerase chain reaction (PCR)-based STR DNA typing systems are used extensively in the field of human identification. Under optimal PCR conditions, the amplicon yield from both alleles of an STR locus is expected to be approximately equivalent. However, it is reasonable to expect that rare genomic sequence polymorphisms will co-localize with well-designed primer sets and induce allele imbalance or "dropouts". Two samples were identified in the course of genotyping thousands of individuals with AmpF/STR Profiler Plus that showed strong disparity in amplitude peak height of heterozygous peaks at the loci vWA and FGA. These samples were reamplified at reduced annealing temperature in an attempt to balance the peak heights. Nucleotide sequencing documented polymorphisms at the PCR primer binding sites of the affected alleles. The results indicate that reducing the annealing temperature to improve primer-binding efficiency at the mismatch and employing an alternative multiplex enhanced the data from both samples. Reducing annealing temperatures could provide a simple general solution to improving data quality for samples where polymorphisms are suspected to cause allele imbalance. Finally, we report on additional polymorphisms surrounding the vWA locus in a genetically diverse population.
Hendrickson
Brant C
BC
Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA.
Leclair
Benoit
B
Forrest
Shawn
S
Ryan
John
J
Ward
Brian E
BE
Petersen
Daniel
D
Kupferschmid
Timothy D
TD
Scholl
Thomas
T
D022981:Allelic Imbalance; D016172:DNA Fingerprinting; D017931:DNA Primers; D006579:Heterozygote; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences; D013696:Temperature
D017931:DNA Primers