Publication Date:
2004
abstract:
One of the many commercial technologies for genotyping single nucleotide polymorphisms (SNPs) is template
direct dye-terminator incorporation with fluorescence-polarization (TDI-FP assay). It is a single-base extension
assay followed by reading the fluorescence polarization values in an appropriate instrument. We have
evaluated the suitability of the TDI-FP technique to detect haploid uniparentally inherited DNA polymorphisms
on the nonrecombining portion of the Y chromosome. A sample of 47 individuals has been genotyped
for 8 Y chromosome biallelic markers. The SNP typing was blindly duplicated by the denaturing high-performance
liquid chromatography (DHPLC) technique for comparison. In the cases under examination the
TDI-FP assay was able to resolve an allelic state fully. Such a result showed 100% concordance indicating
how efficiently the TDI assay can be used to genotype Y chromosome DNA SNPs. However, a percentage of
indeterminate genotypes remained unresolved by simple visual inspection: it varied from 0% to 11% depending
on the SNP locus and on the success of amplification. This is consistent with previous findings. A
maximum likelihood classificatory analysis allowed some of the indeterminate genotypes to be assigned and
some potentially misclassified samples to be identified. Their percentage remains relatively high despite retyping
and therefore alternative techniques for these noncompliant situations are required.
Iris type:
01.01 Articolo in rivista
List of contributors:
Crobu, Francesca
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