Two problematic human polymorphic Alu insertions.
Analysis of two previously described polymorphic Alu insertions (Sb19.3 and NBC3) in world-wide human populations generated genotypic frequencies grossly in violation of Hardy-Weinberg equilibrium expectations. GenBank searches at the National Center for Biotechnology Information (NCBI) and sequencing analyses revealed that samples homozygous for the Sb19.3 Alu insertion amplify a band indistinguishable in size to the lack of insertion amplicon, corresponding to a paralogous locus on chromosome 4. This locus displays a very similar sequence (84%) to that flanking the Sb19.3 Alu insertion located at chromosome 19. Moreover, we have determined that NBC3, a different Alu insertion, is not located in the pseudoautosomal region of the Y-chromosome, as previously reported, but in position Yq11.2. Also, the band that mimics the lack of insertion amplicon corresponds to a paralogous locus located at chromosome X with a similarity of 92% to the sequence flanking the NBC3 Alu insertion. Finally, the utilization of newly designed primers avoided amplification from the paralogous loci and allowed a reliable assignation of genotypes for both loci. Unlike previously reported, using our new primers the Y-specific locus NBC3 was found not to be polymorphic in the populations analyzed.
Luis
Javier R
JR
Department of Biological Sciences, Florida International University, Miami, FL, USA.
Terreros
Maria C
MC
Martinez
Laisel
L
Rojas
Dina
D
Herrera
Rene J
RJ
D020087:Alu Elements / Q000235:genetics*; D017931:DNA Primers; D003951:Diagnostic Errors; D005006:Ethnicity / Q000235:genetics; D005787:Gene Frequency; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods / Q000592:standards; D016133:Polymerase Chain Reaction / Q000592:standards; D011110:Polymorphism, Genetic
D017931:DNA Primers; D005819:Genetic Markers