Null allele sequence structure at the DYS448 locus and implications for profile interpretation

Abstract

Null alleles can occur with any PCR-based STR typing system. They generally are due to deletions within the target region or primer binding sites or by primer binding site mutations that destabilize hybridization of at least one of the primers flanking the target region. Although not common, null types were detected at the DYS448 locus in seven out of 1,005 unrelated males in the Hispanic population. Of these DYS448 null types, four individuals displayed an apparent duplication at the DYS437 locus. The additional allele observed at the DYS437 locus is in actuality a smaller-sized DYS448 amplicon, which is the result of a deletion of the invariant N42 base pair domain and downstream repeats within the DYS448 locus. Thus, some DYS448 null types are not truly null. A true DYS448 null allele carried numerous primer binding site variants and a large deletion including the N42 base pair domain and surrounding or downstream repeat regions. The presence of null alleles is not a real concern for interpretation of Y STR loci evidence; current methods for interpreting Y STR profiles easily accommodate such phenomena.

Development and validation of I-DNA1: a 15-Loci multiplex system for identity testing

“…The sample was analysed in triplicate by both systems, and the results were the same. Similar discordances reported in other studies have proved to be due to mutations which probably coincided with the 3′ end binding region of one of the primers [30,31].…”

Development and validation for identity testing of I-DNADuo, a combination of I-DNA1 and a new multiplex system, I-DNA2

“…A concordance of 99.9% between the genetic profiles of the two components of the kit I-DNADuo was observed, a result similar to those of other concordance studies [8,9]. Previous studies have reported that these discordances were due to mutations which probably coincide with the 3′ end binding region of one of the primer pairs, so the combination of two kits with different primers is therefore of great interest in detecting and preventing allelic dropouts [10][11][12].…”

Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM)

“…Null alleles at the locus DYS448 have been reported previously, with relatively high frequencies in Asians [20][21][22]. Null alleles can occur due to primer binding sites mutations or sequence deletions within the STR regions or primer binding regions [20]. Since different method might use different primers, it seems that some deletions may occur within the detected regions of DYS448 locus, which results in amplification failures of all the primer pairs [23].…”

“…These two samples were then typed with the Yfiler ® Plus PCR Amplification Kit (Thermo Fisher) and the AGCU Database Y24 Fluorescence Detection Kit (AGCU), and similar dropout phenomena were observed. Null alleles at the locus DYS448 have been reported previously, with relatively high frequencies in Asians [20][21][22]. Null alleles can occur due to primer binding sites mutations or sequence deletions within the STR regions or primer binding regions [20].…”