A compromising position for a variant: A new allele for D1S1656 that invades its neighbors and can lead to missinterpretations

Abstract

Short tandem repeats (STRs) are the markers of choice for purposes of human forensic identification because of their considerable degree of polymorphism. This variability may occasionally become a challenge for the analyst when a new variant invades the allele distribution range of the neighboring locus. We present here a novel variant at locus D1S1656 showing a molecular length of 211.32 bp corresponding to 21.3 repeating units. This variant is superimposed on the D12S391 locus when the Global Filer™ (Thermo Fisher Scientific Inc., USA) is used, invading the shortest allele range and being assigned as Off-ladder (OL). In contrast, typing with PowerPlex® Fusion (Promega Corp., Madison, USA) overlaps the D2S441 locus, generating an allele that is recognized as 8. In both cases the invasion was observed as a tri-allele pattern. The results were confirmed by DNA re-extraction and typing with the two independent commercial megaplexes described above. The variant was detected during analysis of a reference sample throughout a paternity exclusion case. This is the first time this variant has been described and reported to the NIST STR Base. Since D1S1656 is included in widely-used multiplex kits from several vendors - Biotype (Dresden, Germany) Qiagen (Venlo, The Netherlands), Promega (Madison, USA) and Thermo Fisher (Foster City, CA, USA) - it would then be recommendable that other forensic labs be aware of this new micro-variant in dealing with similar interpretation challenges and that the kit producers take this fact into account in designing new multiplex kits.