Analysis of unusual mutation patterns within father-son pairs using a ForenSeq DNA Signature Prep Kit and a YFiler Plus PCR Amplification Kit

Abstract

The application of Y-chromosome analysis is expanding in fields such as forensic science and genealogy. By researching the potential polymorphisms this chromosome can present, we can further our ability to assess DNA profiles for these disciplines to avoid erroneous exclusions of paternal linkage, wrongful convictions based on forensic evidence, and other misinformed genetic conclusions. The conservation of Y-haplotypes during transmission occurs due to a relative lack of genetic recombination events in the inheritance of the Y-chromosome [1]. However, random mutation events can occur in a paternal line resulting in haplotype changes. These changes can include allele duplications and deletions that occur at the STR and SNP loci used in forensic DNA analysis. This can become important in cases of sexual assault where male-female mixture samples have low amounts of male DNA such that the male signal is not amplified in currently used STR multiplexes [7]. In this study, we analyzed a father and his eleven sons using two different methodologies for genetic analysis; next generation sequencing and capillary electrophoresis. The samples were obtained from the Coriell Institute for Medical Research located in Hamden, NJ, in the form of frozen DNA extracts isolated from a blood-sourced lymphocyte cell culture [22]. DNA from these samples was tested with the ForenSeqTM DNA Signature Prep Kit [14] (Verogen, San Diego, CA) primer set A and the YFilerTM Plus PCR Amplification Kit [24] (Thermo Fisher Scientific, Waltham, MA). Using these two platforms, three Y-STR loci were identified as discordant between the father and all of his eleven sons. In all three instances, the father possessed the same allele as the sons as well as one additional allele. At two of these loci (DYS449 and DYS635), the additional allele was one repeat (4bp) longer than that of the shared allele. At the other locus (DYS458), the additional allele was three repeats (12bp) longer than that of the shared allele. Following read count and peak height analysis, it was concluded that these double allele loci are not the product of stutter and are potentially the product of a non-inheritable mutation. With the knowledge that the DNA was extracted from a blood lymphocyte cell culture, it is believed that a somatic mutation may be present in the cell line. We are not able to determine whether the mutations exist in the blood of the father (true somatic mutations) or occurred as a result of the cell culture process. Throughout the study, details concerning the position of these loci on the Y-chromosome, the repeat motifs of the alleles, and the potential for duplication and/or stutter as the originating event are discussed in an effort to further understand this phenomenon. Potential locus duplications were compared to those reported on the National Institute of Standards and Technology STRBase [21] list of allele variations and also to information found in literature. The observed DYS635 locus had an allele designation of 21,22 which is reported on STRBase. The DYS449 and DYS458 loci showed potential allele-specific locus duplications that were not found on STRBase. The implications of potentially undocumented non-inheritable allele patterns in the Y-chromosome, such as this, are significant when considering comparisons between DNA obtained from germline cells (sperm) versus a known casework sample which is usually obtained from blood or saliva [7].