Phenotypic Single Nucleotide Polymorphisms Research Articles

An automated independent workflow for the analysis of massively parallel sequence data from forensic SNP assays.

Illumina and Thermo Fisher Scientific have developed assays that permit the sequencing of forensically relevant single nucleotide polymorphisms (SNPs), along with software to determine the associated genotypes. Currently there is no method to either independently confirm the genotypes determined using the manufacturer's software, or to compare genotypes and quality metrics among samples processed using both platforms. This paper outlines an automated workflow developed in CLC Genomics Workbench that permits accurate, fast and independent analysis of SNP sequence data from either platform. To facilitate the straightforward comparison of genotypes generated from both the manufacturer's software and the independent CLC analysis, a Python script was written. Data for a total of 323 forensically relevant ancestry, identity and phenotypic SNPs can be analyzed, and the resulting genotypes, coverage, quality flags and major allele frequencies are easily compared across samples and platforms.

Prediction of human eye colour using highly informative phenotype SNPs (PISNPs)

ABSTRACTOne of the rapidly developing areas in human genetics and genomics is detection of candidate Single Nucleotide Polymorphism (SNPs) for human complex traits. These findings can be used in the field of forensics for predicting the externally visible characteristics (EVCs) of a given individual based on a sample of DNA alone. Eye colour is currently the most thoroughly investigated EVC for forensic genetic applications. In this study, eye colour prediction performance of two currently available major methods was assessed in a set of 100 individuals from Turkey by applying the two statistical approaches of multinomial logistic regression (MLR) and Bayes analysis using each statistical approach’s online portal (https://hirisplex.erasmusmc.nl/ and http://mathgene.usc.es/snipper/eyeclassifier.html) designed for SNP-based forensic prediction for this phenotype. On one hand, eye colour prediction results for IrisPlex SNPs have a high success rate for correctly predicting blue/brown phenotypes but not for green-hazel or intermediate dark phenotypes. On the other hand, Snipper analysis improved detection of intermediate phenotypes but increased the number of unclassified individuals given the prediction probability threshold applied. This study adds data that can be used as a reference for future eye colour prediction investigations in forensic cases.

A mini-multiplex SNaPshot assay for the triage of degraded human DNA

Short Tandem Repeat (STR) genotyping is currently the primary DNA-based method for human identification, however it can have limited success when applied to degraded human remains. Massively parallel sequencing (MPS) provides new opportunities to obtain genetic data for hundreds of loci in a single assay with higher success from degraded samples. However, due to the extra requirement for specialised equipment, expertise and resources, routine use of MPS may not be feasible or necessary for many forensic cases. Here we describe the development of a mini-multiplex SNaPshot screening tool (Miniplex) for human samples which allows the qualitative comparison of short mitochondrial and nuclear DNA targets, as well as the interrogation of biogeographic ancestry, lineage, and phenotype single nucleotide polymorphisms (SNPs). This tool is useful to triage samples based on sample quality prior to downstream identification workflows and provides broad biological profile data for intelligence purposes.

Beyond the STRs: A comprehensive view of current forensic DNA markers characterized in the PCR-based DNA profiling standard SRM 2391D

Capillary electrophoresis (CE) of the Combined DNA Index System (CODIS) core set of 20 Short Tandem Repeat (STR) markers [1] is the primary genotyping method for forensic human identification in the U.S. With the emergence of new technologies beyond CE testing, other categories of forensic DNA markers are now more readily available. The next iteration of the PCR-Based DNA Profiling Standard Reference Material, SRM 2391d, will contain allele calls and sequence information for forensically relevant markers available in commercial kits. The SRM components will be characterized using CE and next-generation sequencing (NGS). With NGS technology, more data can be mined from these reference samples than previous generations of this SRM. This paper will focus on data from the forensic DNA markers beyond the common autosomal, Y-STR, and X-STR markers to include: insertion/deletions, ancestry single nucleotide polymorphisms (SNPs), identity SNPs, phenotypic SNPs, microhaplotypes and mitochondrial whole genome sequencing. The primary emphasis will be an analysis of the information gained from using NGS vs CE technology with the reference samples going “Beyond the STRs”.

Massively parallel sequencing of forensically relevant single nucleotide polymorphisms using TruSeq™ forensic amplicon.

The TruSeq™ Forensic Amplicon library preparation protocol, originally designed to attach sequencing adapters to chromatin-bound DNA for chromatin immunoprecipitation sequencing (TruSeq™ ChIP-Seq), was used here to attach adapters directly to amplicons containing markers of forensic interest. In this study, the TruSeq™ Forensic Amplicon library preparation protocol was used to detect 160 single nucleotide polymorphisms (SNPs), including human identification SNPs (iSNPs), ancestry, and phenotypic SNPs (apSNPs) in 12 reference samples. Results were compared with those generated by a second laboratory using the same technique, as well as to those generated by whole genome sequencing (WGS). The genotype calls made using the TruSeq™ Forensic Amplicon library preparation protocol were highly concordant. The protocol described herein represents an effective and relatively sensitive means of preparing amplified nuclear DNA for massively parallel sequencing (MPS).