Science          

The technology being used by Casework Genetics to resolve mixtures in forensic samples uses the genetic variant designated as Single Nucleotide Polymorphisms, more commonly known as SNPs (pronounced “snips”).  This is not the first time SNPs have been used in forensics.  In fact, RFLPs, the very first genetic variant used for DNA identification, were in reality SNPs.  The variation in restriction enzyme digestion fragment lengths is caused by SNPs in the enzyme recognition sites.   SNPs in enzyme recognition sites render them inoperational, resulting in varying fragment lengths.  Other forensic SNP products include the DQ Alpha Polymarker.  More recently there have been papers proposing the use of SNP panels consisting of ~50-100 SNP loci (Kidd 2006, Budowle and van Daal).  The distinguishing feature of our technology is that we are using over 1 million SNP loci to provide identification.  The discrimination potential of a million is enormous and it is difficult to overstate the differences between High Density SNP Arrays and any current DNA identification technology.

SNP FACTS AND FEATURES

• SNPs are the largest class of variants in the Genome

• By convention, SNP designation means a variant is common, that is it occurs in at least 1% of the population. 

• Heterozygosity is often discussed in terms of Minor Allele Frequency (MAF)

• SNP minor allele frequencies can vary significantly from 50% to 1%

• Typical MAFs are in the range of 10%

• Estimates for the number of SNPs in the human genome range from 3 to 10 million

• With 3 billion bases in the Human Genome,  SNPs should be distributed every 330 to 1000 bases.

• SNP Insertions – Addition of a single nucleotide

• SNP Deletions – Removal of a single nucleotide

• SNP Substitutions

• Substitutions constitute ~99% of SNPs

• May be tri-allelic, but nearly all are bi-allelic

• For bi-allelic SNPs,2 out of 3 substitutions are due to a T to C transition

Platform                                                                                                                           

Technology development is extremely expensive and necessarily driven by large markets such as medical research.  This, and the existence of large, fixed databases that are dependent on sieving technology are reasons that little revolutionary technology development has occurred with STR analysis.

While STR variants are little used in medical research or diagnostics, Genome Wide Association Studies (GWAS) are a major driver for the development of High Density SNP arrays.  GWAS  efforts search for SNPs that are associated with disease.   The results of these associations are in identifying targets for therapeutics and for identifying disease markers predicting risk for disease.  Because medical applications can be subject to intense regulation, High Density SNP Arrays were developed with stringent quality standards.  While the cost of developed was immense, it was justified by the large medical market.

Algorithms developed in 2008 at UCLA and Translational Genomics in labs working on GWAS suggested that  High Density SNP Arrays could be used to resolve forensic samples containing mixtures of contributing DNA.  Casework Genetics has exclusive license to this technology for use in human identification.  Casework Genetics is leveraging the development born by the medical research industry to bring these technological advancements to forensics.   Together with Casework’s in-house inventions, this powerful technology allows significant advances in the performance of Human DNA Identification for forensics. 

Casework Genetics has partnered with Illumina, the largest genomic research technology provider in the world.  Among the many genetic platforms Illumina offers, we have selected the Infinium Assay for forensic validation.  This a turnkey assay that runs on Illumina’s iScan instrumentation.  All the biochemistry, including a non-PCR amplification methodology operate identically to the GWAS products and no specialized modifications are required for forensic applications.  Therefore, we take advantage of the years of development put into this system.  It is only in the analysis of the post-assay data that we apply algorithms that make the data relevant to human identification.  This post-assay analysis is compatible with Excel and can be easily formatted into reports specialized for forensic applications.  The iScan system is available for use with a fluidics robot, thereby increasing throughput and improving assay reproducibility and reliability.