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Updated: Feb 7, 2026

Massively Parallel Reporter Assays in Cultured Mammalian Cells
Published on: August 17, 2014
An automated independent workflow for the analysis of massively parallel sequence data from forensic SNP assays
Nicholas T Vlachos1, Kelly A Meiklejohn1,2, James M Robertson3
1Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA.
Abstract:
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.
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