engleski

VALIDATION AND ASSESSMENT OF AN OPTIMIZED MASSIVELY PARALLEL SEQUENCING WORKFLOW FOR WHOLE MITOCHONDRIAL GENOMES OF REFERENCE SAMPLES

Massively parallel sequencing (MPS) technology shaped the era of forensic genomics, particularly regarding mitochondrial DNA (mtDNA), one of the most valuable markers in cases when conventional nuclear DNA typing fails. The technology enabled higher throughput and greater sensitivity, which comes with a greater possibility of errors. In order to produce reliable forensic results, validation is the first step when incorporating new methodology into routine casework. The work presented here is part of our ongoing internal validation of MPS workflow for sequencing whole mtDNA from reference samples using Nextera® XT (Illumina®) protocol on MiSeq FGx™ instrument. Through studies of sensitivity, mixtures, repeatability and reproducibility, as well as concordance and contamination studies, we aimed to ensure accuracy and reliability of generated data from manually prepared libraries. To cover the entire mitochondrial genome, reference samples were enriched by long range PCR, resulting in two overlapping fragments of length 9.1 kb and 11.2 kb. Three different DNA polymerases were tested for optimal conditions, prior to library preparation step. Repeatability and reproducibility were assessed by using different sample types (blood and saliva) in multiple PCR and technical replicates, across different operators and different library normalization methods (magnetic beads, fluorometry and capillary gel-electrophoresis), and across two different sequencing platforms. Contamination studies were used to set thresholds for the analysis of sequencing data. We demonstrate through concordance study between MPS and Sanger results that accurate and reliable haplotypes can be obtained using our optimized Illumina protocol for whole mtDNA sequencing from reference samples.

massively parallel sequencing, mitochondrial DNA (mtDNA), validation study

nije evidentirano