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                            Funding & Awards
 Validation of Illumina's MiSeq FGx NGS Platform for Transition to Casework
Award Information
Awardee
              City of New York, Office of Chief Medical Examiner
Award #
              2015-DN-BX-K005
Funding Category
              Competitive
Location
                    New York, NY
Congressional District
              7
Status
              Closed
Funding First Awarded
              2015
Total funding (to date)
              $150,000
Original Solicitation
              NIJ FY 14 Research and Development for Publicly Funded Forensic Science Laboratories to Assess the Testing and Processing of Physical Evidence
Description of original award (Fiscal Year 2015, $150,000)
The basis of individual identification in modern forensics is DNA typing by short tandem repeats (STR). This technique has brought a standardized, quantitative method with strong statistical underpinnings to the criminal justice system that has dramatically improved just and impartial outcomes. While the fundamental principles behind STR typing have not changed, new instrumentation and informative biological markers developed over the past few years have the potential to address the limitations of current techniques as well as the need for increased throughput at lower costs.
Current DNA analysis methods for individual identification have technical, cost and throughput limitations. These methods are based on capillary electrophoretic sizing of selected amplicons, some of which would not be accepted today due to poor population frequency distributions of PCR amplification problems. Capillary electrophoresis (CE) itself has inherent limitations. It is a single reaction detection method without capabilities for multiplexing and is consequently slow. It can only measure amplicon lengths and consequently fails to detect sequence specific information that could improve STR analysis. Finally it is approaching the maximum number of STRs it can process, thus effectively abandoning improvement from new STRs and SNPs that could improve individual identification, mixture deconvolution and hereditary analysis  at least in a single system.
The forensic community is beginning to evaluate next generation sequencing (NGS) as a means to overcome these problems. Such instruments not only add additional sequencing information, but have a nearly unlimited capacity for additional STRs as well as single nucleotide polymorphisms (SNPs) markers, thereby enhancing individual identification. These instruments also have the potential for significant improvements in throughput at lower costs.
The goal of this application is to validate the Illumina MiSeq FGx forensic sequencing platform with the aim of transitioning our laboratory from CE to NGS. To achieve these ends four Specific Aims are proposed: i) To compare NGS detection sensitivity, precision and accuracy against our current CE platform, ii) To evaluate NGSs ability to improve mixture deconvolution through use of STRs and SNPs, iii) To compare outcomes of NGS and CE using degraded DNA, and iv) To evaluate throughput and costs between to the two systems.
We believe this application directly addresses the goals of the solicitation as it will result in the production of a validated method that may be replicated in other laboratories, and will have a direct and immediate impact on laboratory efficiency and assist in making laboratory policy decisions.

ca/ncf



  
Grant-Funded Publications
        
                      Evaluation of ArmedXpert software tools, MixtureAce and Mixture Interpretation, to analyze MPS-STR data
                  Analyzing degraded DNA and challenging samples using the ForenSeq (TM) DNA Signature Prep kit
                  Validation of Illumina’s MiSeq FGx NGS Platform for Transition to Casework
                  Qualitative and Quantitative Assessment of Illumina's Forensic STR and SNP Kits on MiSeq FGx (TM)
                  Systematic Assessment of the Performance of Illumina's MiSeq FGx((TM)) Forensic Genomics System

  
Date Created: September 20, 2015
    
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