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Next-Generation Sequencing Technologies and Forensic DNA Analysis

by
Brittania Bintz, M.S., Forensic Research Scientist, Western Carolina University
| Oct 16, 2013

forensic genomicsI hold a B.S. in Microbiology from the University of South Florida, and an M.S. in Chemistry from Western Carolina University. I currently work in the laboratory of Mark R. Wilson at Western Carolina University in Cullowhee, NC. The overarching goal of our research is to assess the viability of next-generation sequencing (NGS) or massively parallel sequencing (MPS) technologies for human mitochondrial DNA analysis in forensic casework and databasing laboratories. 

I have been attending the International Symposium on Human Identification (ISHI) for four years. Throughout my tenure at this meeting, I have excitedly witnessed a dramatic increase in the number of presentations highlighting NGS technologies for use in forensic DNA analysis. I’m not the only one who has noticed this trend. Dr. Seth Faith from Battelle graphically outlined the increase during a talk.  It is not insignificant that in 2010, a single NGS-related poster was presented at ISHI; increasing to 22 total presentations featuring NGS at this year’s meeting. This increase illustrates how rapidly this technology is evolving, and how important it is becoming to the forensic community.

For the past three years, I have been given the opportunity to present my research in poster format at ISHI. This year I interacted with more practitioners than ever before, suggesting that the forensics community is embracing NGS. During my presentation1, I was delighted to see that most people were very excited about my work, and genuinely interested in NGS. A few analysts communicated concerns regarding topics such as storage and archiving of data, and implications of sample pooling during library preparation. While these topics should be addressed, I don’t feel that they are significant enough to prevent laboratories from considering how beneficial these technologies can be.

The keynote speaker of the meeting was Dr. Kevin Davies, author of The $1000 Genome. Dr. Davies discussed the evolution of DNA sequencing since the Human Genome Project commenced in 1990, leading to advancements in low-cost, rapid genome sequencing with the advent of NGS technologies. He discussed how these advances are leading to sequencing entire genomes for a cost of $1,000 and how this will impact personalized medicine and clinical genomics. These advances will also ultimately impact forensic genetics, as evidenced by the content of the 24th ISHI meeting.

This year’s symposium also brought with it a dedicated workshop entitled “Advancing Human Forensic DNA with Next-Generation Sequencing Technologies”. During this workshop, experts in the field discussed advances in NGS research. Dr. Mark Wilson discussed high-throughput sequencing of whole human mitochondrial genomes using different approaches for challenging casework-type samples and robust reference samples ultimately increasing the discriminatory power of mtDNA. Additionally, Dr. Mitchell Holland from Penn State University discussed evaluation of heteroplasmy in mtDNA using NGS technologies2. Dr. Seth Faith and his team at Battelle are assessing the utility of multiple NGS platforms for analysis of forensic STR markers, and are developing user-friendly customized software solutions that will enable laboratories to view the resulting data in a way that is similar to the electropherograms generated by capillary electrophoresis instruments3-5. Other laboratories, including Dr. Bruce Budowle’s lab at the University of North Texas Health Science Center (UNTHSC), are working to develop highly-multiplexed panels that probe phenotypic, ancestry informative, and identity SNPs, as well as autosomal, X, and Y-STRs in a single amplification reaction and sequencing run.

The take-home message of this workshop was clear: NGS technologies are powerful, enabling rapid, low-cost sequencing of multiple targets per sample. Additionally, NGS can increase the likelihood that an analyst will obtain information from a compromised or degraded sample due to the reduced size of some markers used for analysis, and can increase the discriminatory power of the analyses due to an increase in the number of markers analyzed.  While there is still much work to be done before NGS finds its way into the crime laboratory, it is only a matter of time before it replaces capillary electrophoresis methods. 

Also this year, Illumina held a vendor showcase. Not surprisingly, this event was standing room only. The showcase featured an animated and entertaining talk from Penn State University’s Dr. Jenifer Smith, who did a great job convincing the audience that sequencing on the Illumina MiSeq is so easy “a cavewoman can do it”. 

We are experiencing a very exciting time in molecular biology. I left the meeting feeling that now, more than ever, the forensic community recognizes the transformative utility of NGS. If not, as Ferris Bueller says “Life moves pretty fast. If you don't stop and look around once in a while, you could miss it”.

References:

  1. Bintz B., Burnside ES, Wilson MR. 2013 A tale of f two platforms: An evaluation of the Roche GS Junior and Illumina MiSeq next-generation sequencing instruments for forensic mitochondrial DNA analysis.
  2. McElhoe J, Holland M, Makova K, Su, M S-W, Nekrutenko A, et al., 2013. Rates and Maternal Transmission of mtDNA Heteroplasmy using a NGS Approach.
  3. McMillan N, Schuetter J, Bornman D, Sander A, Rigsby D, et al., 2013. An Initial Evaluation of Next-Generation Sequencing Technology for STR-Based Mixture Deconvolution Using PCR-Enriched Samples.
  4. Heizer E, Hester M, Minard-Smith A, Bornman D, Young B., 2013. Characterization of STR Allelotyping Data from Next-Generation Sequencing Workflows.
  5. Bornman D, Carnell R, Tornes I, Kuhlman A, Yavas G, et al., 2013. An Open Framework Application for Analyzing STRs and Other Forensic Markers from Next-Generation Sequencing Data.

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