Is MPS right for your forensics lab?

Today’s post was written by guest blogger Anupama Gopalakrishnan, Global Product Manager for the Genetic Identity group at Promega. 

Next-generation sequencing (NGS), or massively parallel sequencing (MPS), is a powerful tool for genomic research. This high-throughput technology is fast and accessible—you can acquire a robust data set from a single run. While NGS systems are widely used in evolutionary biology and genetics, there is a window of opportunity for adoption of this technology in the forensic sciences.

Currently, the gold standard is capillary electrophoresis (CE)-based technologies to analyze short tandem repeats (STR). These systems continue to evolve with increasing sensitivity, robustness and inhibitor tolerance by the introduction of probabilistic genotyping in data analysis—all with a combined goal of extracting maximum identity information from low quantity challenging samples. However, obtaining profiles from these samples and the interpretation of mixture samples continue to pose challenges.

MPS systems enable simultaneous analysis of forensically relevant genetic markers to improve efficiency, capacity and resolution—with the ability to generate results on nearly 10-fold more genetic loci than the current technology. What samples would truly benefit from MPS? Mixture samples, undoubtedly. The benefit of MPS is also exemplified in cases where the samples are highly degraded or the only samples available are teeth, bones and hairs without a follicle. By adding a sequencing component to the allele length component of CE technology, MPS resolves the current greatest challenges in forensic DNA analysis—namely identifying allele sharing between contributors and PCR artifacts, such as stutter. Additionally, single nucleotide polymorphisms in flanking sequence of the repeat sequence can identify additional alleles contributing to discrimination power. For example, sequencing of Y chromosome loci can help distinguish between mixed male samples from the same paternal lineage and therefore, provide valuable information in decoding mixtures that contain more than one male contributor. Also, since MPS technology is not limited by real-estate, all primers in a MPS system can target small loci maximizing the probability of obtaining a usable profile from degraded DNA typical of challenging samples. Continue reading

Forensic Scientists Improve Sexual Assault Kit Turnaround Time with Y-Screening

The backlog of sexual assault kit samples in crime laboratories across the nation is a topic that hit the spotlight when a group of journalists uncovered the issue in an open records search of crime lab records in 2015. Reasons for the backlog include lack of staff, lack of funding, and simply, lack of time or a decision not to prosecute the case. Processing samples can be a labor-intensive process.

We recently interviewed Lynndsey R. Simon, Forensic Scientist II and Alternate CODIS Administrator from the Columbus Police Forensic Services Center to discuss some recent changes in sample processing in their laboratory that are helping to alleviate some of the backlog. She will be presenting a talk at the upcoming International Symposium on Human Identification (ISHI) in September.

The Columbus Police Forensic Services Center is a smaller forensic laboratory and according to Simon, one of the biggest challenges they face is strained resources. The DNA extraction and processing kits that forensic laboratories use are very expensive, and the number of DNA samples that laboratories are getting for DNA analysis are increasing. With limited resources and funding, maximizing efficiency and finding the best solutions for the laboratory becomes critical. Continue reading

Meet Jon Drobac, Manager Global Technical Support and Training on the Spectrum CE Team

29160613_lPromega will introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines–from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Jon Drobac, Global Technical Support and Training Manager.
Continue reading

Meet Katie Herbrand, Genetic Identity Supervisor on the Spectrum Team

29160613_lPromega will introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines–from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Katie Herbrand, Genetic Identity Supervisor in Production. Continue reading

Meet Sue Wigdal, Senior Quality Assurance Scientist on the Spectrum Team

29160613_lPromega will introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines–from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Sue Wigdal, Senior Quality Assurance Scientist. Continue reading

Meet Lisa Misner, Technical Support and Training Specialist on the Spectrum Team

29160613_lPromega will introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines–from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Lisa Misner, Technical Support and Training Specialist. Continue reading

Meet Jonelle Thompson, Validation Services Manager for the Spectrum CE Instrument

29160613_lPromega will soon introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines—from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Jonelle Thompson, Validation Services Manager. Continue reading

Ten Validation Tips You Need to Know

exampleForensic lab validations can be intimidating, so Promega Technical Services Support and Validation teams shared these tips for making the process go more smoothly.

  1.  Prepare Your Lab. Make sure all of your all of your instrumentation (CEs, thermal cyclers, 7500s, centrifuges) and tools (pipettes, heat blocks) requiring calibration or maintenance are up to date.
  2.  Start with Fresh Reagents. Ensure you have all required reagents and that they are fresh before beginning your validation. This not only includes the chemistry being validated, but any preprocessing reagents or secondary reagents like, polymer, buffers, TE-4 or H2O.
  3. Develop a Plan. Before beginning a validation, take the time to create plate maps, calculate required reagent volumes, etc. This up-front planning may take some time initially, but will greatly improve your efficiency during testing.
  4. Create an Agenda. After a plan is developed, work through that plan and determine how and when samples will be created and run. Creating an agenda will hold you to a schedule for getting the testing done.
  5. Determine the Number of Samples Needed to Complete Your Validation. Look at your plan and see where samples can be used more than once.  The more a sample can be used, the less manipulation done to the sample and the more efficient you become.
  6. Select the Proper Samples for Your Validation. Samples should include those you know you’ll obtain results with be similar to the ones you’ll most likely be using, and your test samples should contain plenty of heterozygotes. When you are establishing important analysis parameters, like thresholds, poor sample choice may cause more problems and require troubleshooting after the chemistry is brought on-line.
  7. Perform a Fresh Quantitation of Your Samples. This will ensure the correct dilutions are prepared. Extracts that have been sitting for a long time may have evaporated or contain condensation, resulting in a different concentration than when first quantitated.
  8. Stay Organized. Keep the data generated in well-organized folders. Validations can contain a lot of samples, and keeping those data organized will help during the interpretation and report writing phase.
  9. Determine the Questions to Be Answered. While writing the report, determine the questions each study requires to be answered. Determining what specifically is required for each study will prevent you from calculating unnecessary data.  Do you need to calculate allele sizes of your reproducibility study samples when you showed precision with your ladder samples?
  10. Have fun! Remember, validations are not scary when approached in a methodical and logical fashion. You have been chosen to thoroughly test something that everyone in your laboratory will soon be using. Take pride in that responsibility and enjoy it.

Need more information about validation of DNA-typing products in the forensic laboratory? Check out the validation resources on the Promega web site for more information for the steps required to adopt a new product in your laboratory and the recommended steps that can help make your validation efforts less burdensome.

 

 

 

Meet Andrea Chow, Sr. Director of Integrated Engineering and Member of the Spectrum CE Team

29160613_l Promega will introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines–from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Andrea Chow, Sr. Director, Integrated Engineering. Continue reading

Massively Parallel Sequencing for Forensic DNA Analysis

HiResToday’s blog is written by guest blogger, Douglas R. Storts, PhD, head of Research, Nucleic Acid Technologies, Promega Corporation.

Massively parallel sequencing (MPS), also called next generation sequencing (NGS), has the potential to alleviate some of the biggest challenges facing forensic laboratories, namely degraded DNA and samples containing DNA from multiple contributors. Unlike capillary electrophoresis, MPS genotyping methods do not require fluorescently-labeled oligonucleotides to distinguish amplification products of similar size. Furthermore, it is not necessary to design primers within a color channel to generate amplicons of different sizes to avoid allele overlap. Consequently, all the amplicons can be of a similar, small size (typically <275 base pairs). The small size of the amplicons is particularly advantageous when working with degraded DNA. Because the alleles are distinguished by the number of repeats and the DNA sequence, additional information can be derived from a sample. This can be especially important when genotyping mixtures. As previously demonstrated (1), this sequence variation can help distinguish stutter “peaks” from minor contributor alleles.

Because there is no reliance upon size and fluorescent label, significantly greater multiplexing is possible with MPS approaches. In addition to autosomal short tandem repeats (STRs), we can also sequence Y-STRs, single nucleotide polymorphisms (SNPs), and the mitochondrial DNA control region. The advantage to this approach is the forensic analyst does not need a priori knowledge whether a sample would benefit most from the different methods of genotyping.

Despite these major advantages, there are limitations to the near-term, broad deployment of current MPS technology into forensic laboratories. The limitations fall into four main categories:  Workflow, costs, performance with forensically-relevant samples, and community guidelines. Continue reading