STR analysis

The Spectrum CE System: Capillary Electrophoresis for This Generation—and the Next

Posted on by Ken Doyle

Massively parallel sequencing (MPS) has gained popularity for specialized forensic applications. However, the amplification of short tandem repeats (STRs) and analysis by capillary electrophoresis (CE) remains the gold standard for the vast majority of forensic laboratories.

Spectrum CE System in the lab

Recently, Promega announced the launch of the Spectrum CE System, a new capillary electrophoresis instrument that supports future 8-color technology while maintaining compatibility with existing 5- and 6-color kits—even ones that Promega does not sell. In a market with limited instrumentation options for CE analysis, the Spectrum CE system offers features designed to streamline the workflow for analyzing casework and database samples.

Cristopher Cowan, Director of Instrumentation R&D at Promega, discusses the key features of the Spectrum CE System.
Continue reading “The Spectrum CE System: Capillary Electrophoresis for This Generation—and the Next”

The Latest Addition to the Lab: A Review of the Spectrum Compact CE System

Posted on by AnnaKay Kruger

When it comes to acquiring new equipment, choosing the right instrument for your lab can be daunting―you want to make a worthwhile investment that will go the distance, both in longevity and overall capacity. In a perfect world, the instruments available to you would have been thoroughly tested and reviewed, especially as they compare to one another, making your job that much easier.

In the case of benchtop capillary electrophoresis (CE) instruments, researchers Nastasja Burgardt and Melanie Weissenberger have done just that. Their article, titled “First experiences with the Spectrum Compact CE System”, appeared in the International Journal of Legal Medicine and offered a comprehensive review of the performance of the recently released Spectrum Compact CE System in a forensic genetics laboratory setting.

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Is MPS right for your forensics lab?

Posted on by Promega

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 “Is MPS right for your forensics lab?”

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

Posted on by Michele Arduengo

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

Ten Validation Tips You Need to Know

Posted on by Promega
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Forensic 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.

Massively Parallel Sequencing for Forensic DNA Analysis

Posted on by Promega

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 “Massively Parallel Sequencing for Forensic DNA Analysis”

Forensic Science in Search of the ‘Disappeared’

Posted on by Terri Sundquist

By Fredy Peccerelli

Guatemala’s method of uncovering human rights violations can help other post-conflict areas, says Fredy Peccerelli.

Skeleton TeethDuring Guatemala’s internal armed conflict (1960–1996) almost 200,000 people are thought to have been killed or ‘disappeared’ at the hands of repressive and violent regimes. Those lives matter. Their families’ demands are clear: they want to know what happened to their loved ones and they want their remains returned. They need truth and justice.

Using forensic sciences, the Forensic Anthropology Foundation of Guatemala (FAFG) is assisting families by returning their loved ones’ remains, promoting justice, and setting the historical record straight.
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From Death Row to Exoneration Thanks to DNA Testing

Posted on by Terri Sundquist

Hands of man prisoner gripping rusty prison barsImagine being convicted of a crime for which you are not guilty—not some minor crime, but one of the most heinous crimes imaginable: the rape and murder of a young girl. Would you feel shock and anger at the injustice? Disappointment in the legal system that could make such a horrible error? Sadness and depression at the thought of spending time imprisoned for a crime that someone else committed? Probably all of those emotions and more. At your sentencing hearing, the situation gets worse; you are sentenced to death. Now, this horrible crime will prematurely claim the life of two innocents: the young girl and you.

This is the situation that Kirk Bloodsworth faced in 1985: a death sentence for the rape and murder of 9-year-old Dawn Hamilton. Although Bloodsworth didn’t know it at the time, DNA testing would eventually prove his innocence and save his life.
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PowerQuant System: Tool for informed casework sample processing decisions

Posted on by Anupama Gopalakrishnan

CottonSwabsIdentification of a crime perpetrator on the basis of DNA fingerprinting is not as easy as some of the CSI shows on television make it out to be. A sample such as blood stain, touch sample or body fluid retrieved at a crime scene is often a challenge for DNA analysts. In many instances, the samples are limited in quantity, found in dirty conditions, exposed to harsh environmental factors and are mixtures of more than one DNA—human and/or non-human. One of the most important aspects of the workflow to successfully obtain a DNA fingerprint profile is accurate quantification of human amplifiable DNA. The more information gleaned from the sample, the better equipped the DNA analyst is to determine the best course of action for obtaining a usable short tandem repeat (STR) profile from challenging samples. Therefore, Promega has developed the PowerQuant™ System, a probe-based 4-target, 5-dye real-time PCR method to a) determine human and male DNA concentrations in a sample, b) detect possible PCR inhibitors c) identify possible mixtures and d) measure DNA integrity. Continue reading “PowerQuant System: Tool for informed casework sample processing decisions”

How a Magazine Ad Helped Convict a Rapist

Posted on by Terri Sundquist

TrialIn May of 1986, a woman in Orange County, Florida, was surprised by a man who entered her apartment and raped her at knifepoint. Despite the fact that she got a glimpse of his face, the chances of identifying and convicting her rapist were slim. Although law enforcement officers did their best to identify the perpetrator, their investigative techniques in the case were limited compared to our current set of forensic tools. That changed when Jeffrey Ashton, an assistant attorney for the state of Florida, saw an advertisement for DNA-based paternity testing in a magazine and began to wonder if DNA testing could also be used to identify the man responsible for the attack.

Continue reading “How a Magazine Ad Helped Convict a Rapist”