Genetic Identity and Forensics

Harnessing the Power of Massively Parallel Sequencing in Forensic Analysis

Posted on by Ken Doyle

The rapid advancement of next-generation sequencing technology, also known as massively parallel sequencing (MPS), has revolutionized many areas of applied research. One such area, the analysis of mitochondrial DNA (mtDNA) in forensic applications, has traditionally used another method—Sanger sequencing followed by capillary electrophoresis (CE).

Although MPS can provide a wealth of information, its initial adoption in forensic workflows continues to be slow. However, the barriers to adoption of the technology have been lowered in recent years, as exemplified by the number of abstracts discussing the use of MPS presented at the 29th International Symposium for Human Identification (ISHI 29), held in September 2018. Compared to Sanger sequencing, MPS can provide more data on minute variations in the human genome, particularly for the analysis of mtDNA and single-nucleotide polymorphisms (SNPs). It is especially powerful for analyzing mixture samples or those where the DNA is highly degraded, such as in human remains. 

Continue reading “Harnessing the Power of Massively Parallel Sequencing in Forensic Analysis”

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”

“GenEthics” – The Implications of Genomic Data

Posted on by Seffie Wilkinson

I majored in genetics because I love Punnett Squares. Don’t get me wrong, I was fascinated by the groundbreaking research going on in fields like oncology and agriculture, but there was something about the simple and logical nature of calculating inheritance patterns that really drew me in. At the time when I confusingly wandered into my advisor’s office to make this life changing academic decision, I had no idea that this degree would help me see the more complicated, “gray area”, of science, changing the way that I look at the world today.

What is “GenEthics” ?

As I’m sure you’ve already guessed, “GenEthics” is the intersection between the fields of genetics and ethics. A broad term involving questions related to the implications of a variety of different topics in genetic research; “GenEthics” covers everything from the modification of stem cells, to gene therapy and GMOs. Since this term encompasses such a large array of topics, I’m going to focus on some of the ethical questions related to your genome.

Genomic data and its applications

If you’ve ever heard of 23andMe or Ancestry.com then you’ve already had an introduction to genomic data. These direct-to-consumer genetic testing companies are a result of advancements in technology that have made the genotyping process relatively cheap and quick. When you submit a sample, they send it to a lab, extract the DNA, and test it for various markers. What’s returned to you is a report of what markers (alleles) you do and don’t have. These reports can tell you everything from what percent German you are, to your status for any of the many alleles of several genes that may increase risk for Alzheimer’s disease. Genomic data has affected a variety of fields; knowledge of the genome has allowed us to catch famous criminals like the Golden State Killer and has provided us with diagnostic markers for serious diseases. But even with all the good that genomic data has done and will do, there is a “gray area” where many questions regarding safety, equality, and privacy lie.

Safety – Should everyone have their genomes sequenced?

Some believe this is the future of healthcare, that everyone will have their genomes sequenced at birth and put into a national database. This would have amazing implications in the research world; access to endless data, and the ability to form conclusions about everything from human disease to intelligence.

This question also brings up a plethora of others, some pertaining to identity safety. In particular, what if this fictitious database is hacked? There have already been smaller-scale database breaches, the most recent being on the MyHeritage website. These breaches are potentially dangerous; the entirety of your personal health information is housed in your genome. With proper scientific guidance, hackers could infer your: gender, ethnicity, disease status, etc. DNA is not like a credit card, there is no way to obtain a new set of genes.

Equality – How do we ensure that everyone benefits from the advancements that genomic data has to offer?

There are many studies being done with the goal of eradicating cancer using precision medicine. This involves finding common tumor-causing variants in patients’ DNA sequences, and treating them based on their genes. These types of studies have the potential to contribute greatly to the field of personalized medicine, but caution needs to be taken to ensure that multiple populations are represented in the study. Ethnic groups have evolved on separate continents and their genetic sequences contain different variations, one set of conclusions about a disease might not apply to all populations.

Privacy: Who has a right to your genetic information?

The Genetic Nondiscrimination Act (GINA) was passed in 2008 to prevent your genetic test results from affecting your qualification for health insurance, or employment prospects. However, this is but a scratch on the surface of possible genomics-related legal issues; the ownership of a DNA sequence is a complete question mark at this time. There are no laws regarding an organization or family members’ right to an individual’s sequence.

Genomic data has the ability to save lives and prevent devastating disease, but it also can cause disputes within families, and between organizations and individuals. The question of DNA ownership brings up many others: if you test positive for a condition, should you inform other at risk family members? Do you have sole claim on your DNA when you have family members that share most of your sequence? When you submit your DNA to an organization what ownership rights do they have?

The Future…

We have come a long way since completion of the Human Genome Project back in 2003, and we will continue to make amazing advances thanks to the field of genetics. The questions I have posed are just a few that lie in the “gray area” we will be venturing into in the future. These questions may seem as if they are just for researchers, doctors, and lawyers, but they really are for everyone. The social and ethical implications of science affect us all; it’s important that we all join the conversation!

Questions of Genome Privacy and Protection

Posted on by Michele Arduengo

In April 2018, law enforcement officials announced the arrest of a suspect in the Golden State Killer case (New York Times 4/27/2018 ). Shortly after the announcement, those same law enforcement officers explained that detectives had used a public forensic genealogy web site to help identify the killer.

What does it mean when a law enforcement agency accesses a public genetic genealogy database to search for a suspect in a crime?

Continue reading “Questions of Genome Privacy and Protection”

The Age of the Genome: Commercial DNA Sequencing, Familial Searching and What We Are Learning

Posted on by Michele Arduengo
Crowd of people at the street, city center
All of these people are 99% the same at the genomic level. The individuals of the human species are far more alike than different.

There are 3 billion (3,000,000,000) bases in my genome—in each of the cells of my body. Likewise, Johanna, the writer who sits next to me at work also has 3 billion bases in her genome. Furthermore, our genomes are 99% the same. Still, that’s a lot of places where my genome can differ from hers, certainly enough to distinguish her DNA from mine if we were both suspected of stealing cookies from the cookie jar. The power of discrimination is what makes genetic identity using DNA markers such a powerful crime solving tool.

The completion of the human genome project in 2003 ushered in a tremendously fast-paced era of genomics research and technology. Just like computers shrank from expensive, building-filling mainframes to powerful hand-held devices we now call mobile phones, genome sequencing has progressed from floor-to-ceiling capillary electrophoresis units filling an entire building to bench top sequencers sitting in a corner of a lab. The $99 genome is a reality, and it’s in the hands of every consumer willing to spit into a tube.

Commercial DNA sequencing services are promising everything from revealing your true ancestry to determining your likelihood to develop dementia or various cancers. Is this progress and promise or is it something more sinister?

As it turns out, that isn’t an easy question to answer. What is probably true is that whole genome sequencing technologies are being put into the hands of the consumer faster than society understands the ethical implications of making all of this genomic information so readily available.

Continue reading “The Age of the Genome: Commercial DNA Sequencing, Familial Searching and What We Are Learning”

Weird samples? Contact Tech Serv to find the right DNA purification kit for you.

Posted on by Johanna Lee

“Dear Tech Serv,
We would like to detect DNA collected from swabs rubbed on the inside thighs of frogs. What would be the best DNA extraction kit to use for this?”

“Hi Tech Serv,
I need to find out a suitable kit for extracting DNA from bird fecal samples. Can I use ReliaPrep™ gDNA Tissue Miniprep System for that?”

These are just some examples of unconventional sample type inquiries that the Promega Technical Services Team receives regularly from scientists around the world. Many of these inquiries land in the hands of Technical Services Scientist, Paraj Mandrekar (a.k.a. “sample type guru”).

Continue reading “Weird samples? Contact Tech Serv to find the right DNA purification kit for you.”

The Bones Didn’t Lie: DNA Proves Viking Warrior was a Woman

Posted on by Kelly Grooms

There is a grave near the Swedish town of Birka that was the final resting place of a Viking warrior. The grave, called Bj 581, was filled with weapons, including a sword, battle knife, axe, armor-piercing arrows, a spear and two shields as well as a full set of gaming pieces with a board, and the skeletons of two horses—a mare and a stallion. First described in the late 1800s, this grave has been held up as the example of what a Viking warrior burial site would look like because it was so well furnished.

Illustration by Evald Hansen based on the original plan of grave Bj 581 drawn by Hjalmar Stolpe; published in 1889. From Hedenstierna-Jonson, C. et al. (2017) Am. J. Phys. Anthropol. 2017, 1–8.
Continue reading “The Bones Didn’t Lie: DNA Proves Viking Warrior was a Woman”

CRISPR: Gene Editing and Movie Madness

Posted on by Alyssa Bear

There are new developments in genetics coming to light every day, each with the potential to dramatically change life as we know it. The increasingly controversial gene editing system, dubbed CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), is at the root of it all. Harnessed for use in genome editing in 20131, CRISPR has given hope to researchers looking to solve various biological problems. It’s with this technology that researchers anticipate eventually having the means to genetically modify humans and rid society of genetic disorders, such as hemophilia. While this is not yet possible, the building blocks are steadily being developed. Most recently, two groundbreaking studies concerning CRISPR have been released to the public. Continue reading “CRISPR: Gene Editing and Movie Madness”

Promega Third Party Forensic-Grade Certification

Posted on by Promega

Promega has become the first major forensic manufacturer to achieve third party certification of the published ISO 18385 standard to minimize the risk of human DNA contamination in products used to collect, store and analyze biological material for forensic purposes.

On February 2, 2016, ISO 18385:2016 was published as the first international standard specific to the forensic manufacturing community. Since the standard was published, companies have begun to self-declare that they comply with the ISO standard. Some companies have gone a step further and reached out to Certification Bodies to provide an unbiased and independent assessment their compliance to ISO18385 through a third-party audit.

When consumers see an ‘ISO 18385 Forensic Grade’ labeled product, it should inspire confidence that the product was produced in accordance with a minimum set of criteria common to all manufacturers.

So what are you actually getting in a Forensic Grade labeled product? Continue reading “Promega Third Party Forensic-Grade Certification”