The Clues in Your Hair: An Introduction to Forensic DNA Analysis

By Jake Beatie

-Featured Image by Carmen Rivera

[Content Warning: Mentions serious criminal behavior (sexual violence & murder) and handling of human remains.]

It’s mid-November in 1985. A hunter stumbles across a large metal drum while strolling through Bear Brook State Park in Allenstown, New Hampshire. Just curious enough to peep inside, the hunter is met with a grizzly sight. The decomposing, plastic-wrapped bodies of two females—one adult and one child—were contained. Fifteen years later, another barrel hiding the bodies of two more children was found. They were completely skeletonized, sitting no more than 300 feet away from the location of the first barrel. Time and the elements had whittled away at what little evidence police had before them, and the identities of the victims remained a mystery. That is, until new developments in extraction techniques allowed for genetic researchers to sequence the DNA of the deceased from the remnants of their hair, a source previously unthinkable to utilize effectively. All four bodies were identified and tied to Terry Peder Rasmussen as the killer. Of the victims, three of them were blood-related (one mother and two daughters), and the fourth was a daughter of Rasmussen.^1,2

OUR INCREASING FASCINATION WITH FORENSIC SCIENCE

The development of criminal law enforcement and civilization go hand-in-hand. As society progresses, the nature of crime becomes increasingly complicated, and thus more advanced techniques in producing and handling more  intricate pieces of evidence are necessary. Known as the father of modern forensic science, Edmond Locard’s crime scene methodology set the precedent for crime scene investigation globally, yet the whole field has been developing for quite literally millennia. Autopsies were introduced 4000 years ago with Egyptian mummification, and determining the cause of death for forensic cases became a common practice in 1200s China. In fact, Collected Cases of Injustice Rectified by physician Song Ci is often cited as the first example of forensic science literature.³

Culturally speaking, the (dramatized) plights of the long arm of law and order are as popular as ever with the myriad of true crime television shows, novels, and podcasts that seek to bring the administration of justice to the comfort of our own homes. This fascination can go so far as to assist with convictions in the real world; a serial rapist was convicted in the town of Chippenham, England in 2011 thanks to a victim making the savvy move to intentionally leave a lock of hair and some saliva in the back of the assailant’s car.⁴

Contrary to that last example, our fixation on using what we see or hear in our favorite crime series doesn’t always lead to positive outcomes. A hotly-debated phenomenon in legal justice is the ‘CSI effect’, which details how a jury’s perception of a criminal case is skewed due to what they’ve seen in fictionalized crime media.⁵ Particularly, a juror that watches crime shows is more likely to see forensic evidence (especially DNA evidence) as infallible, to the point where they might be hesitant to convict an otherwise guilty suspect.⁶ The public has come to love forensic evidence, and they put it on this grand pedestal without really understanding how a sample is used, or what avenues researchers take to obtain information or leads from that sample.

Years of research and technological advancements have allowed us to truly unlock the potential of trace DNA samples. Without the ingenuity of countless scientists, technicians, and engineers devoted to creating these avenues, forensic DNA evidence wouldn’t have nearly the acclaim it has today. Hopefully, by the end of this piece, you can look back on your favorite CSI: Las Vegas episode and think about just how far science has come to be able to fool-proof that one piece of DNA evidence.

GENETICS VS. GENOMICS: A MACRO-LEVEL DEVELOPMENT

Before we get into the nitty-gritty of how the law can harness the power of DNA evidence, we need to first understand what people are talking about regarding genetics. Stripped down to its very basics, genetics is the study of heritability. 

The origins of the field trace back to the Austrian monk Gregor Mendel, who famously took note of the physical traits of pea plant offspring such as seed color, shape, stalk height or flower color. After calculating the frequency in which specific physical traits, also known as phenotypes, Mendel assigned pairs of alleles—representing the genetic component of heritability—to each phenotype. When they combine in specific ways, they can give rise to different traits. From these relationships, Mendel hypothesized the basic rules for how alleles are passed to offspring. Modern genetics takes what we learned from Mendel and aims to effectively answer several questions about the interactivity of our genes. How does a recessive allele lead to an inherited disease such as sickle-cell anemia? How does the distance between two genes affect how often they’re expressed together? How is the expression of our genes affected by external factors through epigenetics? 

Yet, when dealing with ALL of the genes within an organism—the genome—this becomes quite an ordeal to keep track of. It begs the question, how do we create, understand, and manage a map as massive as the entire library of genes within a person?  

To solve this problem of the genome, we then turn to its respective field: genomics. Genomics isn’t an entirely new concept; botanist Hans Winkler came up with this term to describe a huge genetic library shortly after the geneticist Wilhelm Johannsen coined the terms for gene, genotype (the genetic makeup that produces physical traits), and phenotype.⁷ We understood the idea of the genome, but simply lacked the means to make these maps. Genome projects only started taking off in the late 20th century, as the first bacterial genome was sequenced in 1995, followed by the genome of budding yeast in 1996, leading eventually to the first draft of the human genome in 2003.^8,9 This draft has since been completed from one end of the genome to the other end thanks to the work of UCSC’s own Karen Miga, Ph.D., and her team of the Telomere-to-Telomere consortium.¹⁰ By having these baseline templates, scientists from all kinds of disciplines—whether it be medicine, counseling, or forensics—can create limitless research opportunities pertaining to the information that lies within us.

FORENSIC GENETICS: WE’VE GOT A MATCH!

One of the major issues that originally limited the usefulness of DNA evidence was the massive amount of sample you needed to get anywhere. A bloodstain roughly the size of a quarter and literal buckets of salt solution were necessary to process a decent sample!⁴ However, this all changed during one biochemist’s drive down a California highway—a quick stroke of genius had eventual Nobel prize laureate, Kary Mullis, thinking what would happen if you could have the DNA ‘reproduce the hell out of itself’.⁴ This idea birthed arguably the most important technique used by molecular biologists today: the polymerase chain reaction, or PCR.

Not only did crime scene investigation change dramatically, but the entire realm of molecular biology was shaken upon Mullis’ invention (I’m sure you’ve heard of, or have even taken, a COVID PCR test recently). The ability to take even the smallest DNA sample and replicate it hundreds of millions of times is paramount to not only expanding the amount of research that can be done on that single sample but also greatly reducing the time it takes to obtain these several copies. For our sake, this brings the time to a potential conviction (or exoneration) down from days to mere hours. The best part? PCR is deceptively simple; the whole process is as easy as 1, 2, 3:

1. The template piece of DNA is treated at a high enough temperature (~90^oC) to separate the two strands.
2. At a lower temperature (of ~50-60^oC), a short, complementary single-stranded DNA piece known as a primer then attaches to the now-opened single template DNA strand.
3. Raising the temperature (to ~70^oC) allows a new strand to form, using an enzyme called polymerase that reads the template strand and prints its complement (specifically, a polymerase taken from a bacteria that can withstand greater temperatures).

Repeat these three steps, and soon enough you’ll have as much DNA as you could possibly need.

So now that we have a surplus of DNA copies, how can we tell my DNA apart from yours? An aspect of human genetics that proves very useful for forensic research is short tandem repeats, also known as STRs. Simply put, STRs are classified as repeating sequences of (around 2-8) DNA base pairs that appear all along the genome. The one key thing to note about STRs that makes them crucial for identification purposes is that they are conserved between generations.

So, if you had a chain of 20 repeats of the sequence “GATTACA” in your DNA, one of your parents is highly likely to have that same 20 repeats. Compare that to your friends or your coworkers; they may only have 10 or 15 of that same sequence. Some specific locations along chromosomes, known as gene loci, contain more highly variable numbers of tandem repeats (VNTRs). Databases such as the FBI’s Combined DNA Indexing System (CODIS) use these VNTR-containing loci to keep a record of nationwide DNA profiles (CODIS utilizes 20 different loci, which increased from 13 at the start of 2017).¹¹ 

It should be said that the United States’ CODIS system relies on stored genetic data from convicted criminals, and while this is still a LOT of information (more than 14 million profiles as of September 2020), this does limit the usefulness of CODIS when it comes to identifying victims and first-time offenders.¹² There’s another glaring issue when it comes to the forensic analysis of PCR products. To be able to reproduce and use a DNA sample from PCR, not only do you need long enough DNA pieces in your sample (greater than 100 base pairs, typically), but you need that sample to be of high quality.¹³ Given the potential nature of a crime scene, high enough quality just isn’t feasible in some cases. And so, the work to fool-proof DNA evidence continues.

Of course, since the days of PCR we’ve tirelessly aimed to improve our sequencing techniques. Whereas PCR is great at making several copies of a small segment of DNA, whole-genome sequencing (WGS) techniques aim to obtain the entire genetic map of an organism. The drive to obtain more information from less sample brings us to the race for better WGS techniques, with biotech giant Illumina leading the charge. The company’s ‘sequencing by synthesis’ technology allows for the production of a map as large as a human genome to be produced in a matter of hours. Comparing WGS results to a master copy like the Human Genome Project sequence we discussed earlier, you can identify individuals even more accurately than through STR analysis. WGS allows researchers to compare even singular bases between individuals and make note of the differences in the sequences. Genetically, this process entails observing single nucleotide polymorphisms (SNPs), and this is the key to expanding the search for an identity that failed to be revealed through traditional forensic testing. Direct-to-consumer genetic tests like the ones you can purchase from 23andMe utilize this very principle in order to determine a whole slew of inheritable information, such as ancestry, behavioral traits or physical health. Whereas traditional forensic testing generally utilizes PCR and STR analysis mentioned above, advancements in WGS technology opened up the emergent field of investigative genetic genealogy (IGG). The use of IGG comes after initial screening (against the most immediate suspects first, then the CODIS database) fails to produce a proper lead. This is where genealogy databases—like 23&Me mentioned earlier—come into play. While we won’t touch too much on the legal issues that could (and have) arisen from allowing law enforcement to access user profiles, there are really two services today that permit the use of user data for investigative purposes: FamilyTreeDNA and GEDmatch.^{14, 15}

UCSC’S CRIME-FIGHTING MACHINE

Now, remember that horror story from the start of this article? What if I told you that this case (and many others like it) was cracked right on this very campus? That’s right; the work of Dr. Ed Green and the UCSC Paleogenomics Lab is geared towards cracking even the coldest of cases. Dr. Green notably worked on the identification of Edith Howard Cook, the corpse of a 19th-century three-year-old found in the basement of a San Francisco home in 2016.¹³ His application of ancient DNA extraction techniques (which allowed him to sequence the entire Neanderthal genome in 2010) can be used for forensic investigations! The success of the Edith Howard Cook case caught the attention of genetic genealogist Dr. Barbara Rae-Venter, who recruited Green to work on the Bear Brook case.¹⁶ 

Within those few years, Green’s laboratory and expertise were being requested for forensic work left, right, and center, which as you could imagine might get a little in the way of the other objectives of the lab. The Paleogenomics lab needed to expand, and so Astrea Forensics was born in 2019. Now, under the direction of Dr. Kelly Harkins-Kincaid, a postdoctoral researcher from the Paleogenomics Lab, Astrea continues to improve the technology necessary to solve even the most uncertain of mysteries. Since its foundation, Harkins-Kincaid and Astrea have been involved in over 95 cases, including some from clients such as the Santa Cruz Sheriff’s Department and the DNA Doe Project, a Sebastopol-based genetic genealogy nonprofit that helps with identifying unknown remains on a national scale.¹⁷ 

So just take a look at that. We started with needing buckets of salt and large drops of blood and worked all the way down to extracting DNA from even the smallest strands of hair. And we’re far from done with improving; WGS technology is always looking to be more efficient, whether it be through even faster and cheaper sequencing, or expanding from where we can extract a DNA sample. By streamlining this whole process, families and loved ones can more quickly be reunited with their lost ones, and criminals can swiftly be brought to justice. 

References

1. Gast, P. (2013, June 16). Cold-case murders of 4 females brought back to life by new images, DNA tests. CNN. Retrieved April 10, 2022, from https://www.cnn.com/2013/06/14/us/new-hampshire-bodies-mystery/ 
2. The Doe Network International Center For Unidentified & Missing Persons. (2013, July 26). 799UFNH – Unidentified Female. Doe Network. Retrieved April 10, 2022, from https://www.doenetwork.org/cases/799ufnh.html 
3. Incognito Forensic Foundation . (2018, August 14). Exploring the History of Forensic Science through the ages. IFF Lab. Retrieved April 1, 2022, from https://ifflab.org/history-of-forensic-science/ 
4. McDermid, V. (2016). Forensics: What Bugs, Burns, Prints, DNA, and More Tell Us About Crime. Grove Press. 
5. Cornell Law School. (2021, June). CSI Effect. Legal Information Institute. Retrieved April 8, 2022, from https://www.law.cornell.edu/wex/csi_effect
6. Mandal, A. (2010, March 29). DNA evidence often overwhelms jurors to convict wrongly says research. News-Medical Life Sciences. Retrieved April 8, 2022, from https://www.news-medical.net/news/20100329/DNA-evidence-often-overwhelms-jurors-to-convict-wrongly-says-research.aspx 
7. Weissenbach, J. (2016). The rise of Genomics. Comptes Rendus Biologies, 339(7-8), 231–239. https://doi.org/10.1016/j.crvi.2016.05.002 
8. yourgenome. (2021, July 21). Timeline: Organisms that have had their genomes sequenced. yourgenome. Retrieved April 2, 2022, from https://www.yourgenome.org/facts/timeline-organisms-that-have-had-their-genomes-sequenced 
9. National Human Genome Research Institute . (2021, February 12). Human Genome Project Timeline of Events. NIH. Retrieved April 10, 2022, from https://www.genome.gov/human-genome-project/Timeline-of-Events 
10. Stephens, T. (2022, March 31). First complete, gapless sequence of a human genome reveals hidden regions. UC Santa Cruz News. Retrieved April 2, 2022, from https://news.ucsc.edu/2022/03/t2t-genome.html 
11. Federal Bureau of Investigation . (n.d.). Frequently Asked Questions on CODIS and NDIS. FBI. Retrieved April 9, 2022, from https://www.fbi.gov/services/laboratory/biometric-analysis/codis/codis-and-ndis-fact-sheet 
12. Federal Bureau of Investigation. (n.d.). CODIS – NDIS Statistics. FBI. Retrieved April 16, 2022, from https://www.fbi.gov/services/laboratory/biometric-analysis/codis/ndis-statistics 
13. Harkins-Kincaid, K. (2021). Cold Case Files: How Astrea Forensics Empowers Law Enforcement [Webinar]. QB3.
14. Guerrini, C. J., Wickenheiser, R. A., Bettinger, B., McGuire, A. L., & Fullerton, S. M. (2021). Four misconceptions about investigative genetic genealogy. Journal of Law and the Biosciences, 8(1). https://doi.org/10.1093/jlb/lsab001
15. Harkins-Kincaid, K. (2020, November). Solve Cold Cases with DNA from Rootless Hair using Genetic Genealogy. The ISHI Report. Retrieved April 17, 2022, from https://promega.foleon.com/theishireport/november-2020/solve-cold-cases-with-dna-from-rootless-hair-using-genetic-genealogy/ 
16. Murphy, H. (2019, September 16). Why This Scientist Keeps Receiving Packages of Serial Killers’ Hair. New York Times. Retrieved April 9, 2022, from https://www.nytimes.com/2019/09/16/science/hair-dna-murder.html 
17. York, J. A. (2021, November 18). Made In Santa Cruz County | Astrea Forensics makes the untraceable traceable. Santa Cruz Sentinel. Retrieved April 14, 2022, from https://www.santacruzsentinel.com/2021/11/18/made-in-santa-cruz-astrea-forensics-makes-the-untraceable-traceable/