Mar 17 2021

Obtaining DNA Profiles from Rootless Hairs

Throughout the years, conventional wisdom has said that rootless hair shafts do not contain DNA, but this couldn’t be further from the truth. In this interview, Ed Green, Professor at the University of California Santa Cruz and co-founder of Astrea Forensics, discusses how his company is generating DNA profiles from rootless hairs and how this work is assisting forensic genetic genealogists in closing cold cases. He also talks about the case that led him to work on forensic cases, how a news story led him to work with Barbara Rae-Venter, and his latest research in comparing the genomes of humans to their Neanderthal ancestors.

For more on his work with Neanderthals, watch our previous interview with Ed: Neanderthal Genes in Modern Humans (https://youtu.be/9Dy1HCWwzds). If you are interested in learning more about forensic genetic genealogy, we invite you to watch our playlist: https://www.youtube.com/watch?v=32SEh8VO–k&list=PLll6Q7aUAtbAA_oqIyS9HuTSPJu95lSjr.

Transcript:

Laura: Hi, thank you for joining us for the International Symposium on Human Identification’s video series for this year. Joining us today is Ed Green. Ed is a Professor of Biomolecular Engineering at the University of California Santa Cruz and a co-founder of Astrea Forensics. Ed, thank you for joining us today and why don’t you start by telling us a little bit about Astrea?

Ed: So, Astrea is a small operation that was born out of the work that my lab started doing in forensics, mostly from DNA from rootless hairs. There are, as you know, I’m sure, there are many crime scenes, many cases, where the only evidence that might yield DNA is rootless hair. That’s been a very challenging sample for most forensic assays, and we’ve developed some great technology for getting DNA out of rootless hair, converting it into sequencing libraries, that are used to learn the DNA sequence information, and then, using this information to get genetic profiles of a different type – SNP profiles that can then be used for forensic genetic genealogy. That part of it, we don’t do at all. We simply get the genotype files. This, when we first kind of put all of this together, there was a trickle of cases coming in that we could handle in the lab, but it became clear over a little bit of time that there’s just no way to do this in an academic lab in a way that is reasonable and responsive and professional for the demand that was there. So, we moved that operation into a commercial entity (Astrea Forensics) and have 10 fantastic people that do this in a much better way than we could really do in an academic lab. It was kind of a little side project in the back of the lab and now it’s done in a way that we can all be happy with and rely on.

Laura: Ok, that sounds very exciting. Working with rootless hair samples – let’s talk a little bit about that. What are some of the challenges that are associated with that?

Ed: Sure, so rootless hair samples are perhaps one of the most misunderstood sample types in forensics. If you watch the tv shows, they will say that there’s no DNA in hair shafts, and that is actually not true at all. It couldn’t be further from the truth, but there’s a reason that there’s this misconception out there, and I think most folks in the forensics community know this. For a long time, and still today, the most common forensics assay is a PCR-based assay to amplify STR markers. In fact, in the field of forensic genetics, a genetic profile, or a DNA profile, or a fingerprint, is pretty much synonymous with this assay. There’s one single assay looking at STR lengths from PCR. And it turns out the DNA that you can get from hair shafts generally fails on this assay or just barely works. Often, working just well enough to let you know that there’s some DNA in there, but we’re not really getting a useful profile or it just fails entirely. So, that observation over and over and over again kind of led the conventional wisdom to be that there’s not much DNA there or there’s not much DNA there. Turns out, that’s just not true at all. It’s just completely, 100% false. There’s plenty of DNA there. It’s just in pieces that are too short to do PCR amplification on, so you have to do something that. That something else is something that we’re very interested in. I run a lab that works with ancient DNA. DNA that may be tens of thousands of years old and the DNA is there in small quantities and very short and fragmented. That’s how DNA is in hair. So, we’ve got this great technology for converting short, small amounts of DNA into libraries that can be sequenced. That (libraries that can be sequenced) sounds cryptic. What is that? Is that a difficult thing? Conceptually it’s very simple. A library that can be sequenced just means that you stick adapters on the end. Little pieces of DNA at the beginning and little pieces of DNA at the end, so that you can go on the sequencer, and that’s it. We have a very efficient way of slapping those adapters on the ends so that it can be sequenced, and then from this information, reading the DNA sequence, make a genotype file, and then the magic people downstream from us that look at this and build out trees, and all of that happens, and the police work happens. But, that’s what our part is. Getting DNA out of rootless hairs. What was the question? Oh it was something about getting DNA out of rootless hairs. Small amounts, super fragmented, but absolutely there.

Laura: That is fascinating, and yes, you were absolutely answering the question. I’d also love to hear how it’s been applied to particular cases (if you can talk about it). I know we interviewed Barbara Rae-Venter last year about her work on the Golden State Killer case, and I think you work together?

Ed: Yeah, Barbara and I do work together. We’ve worked together on lots of cases. She’s fantastic. More than even working together, she is kind of why we’re doing this at all. I got into forensics kind of sideways. There was a little girl who was dug up in a casket underneath a house, where some homeowner was doing some work, they were out of town, and the construction workers came in to dig a post hole and hit a casket. They pull this thing up, and who is this girl? What is going on? It was a super interesting, kind of long ordeal. Not really a forensics case. It was someone who died tragically, but not really criminally. They assembled a team, and brought us in to do the hair work (try to get DNA out of her hair) and hopefully that would be useful in trying to figure out who she was. Super long project. Alyssa Davy is the person who kind of brought all this together, figured out who the girl was. She brought a living relative in and tested the DNA, and that was all great. So, we reburied this little girl. Turns out she had died in 1876, and they buried her in a cemetery in San Francisco. When they moved all of the bodies out of all of the cemeteries down to Baily City, they just missed one. It was a huge operation and they were just not as thorough as they should have been, so missed this little girl. This was kind of an interesting project. It was on the local news out here. Turns out that “local” is the same for me and Barbara (central coastal California). She saw that and in typical Barbara fashion just called me on the phone and said something to the effect of, “That was cute. Would you like to do real work?” We had a conversation and she got me involved and it’s been great. It’s been great working with Barbara. We’ve done many cases together. When I say together, we do a very defined part of it and have a very defined end point. She has a very defined part of it and doesn’t really overlap with our part at all. We get it right up to the genotype file and then deliver it to law enforcement or Barbara (whoever the genealogist is that’s handling it), and then they go do their thing. It’s been great. Barbara is wonderful.

Laura: That’s fantastic. I love that story about how she called you. What a great partnership and a wonderful way that it started.

Ed: Yeah, and if you talk to her, she’ll say that she discovered me, which is oddly flattering, you know? To be a person who was discovered. Anyway, yeah, I like working with Barbara.

Laura: I love that! Well, we discovered you, I know, at least a couple of years ago. I know we talked to you about some work that you were doing with Neanderthal genes. Is there anything you want to talk about? Any updates there? Does that influence anything that you’re doing today? Was that entirely separate?

Ed: Yeah, so a long time ago, I worked my whole life was getting DNA out of Neanderthals and doing work on that. My post-doc work. We still have an interest in this for sure in the lab. The big thing we’re doing now, and we’ll have a paper soon, is looking at human genetic variation and Neanderthal genetic variations and pinpointing places in the human genome where we know no one has the Neanderthal gene. It’s kind of known that humans and Neanderthals admixed. Many humans carry a legacy of this admixture. Genes from Neanderthals in particular places. No one has too much of this, and it’s kind of randomly scattered across the genome. The different Neanderthal bits. The question that we want to answer was well, what about the places where nobody has the Neanderthal gene? What genes are these? We’re operating under the hypothesis that the places where nobody has what Neanderthals had on offer might underlie the important human-specific genes. The things that make us uniquely human, and when Neanderthal genes came back in, regions of the genome, that maybe were different. Maybe we had some novelty there that their version wasn’t good enough anymore. So maybe we could pinpoint these. So, that’s a computational machinery that finds these in a very efficient way, and a big new interest in the lab is working with these (and this is going to be weird) brain organoids. These little brains in a dish that you can grow, and using CRISPR technology, to (when you find these regions where humans are different from all Neanderthals) go in and snip that out and snip in the Neanderthal version, the archaic version, and see how that changes the little brain in a dish.

Laura: Wow, that is like next level. It sounds crazy!

Ed: Well most of the super cool parts that are done with collaborators. People who are really expert in those parts of it, but it’s a good team. It’s going to be a fun project to work on.

Laura: That’s very exciting. Maybe that segues into kind of the final, wrap up question. What’s next for you? What do you see for the future in your field? Where is this all going? And we’re asking you to guess a little bit.

Ed: Yeah, well like Yogi Beara said, “It’s hard to predict things, especially about the future.” I don’t know. I just hope that it doesn’t all blow up. Forensic genetic genealogy; I’ve seen first-hand how this can really be a force for good and solve really important cases. Cases that really need to be solved. It can do that. And, with that power, we head down a path that kind of has blinders on, but it’s possible to do that, so let’s do that. There are bigger issues. There are deeper issues about the databases, how they are accessible, how they ought to be accessible, and I don’t claim to have any deep wisdom on this, but generally it’s good if policy doesn’t get out too far ahead of society’s collective understanding of what’s going on. We get in trouble when that happens. When either scientists or policy makers or anybody really, who has their hand on the lever of power, does something beyond everybody else’s ability to understand what’s going on. We should try to do things like this. Do outreach explaining the technology, explain what’s going on. Good and bad. Worts and everything. And then let us collectively as a society figure out how this ought to go. What should we do? And step slowly. I know that people (practitioners of this) get frustrated when lay people say something that betrays misunderstanding, and then they say, “well, why should we listen to people who don’t know anything about this?” The other side of this is the laypeople who don’t know anything about this are eventually going to decide how this is going to be done or not, so let’s just all be on the same team like we are all on the same team. We all want the same team. Everybody wants this to turn out well. Everybody wants there to be good, fair, non-abused tools of law enforcement to do their job. I think that we can get there as long as people continue to have patience and continue to make this an effort that we’re all participating in, and we’re all thinking about, and can all weigh in on and no one feels (rightly or wrongly) that they are being taken advantage of.

Laura: That is a fantastic answer, and I think especially perfect, given the world that we’re living in right now with COVID and everything that we’re dealing with.

Ed: Yeah, can we live in a different world? I’m kind of getting tired of this one.

Laura: I know. I miss people.

Ed: Yeah, Zoom’s horrible.

Laura: What can you do?

Ed: Yeah, what can you do?

Laura: Ed, thank you so much for talking with us. We really appreciate it.

Ed: Oh this was fun Laura, anytime.

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