Best Evidence: NIST’s John M. Butler on Advances in Forensics

Scientist Interview: September 2011

John M. Butler

Given the parade of such reliably sensational spectacles as the trial of O.J. Simpson in 1995 or the recent proceedings involving the murder conviction of American student Amanda Knox in Italy, not to mention the current abundance of television shows centered around crime-scene investigation, laypersons have by now become familiar with the role of forensic DNA testing—DNA fingerprinting, as it’s popularly known—in criminal cases and the identification of remains.

The methods of using DNA to establish, in effect, "who done it?" or "who is it?" were originally developed by British researchers in the 1980s. Since then, the technology of DNA fingerprinting has been enhanced and accelerated to the point that analyses that used to take weeks are now routinely done in a single working day, while individuals can be identified by ever-smaller fragments of remains—a single hair, a piece of bone.

Among the researchers who have taken the lead in honing the capabilities of DNA analysis is John M. Butler of the National Institute of Standards and Technology (NIST). Recently, this publication’s July/August 2011 survey placed Butler atop the list of high-impact authors in legal medicine and forensic science over the last decade, with 36 papers averaging almost 28 citations each, a considerable number for such a comparatively small field. His 2003 Journal of Forensic Sciences article, for example, “The development of reduced size STR amplicons as tools for analysis of degraded DNA,” has alone been cited more than 100 times (see table below), ranking it among the field’s top-five most cited since 2001.

Butler, 42, received his bachelor of science degree in chemistry from Brigham Young University in 1992 and his Ph.D. in chemistry three years later from the University of Virginia. In the fall of 1995, Butler joined NIST as a postdoctoral fellow. He spent two years in the commercial sector, working for Gene Trace Systems between 1997 and 1999, and then returned to NIST as a fellow and group leader of the Applied Genetics Group in the Biochemical Science Division, where he’s remained.


SW: As you describe it, your experience in graduate school was a fortuitous one and quite different from what most students get to do. How did that come about?

When I applied to graduate school to do forensic sciences, I applied to only three schools: Cornell, because that’s where my father had received his Ph.D.; Northwestern, because they had the first forensic science program in the country; and the University of Virginia, because they had a professor named Ralph Allen who had won many awards from the FBI for his work. And one of my goals at the time was to work at the FBI laboratory, since that was the best in the country in forensic science. When I went to Virginia to visit, Ralph Allen took me to Quantico, to the FBI Academy, where he was in charge of the accreditation of forensic science being taught there. He also told me he could get me into the FBI laboratory as a visiting scientist while I was doing my doctoral work.

So I cancelled my applications to Cornell and Northwestern and went to Virginia. I finished up at Brigham Young in August of 1992, then started in Charlottesville the next month and in May 1993 began working at Quantico, where I stayed for the next two years. I lived at Quantico and worked in their forensic science research unit. And it happened to be right during a critical time when the wave was just breaking on forensic DNA analysis, and I was able to surf that wave and help bring in my interest in instrumentation and developing new technologies.

SW: You say you “caught the wave” of forensic DNA analysis. What was that wave at the time, and what role did you play?

That was really when short tandem repeats—STRs, the technology used today for DNA testing—was just being developed. And I was working, from an analytical chemistry standpoint, on doing a better job of measuring and analyzing DNA in an automated fashion with instrumentation. Until then, everybody had been running slab gels, which are just like big things of Jell-O. It wasn’t very automated. You had to load the gels by hand, and turn off the voltage before the DNA bands ran off the end of the gel. It was very difficult to scan and get quantitative data. So there were a lot of steps in this method that you couldn’t do in an automated fashion.

Highly Cited Papers by John M. Butler & Colleagues,
Published Since 2002

(Listed by citations)
Rank Papers Citations
1 J.M. Butler, Y. Shen, B.R. McCord, "The development of reduced size STR amplicons as tools for analysis of degraded DNA," J. Forensic Sci., 48(5): 1054-64, 2003. 104
2 L. Gusmao, et al., "DNA Commission of the International Society of Forensic Genetics (ISFG): An update of the recommendations on the use of Y-STRs in forensic analysis," Forensic Sci. Intl., 157(2-3): 187-97, 2006. 99
3 J.M. Butler, et al., "A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers," Forensic Sci. Intl., 129(1): 10-24, 2002. 92
4 P.M. Vallone, J.M. Butler, "AutoDimer: a screening tool for primer-dimer and hairpin structures," Biotechniques, 37(2): 226-31, 2004.   90
5 J.M. Butler, "Genetics and genomics of core short tandem repeat loci used in human identity testing," J. Forensic. Sci., 51(2): 253-65, 2006.    78

I became an advocate for a new technology called capillary electrophoresis. My thinking was, "Here’s this new way to do things. It’s automated. It has much better precision and accuracy. You can use a smaller amount of sample. It’s more sensitive." That’s what I brought to the table and what I worked on. And I developed a lot of methods that the FBI and others are still using. I worked directly with Bruce McCord, an analytical chemist, and Bruce Budowle, who was leading the effort with DNA at the FBI. Dr. Budowle had helped with the development of restriction fragment length polymorphisms—RFLP, the predecessor of STRs—which the FBI started using in 1988. And it was through my work with Bruce McCord that I met Dennis Reeder, who at that time was the group leader of DNA technologies at NIST, and he asked me to come to work there and apply for the post-doctoral program that I eventually got.

SW: Your most influential research is on mini-STRs. What exactly are they, and what makes them so important?

In a mass spectrometer, the challenge is to get a sample from either a liquid state or a solid state into a gas phase, so that it will work inside a vacuum, inside of the flight tube of the mass spectrometer. To get that to happen with DNA, you have to make the DNA molecules as small as possible. What varies between people in a DNA profile is found in these short tandem repeats. You have a sequence, like GATA, that’s repeated over and over again, 10 or 12 times. What we did during the two years in the late 1990s that I worked at a company called Gene Trace is put primers next to the repeats, as close as we could, and make these small amplicons—PCR (polymerase chain reaction) products.

When I came back to NIST around late 1999, I was contemplating projects that might be useful to pursue, and I thought about putting fluorescent dyes on these small PCR primers, to make small amplicons, thinking they might work well with degraded DNA, with DNA that’s been fragmented into smaller pieces. So mini-STRs are just a smaller version of STRs.

Let me back up for a minute: The reason that RFLP technology didn’t work very well is that it required a lot of DNA to do an identification. It required DNA that wasn’t damaged or broken apart. It worked via the use of DNA technology—restriction enzymes—to cut DNA at specific locations, and then you had a probe that would bind to the DNA, to a long repeated sequence called a variable number tandem repeat.

The problem was that you couldn’t automate that technology. It was essentially an art form to get good results. There were issues of quality control, and you couldn’t run a lot of samples with RFLP. It was very slow, taking weeks to get a result. In the O.J. case, for instance, it took about eight weeks. With STR typing, you now can get results in about eight hours, start to finish. So it’s a major change in terms of speed, also in the throughput. You can run a lot more samples in parallel now, and with capillary electrophoresis you can run them in an automated fashion

Mini-STRs were just smaller versions of STRs. You could use even less DNA. When 9/11 happened, that gave us a real motivation to get this going. Working with Bruce McCord, we further developed the methods to help with the World Trade Center investigation. The need there was to analyze samples that had been very badly damaged. As it turned out, the last 20% of people identified from the World Trade Center were identified because of mini-STRs—the most damaged DNA from which they could get a result.

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