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Q&A with John Butler, NIST chemist
Dr. John Butler is a research chemist within the Biotechnology Division at NIST. He has written Forensic DNA Typing: Biology and Technology behind STR Markers (Academic Press, 2001), which received high honors from the British Medical Association Book Competition in November 2001 and is now the leading textbook in the field. President George W. Bush recognized Dr. Butler in July 2002 as one of 60 young scientists to receive the prestigious Presidential Early Career Award for Scientists and Engineers (PECASE). Dr. Butler leads the forensics/human identity testing project team at NIST and has been involved in the field for the past ten years developing new methods and technologies for forensic DNA typing. How did you get involved in the WTC ID project? Due to the nature of the World Trade Center disaster, it quickly became evident that traditional methods for performing DNA typing were not likely to be fully successful in identifying all of the recovered remains. Traditional DNA ID methods depend on the presence of long, intact segments of DNA in order to accurately type the sample. The DNA in many of the samples recovered in this situation were so fragmented that these standard methods were ineffective. In early November 2001, Dr. Robert Shaler, the director of the WTC DNA identification effort, contacted me and asked if I would be willing to develop some new DNA tests to help in the identification effort. I agreed to fast track our research efforts over the next several months and produce some test materials for his laboratory to try by January 2002. Dr. Shaler’s laboratory, New York City’s Office of the Chief Medical Examiner (NYC OCME), is charged with identifying all of the remains by whatever means possible. He had heard me present some of our early research efforts in analyzing small regions of DNA at several scientific meetings. Dr. Lisa Forman from the U.S. Department of Justice’s National Institute of Justice has funded our research efforts in human identity testing at NIST over the past several years, and she gave Dr. Shaler my contact information. I collaborated with Dr. Bruce McCord from Ohio University and one of his postdoctoral students, Yin Shen, throughout December 2001 and January 2002 to produce several new DNA assays, which we termed “miniSTRs” or “miniplexes”. What other agencies and companies are involved? The lead investigative agency in the WTC DNA identification effort is the NYC Office of the Chief Medical Examiner whose forensic biology laboratory is headed by Dr. Robert Shaler. The New York State Police (NYSP) in Albany assists them in the WTC effort. In October 2001, OCME and NYSP asked the National Institute of Justice to bring together a group of experts to advise Dr. Shaler and the NYC OCME’s DNA laboratory and help resolve some of the challenges with this large mass disaster. This group became the WTC Kinship and Data Analysis Panel (KADAP). KADAP is made up of approximately 25 scientific experts who have gathered every other month since October 2001 to work out many of the challenges involved in evaluating and accepting new technologies for analysis of WTC remains. KADAP members include officials from OCME, NYSP, and the New York State Department of Health along with federal employees from U.S. Departments of Defense (Armed Forces DNA Identification Laboratory), Health and Human Services (National Institutes of Health), Commerce (National Institute of Standards and Technology), and the U.S. Department of Justice. In addition, academic researchers from Yale University, Harvard Medical School, Johns Hopkins University, and several other universities are part of KADAP. Several companies are involved in the WTC identification efforts. Scientists from Myriad Genetic Laboratories (Salt Lake City, UT), Gene Codes Forensics (Ann Arbor, MI), and DNA-VIEW (Oakland, CA) have written software to aid in the analysis and matching of genetic data from the WTC victims and their family reference samples. Myriad Genetics ran family reference samples and WTC victim personal effects with traditional short tandem repeat (STR) typing methodologies. The Bode Technology Group (Springfield, VA) has run and continues to test bones from WTC victims using conventional STR typing and miniSTR typing. Celera Genomics (Rockville, MD) has performed mitochondrial DNA sequencing. Orchid GeneScreen (Dallas, TX) is involved in performing single nucleotide polymorphism (SNP) analysis using small sections of DNA. When and why did you first develop your mini-STR approach? I first started working on smaller PCR products for STR markers in June 1997 when I began work at GeneTrace Systems in Menlo Park, California. GeneTrace was trying to develop a new technology for rapidly analyzing STRs with time-of-flight mass spectrometry. Primers were designed as close as possible to the STR repeat regions in order to retain the variability of the STR alleles but reduce the size of the PCR product. The smaller PCR products were necessary to improve the ionization of the DNA for detection in the mass spectrometer. I presented our work in this area at the International Symposium on Human Identification in October 1997 and mentioned then that these primer sets would probably be useful for degraded DNA samples in addition to aiding analysis via mass spectrometry. Full details on this miniSTR work, including these new primer sequences, were published in an October 2001 special report by the National Institute of Justice which funded the work. In late 1999, I left GeneTrace and went to NIST to work as a research chemist. Deciding to pursue this idea of making the STR PCR products smaller for possible application in forensic casework, I put fluorescent dye labels on several of the primers and demonstrated this work in a poster at the October 2000 International Symposium on Human Identification. There was not a lot of interest in our efforts at that time because everyone was so busy working with the new megaplex STR kits. This work however demonstrated that the original primers I had designed could be used with conventional capillary electrophoresis instrumentation. In the summer of 2001, I began collaborating with Bruce McCord at Ohio University on the miniSTR project. When I received the request from Dr. Shaler in November 2001, we were in a good position to accelerate our efforts. We laid out the various miniSTR markers into different combinations we termed “miniplexes” to cover all 13 of the core STR loci. The Ohio University group, also funded by NIJ, began working on the software necessary to make the allele calls (Genotyper macros) while I created the allelic ladders and began testing the new primer combinations on population samples to verify their performance. Materials were sent back and forth between our two laboratories in order to meet our goal of producing materials for OCME by the end of January 2002. We dubbed the materials provided to OCME as the “Big Mini” assay. While “Big Mini” worked in the hands of OCME personnel according to the specifications we provided with it, they wanted the test made more sensitive and to be capable of working robustly on an industrial scale in order to process thousands of samples from the WTC site. These goals went beyond our initial research efforts. But scientists at the Bode Technology Group approached OCME with an idea for scaling up the miniSTR concept. How was your approach modified for the WTC project? In early April 2002, the information and assay design from our miniSTR tests was provided to Dr. Jim Schumm at the Bode Technology Group (BTG) so that their group could scale up our initial work. BTG had contracted with OCME to analyze the remains recovered from WTC victims and was therefore well positioned to run miniSTR assays; Dr. Schumm worked with our data as a framework and building on our foundation constructed two “BodePlexes”. These miniSTR assays incorporate the strategy and many of the same components as we initially developed with our miniplexes at NIST and Ohio University. What other new DNA technologies are being used in the WTC project? OCME has involved multiple approaches to analysis of highly degraded DNA samples to try and recover as much information as possible from the WTC remains. Besides the miniSTR approach, mitochondrial DNA (mtDNA) sequencing and single nucleotide polymorphisms (SNPs) are being used. Celera Genomics (Rockville, MD) is performing the mtDNA sequencing and Orchid GeneScreen (Dallas, TX) is doing the SNP testing.
Family members were contacted shortly after 9/11 and asked to bring in personal effects from victims or to provide biological reference samples. These personal efforts or family reference samples are then processed with DNA typing tests and the resultant profiles are searched against DNA profiles generated from remains recovered at the WTC site in order to make an identification.
I do not know exactly how individual families reacted to receiving notice that their loved one had been identified since I do not interact with the families. Some families are probably grateful to have closure. For others, old wounds may be re-opened. In any case performing the work is important to honor the dead and give solace to the living relatives. On Sept 11, 2002, I was privileged to visit Memorial Park in Manhattan where the remains of the WTC victims are stored. It was a sobering place that caused me to reflect on the blessings we enjoy in this great land. In no other nation on earth would this kind of effort be expended to identify the dead. This effort speaks to the value of each individual in America. Has this project been particularly interesting or satisfying to you personally? Like most Americans immediately after the terrorist attacks of September 11, 2001, I wanted to do something to help our nation. I feel fortunate to have been in a position to be able to assist in a small way with the WTC DNA identification work. It has been rewarding to meet and work with other talented scientists as part of the National Institute of Justice’s Kinship and Data Analysis Panel. The most satisfying thing to me personally is to see the dedication of good people and excellent scientists in this on-going effort. On my laptop computer screen, I have a picture of Ground Zero that I took on the eve of the first anniversary of September 11. It reminds me to never forget the victims of 9/11 and the efforts being put forth to identify them as part of the largest forensic DNA case in history.
Degraded DNA is common to forensic cases and missing persons investigations. Any improvement in this area will be beneficial to the field of forensic DNA typing now and in the future. Improving technology extends the range of cases and the depth of information that may be recovered from old or highly degraded specimens. We will continue to work on improving the miniSTR approach because it does hold promise for aiding analysis of damaged DNA. reated on 5/27/03 |
