Our Research

In addition to genomic methods we have been investigating the potential of epigenetic procedures in DNA typing. Epigenetic processes control gene expression and can be influenced by environmental factors as well as other factors. Initially we studied the application of epigenetics for trace determination of body fluid type. Determination of the type of DNA at a crime scene is critical in certain forensic cases such as sexual abuse, as the type of DNA present can indicate the difference between a handshake (skin) or an assault (blood or semen). We have also worked on the determination of a suspects age, smoking status and more recently have begun investigating effects of diet and drug abuse. We utilize a variety of genomic tools in this work including massively parallel sequencing, pyrosequncing, microfluidic electrophoresis and bisulfite modified PCR.

Alghanim, H.; Wei, W, and McCord, B. A DNA methylation based assay for the determination of smoking status using pyrosequencing, Electrophoresis 2018, 39, 2806–2814.

Alghanim H, Antunes J, Silva DSBS, Alho CS, Balamurugan K, McCord B. Detection and evaluation of DNA methylation markers found at SCGN and KLF14 loci to estimate human age. Forensic Sci Int Genet. 2017 Nov;31:81-88

Madi,T.; Balamurugan,K; Bombardi,R.;Duncan, G.; McCord,B. The determination of tissue specific DNA methylation patterns in forensic biofluids using bisulfite modification and pyrosequencing Electrophoresis, 2012, 33(12) 1736-1745.

We can also use real time PCR for DNA quantification and use melt curve analysis for epigenetic tissue typing. The figure below demonstrates how we utilize real time PCR with melt curve analysis to detect trace levels of semen on forensic samples and discriminate it from other body fluids using epigenetics with bisulfite modified PCR.

Joana Antunes, Deborah S.B.S. Silva, K. Balamurugan3; G. Duncan, C. S. Alho2, B. McCord. High Resolution Melt analysis of DNA methylation to discriminate semen in biological stains, Analytical Biochemistry, 2016, 494: 40-45

Lee, S.; Buel, E.; McCord, B., Advances in Forensic DNA Quantification: A Review, Electrophoresis, 2014, 35, 3044-3052

Opel, Kerry L.; Fleishaker, Erica L; Nicklas, Janice A.; Buel, Eric; McCord, Bruce R. “Evaluation and Quantification of Nuclear DNA from Human Telogen Hairs,” J. Forensic Sciences, 2008, 53(4) 853-857

Forensic DNA analysis is one perfect example of a procedure which can be reduced in size. The separation technique, capillary electrophoresis is highly efficient and easily converted from capillary to chip detection schemes. . By investigating different injection procedures and optimizing the polymer sieving buffers used to separate the DNA we begin to develop new separations. Under the right conditions and chemistry, separations taking 35 minutes on a capillary based sequencer can be placed on a chip and run inless than 2 minutes Another important step is developing appropriate extraction procedures and coupling high speed PCR. We are currently working to develop fast PCR and utilizing a variety of rapid and direct procedures for the extraction from blood and saliva samples. At present we can perform a direct PCR with no extraction in 10 minutes and amplification of extracted and purified DNA in 6 minutes.

Gibson-Daw, G., Albani, P., Gassmann, M., McCord,B. Rapid microfluidic analysis of a Y-STR multiplex for screening of forensic samples, Anal Bioanal Chem 2016. doi:10.1007/s00216-016-9950-9.

Aboud, M.;Gassmann, M.; McCord, B., Ultrafast STR separations on short channel microfluidic systems for forensic screening, and genotyping, J. Forensic Sci, 2015, 60(5), 1121–1390.

Massively parallel sequencing is a disruptive technology in the forensic world. It greatly increases the information you can obtain for human identification from miniscule forensic stains. In the past once DNA was extracted, an examiner would have to choose what kind of assay would take place- autosomal STRS, Y STRs, phenotypic SNPs, ancestral SNPs etc. With this new technology, it is now possible to simultaneously perform all these assays and more. We are currently investigating methods for epigenetics, genomics, and metagenomics using instruments such as the Qiagen GeneReader, the Illumina FGX and the Oxford Nanopore Minion.

Brian A. Young, Katherine Butler Gettings, Bruce McCord, Peter M. Vallone. Estimating Number of Contributors in Massively Parallel Sequencing Data of STR loci, FSI Genetics, 2019, 38, 15–22.

Bruce McCord, Quentin Gauthier, Sohee Cho, Meghan Roig, Georgiana Gibson-Daw, Brian Young, Fabiana Taglia, Sara Casado Zapico, Roberta Fogliota Mariot, Steven B. Lee, and George Duncan, Forensic DNA Analysis, Analytical Chemistry, 2019, 91 (1), pp 673–688

A key issue in understanding how to produce fast and efficient DNA typing is understanding the effects of inhibitors. Forensic DNA samples can be affected by coextracted materials (PCR inhibitors) present at a crime scene. Using Multi plex PCR amplification and real time PCR with high resolution melt capability, we are examining a variety of PCR inhibitors with respect to DNA sequence and polymerase binding. We model their effects and work on better ways to reduce inhibition to permit forensic scientists to improve the quality of their data. For example the two PCR inhibitors shown below originate from soil (tannic acid) and from biological fluids (bile salts) nut have very different effects of PCR. Tannic acid inhibits the polymerase affecting the slope of the amplification curve and generally affecting the larger ampicons. Bile salts inhibit the DNA template, having more sequence specific effects and reducing the availability of the template (affecting Ct value but not the amplification curve.)

Lilliana I. Moreno and Bruce McCord, Understanding metal inhibition: The effect of copper (Cu2+) on DNA containing samples and a proposed solution, Forensic Chemistry, 2017, 4, Pages 89–95.

Pionzio, A. ; McCord, B. The Effect of Internal Control Sequence and Length on the Response to PCR Inhibition in Real-Time PCR Quantitation, FSI: Genetics, 2014, 9, 55–60.

Thompson, R. Duncan, G. McCord, B. An investigation of PCR inhibition using Plexor® based quantitative PCR and short tandem repeat amplification, J. Forensic Sci. 2014, 59(6), 517-529.

Maribel E. Funes-Huacca1, PhD; Kerry Opel2, Ph.D; Bruce McCord1, PhD. A comparison of the effects of PCR inhibition in Quantitative PCR and forensic STR Analysis, Electrophoresis, 2011, 32(9), 1084–1089.

Opel, K.; Chung, D.;McCord, B. A Study of PCR Inhibition Mechanisms Using Real Time PCR, J. Forensic Sci, 2010, 55(1) 25-33.

There is a large backlog in the USA in the processing of rape kits following sexual assaults. We are using high pressure cycling, magnetic bead extraction and chemical digestion to selectively recover male and/or female DNA from these kits in order to improve sample processing and speed up data recovery.

Martinez V, Nori D, Dimsoski P, McCord B. Pressure-based alkaline lysis with immunocapture, a method for enhanced recovery in differential extraction. Electrophoresis. 2017 Nov;38(21):2777-2785

Nori, D.V. & McCord, B.R. The application of alkaline lysis and pressure cycling technology in the differential extraction of DNA from sperm and epithelial cells recovered from cotton swabs, Anal Bioanal Chem 2015, 407, 6975-6984.

Recently we have begun investigation of the human microbiome as an alternative method for identification of human DNA at crime scenes. It has been estimated that human beings have many more microbial cells in their bodies than they have human cells. Some of these microbes are symbiotic, others are neutral in their effects while still others are virulent. This bacterial aura follows us wherever we go and is transferred to and from the surfaces we touch and through human interactions. There are situations in which the microbiome can be used to examine deceased individuals, soils as well as determine the presence of individuals and their phenotypes at crime scenes. We are developing methods for analysis of this data using techniques such as SSCP, pyrosequencing and massively parallel sequencing.

Moreno LI, Mills D, Fetscher J, John-Williams K, Meadows-Jantz L, McCord B., The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition. J Microbiol Methods. 2011 84(3):388-93.

King, S.; McCord, B.R.; Riefler, R.G. Capillary electrophoresis single-strand conformation polymorphism analysis for monitoring soil bacteria, Journal of Microbiological Methods, 2005, 60, 83-92.

Recently we have begun developing a quick, robust and easy method for species identification using pyrosequencing technique. The aim of this project is to help investigators identify non-human samples in a crime scene. To the best of my knowledge, although many studies on species identification were performed almost a decade ago, there is no commercial kit available in the market for crime labs to use. It can be critical in the court to identify a non-human biological sample found in a crime scene as it can give an investigative lead to the case.

The recent explosion in the numbers and types of dangerous drugs on the market has resulted in a huge problem with overdose deaths and emergency room visits. These drugs are manufactured in clandestine laboratories and include a wide variety of structural variants of opioids, cannabinoids, cathinones, and many other novel psychoactive substances. This wide variety of structures makes it very difficult to design a single method to detect all different forms of a drug. Methods, such as immunoassay, which were used in the past can suffer from false negatives due to the poor cross reactivity between a designer drug and the drug target used to produce the test. To combat this problem we are exploring surface enhanced Raman spectroscopy. This procedure uses metallic nanoparticles to enhance the local electrical fields of the compound/nanoparticles and laser excitation to detect them.

Wang, L.; Deriu, C.; Wu, W.; Mebel, AM.; McCord, B. SERS, Raman, and DFT analyses of Fentanyl and six analogs, J. Raman Spect., in press.

Mostwatt, T; McCord, B. Surface Enhanced Raman Spectroscopy (SERS) as a Method for the Toxicological Analysis of Synthetic Cannabinoids, Talanta. 2017, 164, 396-402.

Doctor, E.; McCord, B., The application of supported liquid extraction in the analysis of benzodiazepines using surface enhanced Raman spectroscopy., Talanta, 2015, 144, 938-43

Chiara Deriu1, Irene Conticello1,2, Alexander M. Mebel1, Bruce McCord, Micro solid phase extraction surface-enhanced Raman spectroscopy (µ-SPE/SERS) screening test for the detection of the synthetic cannabinoid JWH-018 in oral fluid, Analytical Chemistry, 2019, 91, 7 4780-4789.

Laboratory on a chip methods involve the development of miniaturized analytical systems. The designs can include multiple steps performed in traditional laboratories such as- extraction, separation and detection.We are also investigating microfluidic procedures for drugs, explosives and environmental toxins. We utilize fluorescence, conductivity and electrochemical detection for sample analysis. More recently we have been experimenting with surface enhanced Raman spectroscopy as a detection method that is more universal, not requiring fluorescence derivatization or electroactive moieties. The figure below illustrates a paper microfluidic device for explosives detection based on colorimetric reactions.

Chabaud, KR; Thomas, JL; Torres MN, Oliveira,S; McCord, BR. Simultaneous colorimetric detection of metallic salts contained in low explosives residue, Forensic Chemistry, 2018,9, 35-41.

Wang L, Musile G, McCord BR. An aptamer-based paper microfluidic device for the colorimetric determination of cocaine. Electrophoresis. 2018 Feb;39(3):470-475

Musile, G.; Wang, L.; Bottoms, J.; Tagliaro, F.; McCord, B., The development of paper microfluidic devices for presumptive drug detection, Analytical Methods, 2015, 7, 8025-8033.

It is common to think of the detection of explosives as based on vapor detection. Unfortunately many explosive materials have very low vapor pressure and if heated, rapidly decompose. Therefore we focus on the detection of explosives using liquid based separation techniques such as ion chromatography, capillary electrophoresis and HPLC. Evidence is swabbed using and the samples are dissolved in a suitable solvent for later analysis. The key for this type of detection is to use sensitive analysis techniques and pay attention to methods for sample preconcentration and recovery. Another issue we focus on is the detection of improvised explosives. These materials often consist of various inorganic salts.

Forensically it becomes important to detect such explosives by mass spectrometry or spectroscopic techniques in order to properly identify the components in the improvsed explosive device. Thus our focus is on developing methods for the detection of improvised low explosives and materials such as fertilizers which can be used as the precursors for such devices. Ion chromatography and UPLC and capillary electrophoresis are excellent techniques for the analysis of these devices. Coupling these methods to electrospray mass spectrometry permits determination of peak identity

Corbin, I ; McCord, B. Detection of ammonium nitrate (AN) and urea nitrate (UN) using non aqueous solvents with electrospray ionization and MS/MS detection, Talanta, 2013, 115, 533-539.

De Perre, C., Prado, A. and McCord, B. R. Rapid detection of urea nitrate and ammonium nitrate spectrometry using infusion with crown ethers. Rapid Comm. Mass Spectrom.,2011 26: 154–162.

Bottegal, M. ; Lang, GL; Miller, M.; McCord, B. Analysis of Ascorbic Acid-Based Black Powder Substitutes by HPLC-ESI-QToFMS, Rapid Communications in Mass Spectrometry 2010 24(9) 1377–1386.

Mathis, J.; McCord, B. The Analysis of High Explosives by LC/ESI-MS: Multiplexed Detection of Negative Ion Adducts, Rapid Communications in Mass Spectrometry 2005, 19(2), 99-104.

Smokeless powders consist of nitrocellulose with a number of additives included to adjust burn rate and improve stability. These include energetic materials such as nitroglycerin and dinitrotoluene, as well as compounds such as diphenyl amine, centralite, and phthalates. These materials make up the additive package of the smokeless powder and can be used to speciate different types of powders In addition each powder has a different morphology, depending on manufacturer or desired burn rate. As the powder ages, the ratio of these components changes due to decomposition of the nitrocelluose. Stabilizers such as diphenyl amine are converted to nitro and nitrosodiphenylamine during this process. In the laboratory, we extract the additive package of the powder with methylene chloride and other solvents and compare the composition between different powders using HPLC, capillary electrophoresis and mass spectrometry. By examining the ratio of different additives we can determine differences between manufacturers and observe lot to lot variations.

Related to smokeless powder analysis is the determination of gunshot residue. Gunshot residue is deposited on the hands of a shooter following the discharge of a weapon. Typically following a crime a suspects hands and clothing may be collected and checked for deposits of metals from the bullet and primer including lead barium and antimony. Recently a number of lead free primers have been produced to reduce contamination of indooor shooting ranges. As a result we have been investigating the use of organic gunshot residue that results from the expulsion of burned and partially burned powder. We use ultra high performance liquid chromatography coupled to multidimensional MS.

Thomas J.L.; Lincoln, D.; McCord, BR., Separation and Detection of Smokeless Powder Additives by Ultra-high Performance Liquid Chromatography with Tandem Mass Spectrometry (UPLC/MS/MS), J. Forensic Sci. 2013, 58(3) 609–615

DePerre, C.; Corbin, I.;Blas, M. ;McCord,B. Separation and Identification of Smokeless Gunpowder Additives by Capillary Electrochromatography, J. Chrom. A, 2012, 1267, 259-265.

Mathis, J.; McCord, B. Mobile phase influence on electrospray ionization for the analysis of smokeless powders by gradient reversed phase liquid chromatorgraphy-EIMS, Forensic Science International, 2005, 154, 159-166

Improvised explosive devices are often produced using simple chemistries that involve mixtures of organic and inorganic oxidizers with metallic or carbonaceous fuels. We develop methods using capillary electrophoresis and ion chromatography to understand the complex residues produced in the blast mixtures. We have also investigated methods for the detection of inorganic explosives using HPLC, and LC/MS. Guest host interactions and the formation of adduct ions have also been studied for improved sensitivity.

Kristy G. Lahoda; Olivier L.Collin ; John A. Mathis; Holly E. LeClair; Steven H. Wise and Bruce R. McCord, A Survey of Background Levels of Explosives and Related Compounds in the Environment, J. Forensic Sciences, 2008 53(4) 802-806

Doyle, J. M.; Miller, M. L.; McCord, B. R.; McCollam, D. A.; Mushrush, G. W. A Multicomponent Mobile Phase for Ion Chromatography Applied to the Separation of Anions from the Residue of Low Explosives, Analytical Chemistry 2000, 72(10), 2303-2307.

McCord, B. R.; Hargadon, K.; Hall, K.; Burmeister, S. Forensic Analysis of Explosives using Ion Chromatographic Methods, Analytica Chimica Acta 1994, 288, 43-56

Using in-line preconcentration techniques such as solid phase, affinity and monolithic extraction, we isolate trace levels of drugs of abuse from biological samples. Recent work using monolithic CEC with benzodiazepines and tricyclic antidepressants (0f potential use in DFSA) demonstrates exceptional separation performance with sensitive mass spectrometric detection.

Fu, H. ; McCord, BR. Separation and analysis of antidepressants by acrylate-based monolithic column capillary electrochromatography with UV detection, Electrophoresis,2016, 37, 2882-2890

Merola, G. Fu, H. Tagliaro, F. McCord, B. Simultaneous chiral separation of 12 cathinone derivatives by cyclodextrin-assisted capillary electrophoresis mass spectrometry, Electrophoresis, 2014, 35, 3231-3241.

Blas, Maximilien; McCord, B. “Determination of trace levels of benzodiazepines in urine using capillary electrochromatography – time of flight mass spectrometry,” Electrophoresis 2008 29(10) 2182-2192

Al Najjar, A;Butcher, J; McCord, B. Determination of multiple drugs of abuse in human urine by capillary electrophoresis with fluorescence detection, Electrophoresis, 2004, 25 (10-11), 1592-1600.

Using fluorescent derivatization and capillary and microfluidic detection techniques we can detect picogram quantities of drugs of abuse in toxicological samples. We develop methods for in-line derivatization of compounds such as opiates and phenethyl amines followed by liquid based detection.

Bishop, Sandra C.; Lerch, Margaret; McCord, Bruce R. “Detection of nitrated benzodiazepines by indirect laser induced fluorescence detection on a microfluidic device,” J. Chromatogr. A 2007, 1154(1-2), 481-484.

Al Najjar, A;Butcher, J; McCord, B. Determination of multiple drugs of abuse in human urine by capillary electrophoresis with fluorescence detection, Electrophoresis, 2004, 25 (10-11), 1592-1600.