George Carmody

Bioinformatics and human identification in mass fatality incidents : The world trade center disaster

Abstract:  Victim identification initiatives undertaken in the wake of Mass Fatality Incidents (MFIs) where high‐body fragmentation has been sustained are often dependent on DNA typing technologies to complete their mandate. The success of these endeavors is linked to the choice of DNA typing methods and the bioinformatic tools required to make the necessary associations. Several bioinformatic tools were developed to assist with the identification of the victims of the World Trade Center attacks, one of the most complex incidents to date. This report describes one of these tools, the Mass Disaster Kinship Analysis Program (MDKAP), a pair‐wise comparison software designed to handle large numbers of complete or partial Short Tandem Repeats (STR) genotypes, and infer identity of, or biological relationships between tested samples. The software performs all functions required to take full advantage of the information content of processed genotypic data sets from large‐scale MFIs, including the collapse of victims data sets, remains re‐association, virtual genotype generation through gap‐filling, parentage trio searching, and a consistency check of reported/inferred biological relationships within families. Although very few WTC victims were genetically related, the software can detect parentage trios from within a victim’s genotype data set through a nontriangulated approach that screens all possible parentage trios. All software‐inferred relationships from WTC data were confirmed by independent statistical analysis. With a 13 STR loci complement, a fortuitous parentage trio (FPT) involving nonrelated individuals was detected. Additional STR loci would be required to reduce the risk of an FPT going undetected in large‐scale MFIs involving related individuals among the victims. Kinship analysis has proven successful in this incident but its continued success in larger scale MFIs is contingent on the use of a sufficient number of STR loci to reduce the risk of undetected FPTs, the use of mtDNA and Y‐STRs to confirm parentage and of bioinformatics that can support large‐scale comparative genotyping schemes capable of detecting parentage trios from within a group of related victims.

Assessing a novel room temperature DNA storage medium for forensic biological samples.

The ability to properly collect, analyze and preserve biological stains is important to preserving the integrity of forensic evidence. Stabilization of intact biological evidence in cells and the DNA extracts from them is particularly important since testing is generally not performed immediately following collection. Furthermore, retesting of stored DNA samples may be needed in casework for replicate testing, confirmation of results, and to accommodate future testing with new technologies. A novel room temperature DNA storage medium, SampleMatrix™ (SM; Biomatrica, Inc., San Diego, CA), was evaluated for stabilizing and protecting samples. Human genomic DNA samples at varying amounts (0.0625-200 ng) were stored dry in SM for 1 day to 1 year under varying conditions that included a typical ambient laboratory environment and also through successive freeze-thaw cycles (3 cycles). In addition, spiking of 1-4 × SM into samples prior to analysis was performed to determine any inhibitory effects of SM. Quantification of recovered DNA following storage was determined by quantitative PCR or by agarose gel electrophoresis, and evaluation of quantitative peak height results from multiplex short tandem repeat (STR) analyses were performed to assess the efficacy of SM for preserving DNA. Results indicate no substantial differences between the quality of samples stored frozen in liquid and those samples maintained dry at ambient temperatures protected in SM. For long-term storage and the storage of low concentration samples, SM provided a significant advantage over freezer storage through higher DNA recovery. No detectable inhibition of amplification was observed at the recommended SM concentration and complete profiles were obtained from genomic DNA samples even in the presence of higher than recommended concentrations of the SM storage medium. The ability to stabilize and protect DNA from degradation at ambient temperatures for extended time periods could have tremendous impact in simplifying and improving sample storage conditions and requirements. The current work focuses on forensics analysis; however this technology is applicable to all endeavors requiring storage of DNA.

VALIDATION STUDIES FOR THE GENETIC TYPING OF THE D1S80 LOCUS FOR IMPLEMENTATION INTO FORENSIC CASEWORK

A series of validation experiments were designed to evaluate, according to the Technical Working Group on DNA Analysis Methods (TWGDAM) guidelines, the analysis of the D1S80 locus for casework implementation. Approximately 400 samples from three different populations (Minnesota Caucasian, Minnesota African Americans, and Minnesota Native Americans) were typed to determine allele frequencies. Simulated forensic type specimens (blood, saliva, hair and semen, or vaginal secretions) were typed to demonstrate that deoxyribonucleic acid (DNA) extracted from various tissues of an individual yield the same D1S80 type. Dilution studies were performed and it was determined that a wide range of input DNA (0.5 ng to 40.0 ng) will consistently yield typeable results. The evaluation of DNA from various animals showed that the D1S80 locus is specific to human DNA within the limits of the parameters tested. The reproducibility of the system was tested by duplicate analysis of approximately 200 population samples. Duplicate samples were analyzed on both horizontal and vertical gel systems. In addition, simulated forensic specimens were analyzed by two independent laboratories: the Minnesota Forensic Science Laboratory (MFSL) and the Roche Biomedical Laboratories (RBL). All analyses, including extraction, quantitation, amplification and typing, were performed independently. All typing results for both laboratories were in agreement. By the analysis of mixtures from various simulated casework type mixtures, it was demonstrated that the D1S80 typing system is suitable for analyzing mixtures. In addition to the simulated casework, evidentiary samples from several adjudicated cases previously analyzed by restriction fragment length polymorphism (RFLP) analysis and/or DQA1 were typed at the D1S80 locus. The D1S80 results were consistent with previous RFLP and/or DQA1 results regarding inclusions/exclusions.

Allele frequencies for the COFILER STR loci in the Canadian Caucasian and Canadian First Nations populations.

Allele Frequencies for the COFILER STR Loci in the Canadian Caucasian and Canadian First Nations Populations

Allele Frequencies for Nine STR Loci in African-American, Chinese, Vietnamese, and Bangladesh Populations

Allele Frequencies for Nine STR Loci in African-American, Chinese, Vietnamese, and Bangladesh Populations

Electrophoretic and heat-stability polymorphism at the phosphoglucomutase (Pgm) locus in natural populations of Drosophila melanogaster.

Genetic polymorphism for electrophoretic and heat-sensitive alleles is known at the phosphoglucomutase (Pgm) locus in Drosophila melanogaster. Analysis of the distribution of electrophoretic and thermosensitive (ts) alleles was carried out in natural populations from Canada and West Africa and compared with already known data on Italian populations [Trippa, G., Loverre, A., and Catamo, A. (1976). Nature 260:42]. The data show the existence of five common alleles, Pgm1.00,tr, Pgm1,00,ts, Pgm0.70,ts, Pgm1.20,ts, and Pgm1.50,tr, and two rare alleles, Pgm0.55,ts and Pgm1.20,tr. The most frequent allele is always Pgm1.00,tr; the second most common allele is always of the ts type. The cumulated frequencies of ts alleles in the populations varies between 11 and 32%. The heat stability polymorphism is present in all populations examined and shows again the uniform geographic pattern that has been found for electrophoretic variation at this locus.

A genetic study of the Identifiler™ System 15 STR loci in the general population of Nicaragua, Central America

Allele frequencies for the 15 short tandem repeats loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA (AmpFℓSTR(®) Identifiler(™)PCR Amplification Kit, Applied Biosystems) were determined in a sample of 322 unrelated individuals from Nicaragua. Statistical analyses were performed using PowerStats v12 and Genepop v4.0. All loci are in Hardy-Weinberg equilibrium and show high discrimination for paternity analysis and forensic genetic applications.

Pupal respiratory complex of Tanypus carinatus Sublette var. (Diptera: Chironomidae)

Abstract The thoracic respiratory organ of the pupa of the genus Tanypus is usually assumed to lack a plastron element. Little information has appealed in the literature regarding the active site(s) of respiration. However, it has been inferred that the aeropyle-like structure at the tip of the organ serves in that role. Detailed examination of Tanypus carinatus Sublette var. respiratory organs by means of the scanning electron microscope, transmission electron microscope, and light microscope indicates the presence of a respiratory complex, whose elements bear structural similarities to those of plastrons, and which covers the entire surface of the respiratory organ. The subsurface meshwork, which previously has been interpreted as only supportive in function, is shown to be tubular, and appears to be intimately connected with the plastron-like surface elements. Functional and evolutionary implications of this plastron-like arrangement are discussed.