Analysis of artificially degraded DNA using STRs and SNPs--results of a collaborative European (EDNAP) exercise

Recently, there has been much debate about what kinds of genetic markers should be implemented as new core loci that constitute national DNA databases. The choices lie between conventional STRs, ranging in size from 100 to 450 bp; mini-STRs, with amplicon sizes less than 200 bp; and single nucleotide polymorphisms (SNPs). There is general agreement by the European DNA Profiling Group (EDNAP) and the European Network of Forensic Science Institutes (ENFSI) that the reason to implement new markers is to increase the chance of amplifying highly degraded DNA rather than to increase the discriminating power of the current techniques. A collaborative study between nine European and US laboratories was organised under the auspices of EDNAP. Each laboratory was supplied with a SNP multiplex kit (Foren-SNPs) provided by the Forensic Science Service, two mini-STR kits provided by the National Institute of Standards and Technology (NIST) and a set of degraded DNA stains (blood and saliva). Laboratories tested all three multiplex kits, along with their own existing DNA profiling technique, on the same sets of degraded samples. Results were collated and analysed and, in general, mini-STR systems were shown to be the most effective. Accordingly, the EDNAP and ENFSI working groups have recommended that existing STR loci are reengineered to provide smaller amplicons, and the adoption of three new European core loci has been agreed.     

Integrated DNA and Fingerprint Analyses in the Identification of 60‐Year‐Old Mummified Human Remains Discovered in an Alaskan Glacier

Abstract: This report describes the identification of a merchant mariner who perished in 1948 when Northwest Airlines Flight 4422, a DC‐4 carrying 24 seamen and six crew members crashed into Mount Sanford, Alaska. Fifty‐one years later, a human forearm and hand were found close by the wreckage of the plane, prompting identification efforts using DNA and fingerprints. There were significant challenges to both the fingerprint and DNA analyses. The hand was badly desiccated, making fingerprint friction‐ridge detail almost invisible and the remains had been embalmed upon discovery, making DNA amplification difficult. We present the results of an interdisciplinary approach that successfully addressed these challenges and ultimately led to the identification of the remains. These efforts relied on efficient fingerprint rejuvenation and imaging techniques that improved print resolution, as well as new DNA extraction techniques optimized for aggressively embalmed remains.     

Application of low copy number STR typing to the identification of aged, degraded skeletal remains

Low copy number (LCN) STR typing was successfully applied to four interesting cases during developmental validation of the approach for degraded skeletal remains. Specific questions were addressed in each case, with the acquisition of STR data largely serving as additional confirmatory or investigatory information in any specific situation, and not necessarily providing the definitive evidence to establish identity. The cases involve missing U.S. service members from World War I, World War II, and the Vietnam War. The variety of these cases, in terms of the questions addressed, the age of the remains, and the type of reference material available for comparison, demonstrates the broad utility of LCN STR typing in the identification of degraded skeletal remains from missing persons.     

NEIGHBORHOOD AND DELINQUENCY: AN ASSESSMENT OF CONTEXTUAL EFFECTS*

The sociological perspectives which helped formulate the study of delinquency and continue to underlie more specific conceptual frameworks—Social Disorganization, Subculture, and Labeling—point to the importance of contextual effects in the dynamics explaining delinquent and criminal behavior. Yet, systematic examination of such effects has been all but neglected. This paper delineates and empirically assesses neighborhood characteristics postulated to represent contextual factors affecting individual delinquency and criminality. Data were collected from a stratified random sample of adolescent males drawn from 12 New York City neighborhoods. The initial model, designed to refine hypotheses specifying community contextual effects, exhibits a highly satisfactory fit to the data. The framework underscores the importance of considering distinct community contextual effects as well as individual-level effects. Two neighborhood-level factors, the effects of which are quite distinct, are important: the community's level of organizational participation and the extent of disorder and criminal subculture. The indirect and direct effects of these factors are elaborated in relation to three measures of de1inquency—namely, self-reported, officially recorded, and severe self-reported delinquency.     

Diagnosing post-mortem treatments which inhibit DNA amplification from US MIAs buried at the Punchbowl

The US military is committed to recovering and identifying the remains of unknown military service members. Casualties of the Korean War were exhumed from the National Memorial Cemetery of the Pacific, or Punchbowl, and submitted to the Armed Forces DNA Identification Laboratory (AFDIL) for mtDNA sequencing. Contrary to AFDIL's experience on other samples from this era, most failed to yield amplifiable DNA. Suspicion fell on mortuary practices that may have been applied to the remains, evidenced by a white powder found with the bones, and general records suggesting the use of formaldehyde-based stablizing agents. To improve the chances of successful identification of the unknown individuals, we looked for the causes underlying this failure. We did this by examining the state of the collagen, the most abundant biomolecule in bone, by using differential scanning calorimetry (DSC) and transmission electron microscopy (TEM). The DSC analyses showed collagens with a range of different thermal stabilities. When these results were compared with the DNA amplification results, a clear correlation between elevated thermal stability and amplification failure was evident. TEM analysis revealed that fibril integrity was maintained after thermal and acid treatments in the samples which failed amplification. Together these two approaches implicate a stabilization agent as the cause of problems with DNA analysis, presumably due to excessive cross-linking. Following the initial study, the ability of DSC to rapidly identify problem samples was tested in a blind study of 14 samples, the method successfully identifying all the problematic samples from Punchbowl. Within this unusual context, DSC analysis is a useful method to assess the likelihood of successful DNA extraction and amplification.     

DNA identification of "Earthquake McGoon" 50 years postmortem

This report describes the genetic identification of James "Earthquake McGoon" McGovern, a WWII fighter ace who perished in Laos while providing supplies to French troops during the French Indochina war. Because reference samples were unavailable for all of the potential casualties, testing of the entire mitochondrial genome, autosomal STRs and Y-chromosomal STRs was performed to increase the genetic information available for analysis. Kinship analyses performed on the evidentiary data and numerous indirect family references for McGovern excluded other possible casualties and definitively established McGovern's identity. This particular case demonstrates the practical utility of novel research technologies and aggressive genetic typing protocols in the identification of aged, degraded remains.