Challenging DNA: Assessment of a range of genotyping approaches for highly degraded forensic samples

It is common in forensic casework to encounter highly degraded DNA samples from a variety of sources. In this category bone and teeth samples are often the principal source of evidential material for criminal investigations or identification of long-deceased individuals. In these circumstances standard STRs are prone to fail due to their long amplicon sizes (since DNA becomes progressively more fragmented as it degrades). To successfully resolve such cases alternative markers can be used and until recently the only other tool available was mitochondrial DNA, which despite being more resistant to degradation, is much less informative. A rapidly developing approach to analyzing degraded DNA is the typing of loci from short-amplicon PCR products based on markers such as mini-STRs and autosomal SNPs. We have performed an analysis of several cases with naturally degraded DNA using established STRs plus mini-STRs and autosomal SNPs in order to make an objective comparison of the performance of each method using challenging DNA. The main aim was to establish the benefits and drawbacks of each marker set to help the practitioner choose the DNA analysis method most suited to the circumstances of each case.     

When Faith Moved Mountains

It is believed that Buddhism reached China through the Silk Road around the first century A.D., and subsequently, Buddhist arts and crafts arrived from countries like India, Nepal and Sri Lanka. An example would be the artworks found in grottoes built along the Silk Road in China. The Mogao Caves near the city of Dunhuang in Gansu Province in northwest China, the Longmen Grottoes near Luoyang in central China's Henan Province, and the Yungang Grottoes near Datong in Shanxi Province in north China are the three most important places in the country where Buddhist grottoes have been found.     

Validation of a method to detect cocaine and its metabolites in nails by gas chromatography-mass spectrometry

The objective of the present work was to compare previously published methods and provide validation data to detect simultaneously cocaine (COC), benzoylecgonine (BE) and norcocaine (NCOC) in nail. Finger and toenail samples (5mg) were cut in very small pieces and submitted to an initial procedure for external decontamination. Methanol (3 ml) was used to release analytes from the matrix. A cleanup step was performed simultaneously by solid-phase extraction (SPE) and the residue was derivatized with pentafluoropropionic anhydride/pentafluoropropanol (PFPA/PFP). Gas chromatography-mass spectrometry (GC-MS) was used to detect the analytes in selected ion monitoring mode (SIM). Confidence parameters of validation of the method were: recovery, intra- and inter-assay precision, as well as limit of detection (LOD) of the analytes. The limits of detection were: 3.5 ng/mg for NCOC and 3.0 ng/mg for COC and BE. Good intra-assay precision was observed for all detected substances (coefficient of variation (CV)<11%). The inter-assay precision for norcocaine and benzoylecgonine were <4%. For intra- and inter-assay precision deuterated internal standards were used. Toenail and fingernail samples from eight declared cocaine users were submitted to the validated method.     

The Advent of Internet Surveys for Political Research: A Comparison of Telephone and Internet Samples

The Internet offers a number of advantages as a survey mode:low marginal cost per completed response, capabilities for providingrespondents with large quantities of information, speed, andelimination of interviewer bias. Those seeking these advantagesconfront the problem of representativeness both in terms ofcoverage of the population and capabilities for drawing randomsamples. Two major strategies have been pursued commerciallyto develop the Internet as a survey mode. One strategy, usedby Harris Interactive, involves assembling a large panel ofwilling respondents who can be sampled. Another strategy, usedby Knowledge Networks, involves using random digit dialing (RDD)telephone methods to recruit households to a panel of Web-TVenabled respondents. Do these panels adequately deal with theproblem of representativeness to be useful in political scienceresearch? The authors address this question with results fromparallel surveys on global climate change and the Kyoto Protocoladministered by telephone to a national probability sample andby Internet to samples of the Harris Interactive and KnowledgeNetworks panels. Knowledge and opinion questions generally showstatistically significant but substantively modest differenceacross the modes. With inclusion of standard demographic controls,typical relational models of interest to political scientistsproduce similar estimates of parameters across modes. It thusappears that, with appropriate weighting, samples from thesepanels are sufficiently representative of the U.S. populationto be reasonable alternatives in many applications to samplesgathered through RDD telephone surveys.     

Results of the GEP-ISFG collaborative study on two Y-STRs tetraplexes: GEPY I (DYS461, GATA C4, DYS437 and DYS438) and GEPY II (DYS460, GATA A10, GATA H4 and DYS439)

A collaborative exercise was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) in order to evaluate the performance of two Y-chromosome STR PCR tetraplexes, which include the loci DYS461, GATA C4, DYS437 and DYS438 (GEPY I), and DYS460, GATA A10, GATA H4 and DYS439 (GEPY II). The participating laboratories were asked to type three samples for the eight markers, using a specific amplification protocol. In addition, two control samples, with known haplotypes, were provided. The results obtained by the 13 different participating laboratories were identical, except for two laboratories that failed to type correctly the same two samples for GATA C4. By sequence analyses, two different GATA C4 allele structures were found. One control sample (allele 21) and two questioned samples (allele 22, correctly typed by all the laboratories, and allele 25) presented the following repeat structure: (TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)n, but different from the one found for allele 26 in one sample included in this exercise, as well as in the second control sample (allele 23), namely (TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)2(TGTA)2(TCTA)n. The collaborative exercise results proved that both Y-tetraplexes produce good amplification results, with the advantage of being efficiently typed using different separation and detection methodologies. However, since GATA C4 repeat presents a complex structure, with alleles differing in sequence structure, efficient denaturing conditions should be followed in order to avoid typing errors due to sizing problems.