Genome-wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains.

Objective A genome-wide high-throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini-sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans. Material and methods The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array (TM) by Fluidigm (R). Results Thirty-eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible. The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified. Discussion The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable

Likelihood ratio and posterior odds in forensic genetics: Two sides of the same coin

It has become widely accepted in forensics that, owing to a lack of sensible priors, the evidential value of matching DNA profiles in trace donor identification or kinship analysis is most sensibly communicated in the form of a likelihood ratio (LR). This restraint does not abate the fact that the posterior odds (PO) would be the preferred basis for returning a verdict. A completely different situation holds for Forensic DNA Phenotyping (FDP), which is aimed at predicting externally visible characteristics (EVCs) of a trace donor from DNA left behind at the crime scene. FDP is intended to provide leads to the police investigation helping them to find unknown trace donors that are unidentifiable by DNA profiling. The statistical models underlying FDP typically yield posterior odds (PO) for an individual possessing a certain EVC. This apparent discrepancy has led to confusion as to when LR or PO is the appropriate outcome of forensic DNA analysis to be communicated to the investigating authorities. We thus set out to clarify the distinction between LR and PO in the context of forensic DNA profiling and FDP from a statistical point of view. In so doing, we also addressed the influence of population affiliation on LR and PO. In contrast to the well-known population dependency of the LR in DNA profiling, the PO as obtained in FDP may be widely population-independent. The actual degree of independence, however, is a matter of (i) how much of the causality of the respective EVC is captured by the genetic markers used for FDP and (ii) by the extent to which non-genetic such as environmental causal factors of the same EVC are distributed equally throughout populations. The fact that an LR should be communicated in cases of DNA profiling whereas the PO are suitable for FDP does not conflict with theory, but rather reflects the immanent differences between these two forensic applications of DNA information

Paraxanthine/caffeine concentration ratios in hair: an alternative for plasma-based phenotyping of cytochrome P450 1A2?

Background and Objective: Although metabolite-to-parent drug concentration ratios in hair have been suggested as a possible tool to study the metabolism of drugs in a non-invasive way, no studies are available that evaluated this in a systematic way. Cytochrome P450 (CYP) 1A2 is a drug-metabolizing enzyme characterized by large inter-individual differences in its activity. The standard approach for CYP1A2 phenotyping is to determine the paraxanthine/caffeine ratio in plasma at a fixed timepoint after intake of a dose of the CYP1A2 substrate caffeine. The aim of this study was to evaluate whether paraxanthine/caffeine ratios measured in hair samples reflect the plasma-based CYP1A2 phenotype. Methods: Caffeine and paraxanthine concentrations were measured in proximal 3 cm segments of hair samples from 60 healthy volunteers and resulting paraxanthine/caffeine ratios were correlated with CYP1A2 phenotyping indices in plasma. Results: Paraxanthine/caffeine ratios in hair ranged from 0.12 to 0.93 (median 0.41); corresponding ratios in plasma ranged from 0.09 to 0.95 (median 0.40). A statistically significant correlation was found between ratios in hair and plasma (r = 0.41, p = 0.0011). However, large deviations between ratios in both matrices were found in individual cases. Although the influence of several factors on paraxanthine/caffeine ratios and hair-plasma deviations was investigated, no evident factors explaining the observed variability could be identified. Conclusion: The variability between hair and plasma ratios complicates the interpretation of hair paraxanthine/caffeine ratios on an individual basis and, therefore, compromises their practical usefulness as alternative CYP1A2 phenotyping matrix

Bodies of Science and Law: Forensic DNA Profiling, Biological Bodies, and Biopower

How is jurisdiction transferred from an individual's biological body to agents of power such as the police, public prosecutor and judiciary, and what happens to these biological bodies when transformed from private into public objects? These questions are examined by analyzing bodies situated at the intersection of science and law. More specifically, the transformation of 'private bodies' into 'public bodies' shall be analyzed by going into the details of forensic DNA profiling in the Dutch jurisdiction. It will be argued that various 'forensic genetic practices' enact different 'forensic genetic bodies'. These enacted forensic genetic bodies are connected with various infringements of civil rights, which become articulated in exploring these forensic genetic bodies' 'normative registers'

Facing the Unborn

(excerpt) An ultrasound video of an unborn child sucking its thumb makes a case against abortion that reason hardly need supplement. But a zygote photographed just after an in vitro conception is not so easily recognizable as a human being or person. Pro-lifers often assume that this difficulty has been overcome by modern science. Since the 1820s, when evidence of ovular fertilization first became known, it has been clear that the life of a human being runs from conception to death

Microelectrophoretic apparatus and process

New gel tray and lid assemblies designed for use in conjunction with slotted electrophoretic membranes were developed to take advantage of recently improved microelectrophoretic accessories which include a multisample applicator capable of applying up to 10 samples consecutively or simultaneously, and a temperature control plate for dissipating the heat produced by electrophoresis in a gel. The trays and membranes can be marketed ready for use as electrophoretic media or impregnated with various specific substrates and dye

Forensic DNA Phenotyping: Improving the Prediction of Eye, Hair, and Skin Color through Quantitative Measurement

poster abstractWithout a match in the DNA database or a reference profile, current methods in forensic DNA profiling fail to give any leads to further criminal investigations. Forensic DNA Phenotyping bridges that gap in the investigation by providing ‘intelligence’ through the identification of externally visible characteristics of the unknown individual from their biological sample left at the crime scene. Recent work on eye and hair color prediction using a tool called ‘HIrisPlex’ has allowed accurate predictions of blue or brown eye color with a precision greater than 95%, and of hair color with a precision of approximately 75% for blond, brown, black and red categories. DNA phenotyping is a new and exciting area of DNA profiling, however there are areas that still require improvement. These include the prediction of intermediate eye colors such as green, or the mechanisms and/or genes involved in age-dependent hair color changes. At this time, categorical skin color prediction is still being developed and will soon be included in the HIrisPlex system, however it is not until the day that pigmentation measurements move toward a quantitative color scale that accuracy will be at a maximum. Our research hopes to target this area specifically. While the predication of categorical measurements is helpful, the term “light brown” is subjective and leads to the possibility of error in interpretation. In order to circumvent this interpretation issue, understanding quantitative color prediction is key. To achieve this, we are in the midst of a database collection of approximately 5000 individuals in which we will perform genome-wide association studies (GWAS) to locate additional eye, hair and skin color genes associated with a quantitative pigment scale phenotype. This database will help create a world-wide representative statistical panel from which quantitative predictive measures can be ascertained. Furthermore, in conjunction with computer programming techniques, it will allow the creation of a user-friendly software program that will enable the prediction of pigmentation-related externally visible characteristics such as eye, hair and skin color. This software has the capacity to be a revolutionary intelligence tool to aid law enforcement investigations by producing a color-print out biological mugshot

The Crime Lab in the Age of the Genetic Panopticon

Scientific evidence really nails this man to the wall, the Harris County, Texas prosecutor told the jurors in closing statements. At trial, George Rodriguez claimed he was innocent and that he had been working a factory the day of the crime. The prosecutor emphasized, however, that the blood type of swabs taken from the victim showed that Rodriguez did commit the crime and that a hair from the crime scene matched him. But seventeen years later, the same hair was tested again, this time using DNA analysis, and the evidence cleared Rodriguez and ultimately led to the crime crime lab being shut down and recreated. The Rodriguez case illustrates why the crime lab has entered a time of crisis. I will discuss that case and the larger story of the transformation of the Houston lab, to introduce the first of three wonderful new books that I review here: Sandra Guerra Thompson\u27s Cops in Lab Coats: Curbing Wrongful Convictions Through Independent Forensic Laboratories. Second, I turn to Erin Murphy\u27s book, Inside the Cell: The Dark Side of Forensic DNA, to explore Murphy\u27s compelling account of why DNA testing is no panacea for these growing problems and may instead actually magnify some of them. These failings raise the larger question whether improved research to support forensic disciplines, national regulation regarding the quality and standards for labs, and constitutional criminal procedure to remedy the poor litigation of forensics in the courtroom can help to address the failings of our crime labs. I suggest that efforts to improve research, regulation, and criminal procedure are beginning to show promise, but that much remains to be done. Third, I will discuss Adam Benforado\u27s book, Unfair: The New Science of Criminal Injustice, which looks broadly at the role of social science and criminal law, but focusing here on cognitive research and expert evidence. Finally, I will discuss how advances in scientific research and technology will reshape the crime lab of the future, creating new challenges and opportunities for criminal justice