Assessing the Forensic Value of DNA Evidence from Y Chromosomes and Mitogenomes.

Y chromosome and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent), which presents different interpretation challenges compared with standard autosomal DNA profiles (inherited from both parents). We review approaches to the evaluation of lineage marker profiles for forensic identification, focussing on the key roles of profile mutation rate and relatedness (extending beyond known relatives). Higher mutation rates imply fewer individuals matching the profile of an alleged contributor, but they will be more closely related. This makes it challenging to evaluate the possibility that one of these matching individuals could be the true source, because relatives may be plausible alternative contributors, and may not be well mixed in the population. These issues reduce the usefulness of profile databases drawn from a broad population: larger populations can have a lower profile relative frequency because of lower relatedness with the alleged contributor. Many evaluation methods do not adequately take account of distant relatedness, but its effects have become more pronounced with the latest generation of high-mutation-rate Y profiles.

Essential Functions of Glycans in Human Epithelia Dissected by a CRISPR-Cas9-Engineered Human Organotypic Skin Model.

The glycome undergoes characteristic changes during histogenesis and organogenesis, but our understanding of the importance of select glycan structures for tissue formation and homeostasis is incomplete. Here, we present a human organotypic platform that allows genetic dissection of cellular glycosylation capacities and systematic interrogation of the roles of distinct glycan types in tissue formation. We used CRISPR-Cas9 gene targeting to generate a library of 3D organotypic skin tissues that selectively differ in their capacity to produce glycan structures on the main types of N- and O-linked glycoproteins and glycolipids. This tissue library revealed distinct changes in skin formation associated with a loss of features for all tested glycoconjugates. The organotypic skin model provides phenotypic cues for the distinct functions of glycoconjugates and serves as a unique resource for further genetic dissection and identification of the specific structural features involved. The strategy is also applicable to other organotypic tissue models.

Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry.

Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R2 = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R2 = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R2 = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.

Y-profile evidence: Close paternal relatives and mixtures.

We recently introduced a new approach to the evaluation of weight of evidence (WoE) for Y-chromosome profiles. Rather than attempting to calculate match probabilities, which is particularly problematic for modern Y-profiles with high mutation rates, we proposed using simulation to describe the distribution of the number of males in the population with a matching Y-profile, both the unconditional distribution and conditional on a database frequency of the profile. Here we further validate the new approach by showing that our results are robust to assumptions about the allelic ladder and the founder haplotypes, and we extend the approach in two important directions. Firstly, forensic databases are not the only source of background data relevant to the evaluation of Y-profile evidence: in many cases the Y-profiles of one or more relatives of the accused are also available. To date it has been unclear how to use this additional information, but in our simulation-based approach its effect is readily incorporated. We describe this approach and illustrate how the WoE that a man was the source of an observed Y-profile changes when the Y-profiles of some of his male-line relatives are also available. Secondly, we extend our new approach to mixtures of Y-profiles from two or more males. Surprisingly, our simulation-based approach reveals that observing a 2-male mixture that includes an alleged contributor's profile is almost as strong evidence as observing a matching single-contributor evidence sample, and even 3-male and 4-male mixtures are only slightly weaker.

How many individuals share a mitochondrial genome?

Mitochondrial DNA (mtDNA) is useful to assist with identification of the source of a biological sample, or to confirm matrilineal relatedness. Although the autosomal genome is much larger, mtDNA has an advantage for forensic applications of multiple copy number per cell, allowing better recovery of sequence information from degraded samples. In addition, biological samples such as fingernails, old bones, teeth and hair have mtDNA but little or no autosomal DNA. The relatively low mutation rate of the mitochondrial genome (mitogenome) means that there can be large sets of matrilineal-related individuals sharing a common mitogenome. Here we present the mitolina simulation software that we use to describe the distribution of the number of mitogenomes in a population that match a given mitogenome, and investigate its dependence on population size and growth rate, and on a database count of the mitogenome. Further, we report on the distribution of the number of meioses separating pairs of individuals with matching mitogenome. Our results have important implications for assessing the weight of mtDNA profile evidence in forensic science, but mtDNA analysis has many non-human applications, for example in tracking the source of ivory. Our methods and software can also be used for simulations to help validate models of population history in human or non-human populations.

How convincing is a matching Y-chromosome profile?

The introduction of forensic autosomal DNA profiles was controversial, but the problems were successfully addressed, and DNA profiling has gone on to revolutionise forensic science. Y-chromosome profiles are valuable when there is a mixture of male-source and female-source DNA, and interest centres on the identity of the male source(s) of the DNA. The problem of evaluating evidential weight is even more challenging for Y profiles than for autosomal profiles. Numerous approaches have been proposed, but they fail to deal adequately with the fact that men with matching Y-profiles are related in extended patrilineal clans, many of which may not be represented in available databases. The higher mutation rates of modern profiling kits have led to increased discriminatory power but they have also exacerbated the problem of fairly conveying evidential value. Because the relevant population is difficult to define, yet the number of matching relatives is fixed as population size varies, it is typically infeasible to derive population-based match probabilities relevant to a specific crime. We propose a conceptually simple solution, based on a simulation model and software to approximate the distribution of the number of males with a matching Y profile. We show that this distribution is robust to different values for the variance in reproductive success and the population growth rate. We also use importance sampling reweighting to derive the distribution of the number of matching males conditional on a database frequency, finding that this conditioning typically has only a modest impact. We illustrate the use of our approach to quantify the value of Y profile evidence for a court in a way that is both scientifically valid and easily comprehensible by a judge or juror.

Importance of nonsynonymous OCA2 variants in human eye color prediction.

BACKGROUND: The color of the eyes is one of the most prominent phenotypes in humans and it is often used to describe the appearance of an individual. The intensity of pigmentation in the iris is strongly associated with one single-nucleotide polymorphism (SNP), rs12913832:A>G that is located in the promotor region of OCA2 (OMIM #611409). Nevertheless, many eye colors cannot be explained by only considering rs12913832:A>G. METHODS: In this study, we searched for additional variants in OCA2 to explain human eye color by sequencing a 500 kbp region, encompassing OCA2 and its promotor region. RESULTS: We identified three nonsynonymous OCA2 variants as important for eye color, including rs1800407:G>A (p.Arg419Gln) and two variants, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile), not previously described as important for eye color variation. It was shown that estimated haplotypes consisting of four variants (rs12913832:A>G, rs1800407:G>A (p.Arg419Gln), rs74653330:A>T (p.Ala481Thr), and rs121918166:G>A (p.Val443Ile)) explained 75.6% (adjusted R (2) = 0.76) of normal eye color variation, whereas rs12913832:A>G alone explained 68.8% (adjusted R (2) = 0.69). Moreover, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) had a measurable effect on quantitative skin color (P = 0.008). CONCLUSION: Our data showed that rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) have a measurable effect on normal pigmentation variation.

Nonoperative treatment improves pain irrespective of radiographic severity. A cohort study of 1,414 patients with knee osteoarthritis.

BACKGROUND AND PURPOSE: The discrepancy between symptoms and radiographic severity of knee osteoarthritis (OA) is well described. However, little is known about whether radiographic severity is predictive of the clinical result of nonoperative treatment. We investigated whether radiographic severity and treatment type were associated with improvements in pain after nonoperative treatment of patients with knee OA. PATIENTS AND METHODS: A 5-year consecutive series of patients deemed not eligible for total knee arthroplasty (TKA) by an experienced orthopedic surgeon was contacted 1-5 years later. Radiographic severity, age, sex, and BMI were registered at the consultation. At follow-up, patients were asked to answer a questionnaire on type of treatment and improvements in pain after treatment. RESULTS: Of 1,848 patients who were not eligible for TKA, 1,414 (77%) completed the follow-up questionnaire (mean age 66 (24-96) years; 55% women). Radiographic severity was not associated with improvements in pain even after adjusting for treatment type, age, sex, and BMI (p > 0.1). The odds ratio of improvement was higher by a factor of 2 in patients who received physiotherapy or multimodal treatment than in patients who did not. INTERPRETATION: Radiographic severity was not associated with improvements in pain after nonoperative treatment. Patients who are not eligible for TKA can confidently be referred to nonoperative treatment even if they have severe radiographic OA. The treatment should preferably be multimodal, including physiotherapy, as recommended in Danish and international clinical guidelines.

The effect of gender on eye colour variation in European populations and an evaluation of the IrisPlex prediction model.

In two recent studies of Spanish individuals, gender was suggested as a factor that contributes to human eye colour variation. However, gender did not improve the predictive accuracy on blue, intermediate and brown eye colours when gender was included in the IrisPlex model. In this study, we investigate the role of gender as a factor that contributes to eye colour variation and suggest that the gender effect on eye colour is population specific. A total of 230 Italian individuals were typed for the six IrisPlex SNPs (rs12913832, rs1800407, rs12896399, rs1393350, rs16891982 and rs12203592). A quantitative eye colour score (Pixel Index of the Eye: PIE-score) was calculated based on digital eye images using the custom made DIAT software. The results were compared with those of Danish and Swedish population samples. As expected, we found HERC2 rs12913832 as the main predictor of human eye colour independently of ancestry. Furthermore, we found gender to be significantly associated with quantitative eye colour measurements in the Italian population sample. We found that the association was statistically significant only among Italian individuals typed as heterozygote GA for HERC2 rs12913832. Interestingly, we did not observe the same association in the Danish and Swedish population. This indicated that the gender effect on eye colour is population specific. We estimated the effect of gender on quantitative eye colour in the Italian population sample to be 4.9%. Among gender and the IrisPlex SNPs, gender ranked as the second most important predictor of human eye colour variation in Italians after HERC2 rs12913832. We, furthermore, tested the five lower ranked IrisPlex predictors, and evaluated all possible 3(6) (729) genotype combinations of the IrisPlex assay and their corresponding predictive values using the IrisPlex prediction model [4]. The results suggested that maximum three (rs12913832, rs1800407, rs16891982) of the six IrisPlex SNPs are useful in practical forensic genetic casework.

Danish surgeons allow the most athletic activities after total hip and knee replacement.

BACKGROUND AND PURPOSE: Counselling patients for or against athletic activities after well performed total hip arthroplasty (THA) and total knee arthroplasty (TKA). Level of evidence is low, and the current international guidelines are based on North American expert opinions in 2001 and 2008. Could technical and operative development and social or cultural differences apply for different counselling? METHODS: All Danish experts in head of departments performing more than 100 THAs or TKAs per year, were invited to fill in a questionnaire regarding the most popular sport activities in the Danish 60-69 years old population RESULTS: Response rate was 74 and 89% for the TKA and THA departments, respectively. A pronounced variation between the departments was observed and compared to the latest published US recommendations in 2007, the present Danish recommendations are significantly more liberal. Athletic activities are now allowed by 87% of the Danish arthroplasty departments. Of these 55% allow for high-impact activities after THA compared to 21% in US in 2007 (p < 0.0001). Recommendations for TKA patients are less liberal. Only 38% of the departments allow for high-impact activities after TKA compared to the 55% after THA (p < 0.0001). INTERPRETATION: Based on the pronounced variation between departments and the fact that a highly significant trend was observed over 5 years on an undocumented basis it was concluded that there is an imminent need for a higher scientific level on this issue­which hopefully can develop in a few years using PROMs in large scale follow-up studies.