Further development of forensic eye color predictive tests

In forensic analysis predictive tests for external visible characteristics (or EVCs), including inference of iris color, represent a potentially useful tool to guide criminal investigations. Two recent studies, both focused on forensic testing, have analyzed single nucleotide polymorphism (SNP) genotypes underlying common eye color variation (Mengel-From et al., Forensic Sci. Int. Genet. 4:323 and Walsh et al., Forensic Sci. Int. Genet. 5:170). Each study arrived at different recommendations for eye color predictive tests aiming to type the most closely associated SNPs, although both confirmed rs12913832 in HERC2 as the key predictor, widely recognized as the most strongly associated marker with blue and brown iris colors. Differences between these two studies in identification of other eye color predictors may partly arise from varying approaches to assigning phenotypes, notably those not unequivocally blue or dark brown and therefore occupying an intermediate iris color continuum. We have developed two single base extension assays typing 37 SNPs in pigmentation-associated genes to study SNP-genotype based prediction of eye, skin, and hair color variation. These assays were used to test the performance of different sets of eye color predictors in 416 subjects from six populations of north and south Europe. The presence of a complex and continuous range of intermediate phenotypes distinct from blue and brown eye colors was confirmed by establishing eye color populations compared to genetic clusters defined using Structure software. Our study explored the effect of an expanded SNP combination beyond six markers has on the ability to predict eye color in a forensic test without extending the SNP assay excessively – thus maintaining a balance between the test's predictive value and an ability to reliably type challenging DNA with a multiplex of manageable size. Our evaluation used AUC analysis (area under the receiver operating characteristic curves) and naïve Bayesian likelihood-based classification approaches. To provide flexibility in SNP-based eye color predictive tests in forensic applications we modified an online Bayesian classifier, originally developed for genetic ancestry analysis, to provide a straightforward system to assign eye color likelihoods from a SNP profile combining additional informative markers from the predictors analyzed by our study plus those of Walsh and Mengel-From. Two advantages of the online classifier is the ability to submit incomplete SNP profiles, a common occurrence when typing challenging DNA, and the ability to handle physically linked SNPs showing independent effect, by allowing the user to input frequencies from SNP pairs or larger combinations. This system was used to include the submission of frequency data for the SNP pair rs12913832 and rs1129038: indicated by our study to be the two SNPs most closely associated to eye color.     

Landmark Typology in Applied Morphometrics Studies: What's the Point?

Landmarks are the hallmark of biological shape analysis as discrete anatomical points of correspondence. Various systems have been developed for their classification. In the most widely used system, developed by Bookstein in the 1990s, landmarks are divided into three distinct types based on their anatomical locations and biological significance. As Bookstein and others have argued that different landmark types possess different qualities, e.g., that Type 3 landmarks contain deficient information about shape variation and are less reliably measured, researchers began using landmark types as justification for selecting or avoiding particular landmarks for measurement or analysis. Here, we demonstrate considerable variation in landmark classifications among 17 studies using geometric morphometrics (GM), due to disagreement in the application of both Bookstein's landmark typology and individual landmark definitions. A review of the literature furthermore shows little correlation between landmark type and measurement reproducibility, especially when factors such as differences in measurement tools (calipers, digitizer, or computer software) and data sources (dry crania, 3D models, or 2D images) are considered. Although landmark typology is valuable when teaching biological shape analysis, we find that employing it in research design introduces confusion without providing useful information. Instead, researchers should choose landmark configurations based on their ability to test specific research hypotheses, and research papers should include justifications of landmark choices along with landmark definitions, details on landmark collection methods, and appropriate interobserver and intraobserver analyses. Hence, while the landmarks themselves are crucial for GM, we argue that their typology is of little use in applied studies. Anat Rec, 302:1144–1153, 2019. © 2018 Wiley Periodicals, Inc.     

Parent Perspectives on Adverse Childhood Experiences & Unmet Social Needs Screening in the Medical Home: A Qualitative Study

ObjectivesTo explore parental perspectives regarding disclosure of child and parental adverse childhood experiences (ACE) and family unmet social needs (USN) and to elicit parental recommendations for screening in the pediatric medical home.MethodsWe conducted a qualitative study using a purposive sample of English- and Spanish-speaking parents in our urban academic community clinic. Between January 2018 and March 2019, each parent underwent one semistructured interview that was audiotaped, transcribed, and independently coded in Atlas.ti by 2 study team members. Data analysis was based in constructivist grounded theory methodology to identify common themes and subthemes.ResultsWe interviewed 25 English-speaking and 15 Spanish-speaking parents who were mostly female, racial/ethnic minorities with ≥1 ACE. English-speaking subjects were more likely to have a high school degree and be single parents. Four themes were identified: 1) Pediatricians should ask about ACE and USN. 2) Disclosure is a longitudinal process, not a discrete event. 3) Barriers to disclosure are significant, involving concrete and emotional risks for the family. 4) Trauma-informed providers and practices support disclosure.ConclusionsFamilies support pediatricians addressing ACE and USN in the medical home despite significant barriers. Even if providers screen using trauma-informed principles, parents may prefer not to disclose ACE initially because they regard disclosure as a stepwise process. These findings contribute to a new conceptual framework for thinking of ACE screening not merely as a way to generate information, but as an interactive, therapeutic relationship-building activity irrespective of whether or when it produces disclosure.     

Variation of X-chromosomal microsatellites in Belarus within the context of their genetic diversity in Europe

More and more X-STR data are becoming available for worldwide human populations for forensic and anthropological investigations, but the European datasets analysed so far represent mainly the central, northern, western and southern part of the continent with populations of Eastern Europe being practically uninvestigated. In the present study, we assessed genetic variation and linkage disequilibrium of 19 X-chromosomal STR markers (DXS7132, DXS7133, DXS7423, DXS7424, DXS8377, DXS8378, DXS9895, DXS10074, DXS10075, DXS10079, DXS10101, DXS10103, DXS10134, DXS10135, DXS10146, DXS10147, DXS10148, GATA172D05, HPRTB) in four regional populations of an Eastern European state of Belarus, including 12 loci incorporated in the Argus X-12 kit. Our results revealed cumulative power of discrimination of the tested X-STR loci to amount to 0.999999999999996 and 0.999999997 in females and males, respectively. Analysis of molecular variance demonstrated regional stratification within the country, excluding the use of a common X-STR database for Belarus in forensic casework. However, development of a separate X-STR database for the northwestern part of the country or exclusion of four loci displaying regional differences from the dataset were shown to eliminate the observed geographic substructure among Belarusians. Comparison of the Belarusian genotypes with X-STR data from other European populations disclosed a geography-driven northeast-southwest gradient extending from Belarus and Finland to Iberia and Italy. This study is the first extensive report on variation of X-STR markers in populations from Eastern Europe and the first comprehensive analysis of diversity of X-chromosomal microsatellites in Europe.     

Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power

This study reports Short Tandem Repeat (STR) sequence-based allele data from 496 Spanish individuals across 31 autosomal STR (auSTR) loci included in the Precision ID GlobalFiler™ NGS STR Panel v2: D12S391, D13S317, D8S1179, D21S11, D3S1358, D5S818, D1S1656, D2S1338, vWA, D2S441, D5S2800, D7S820, D16S539, D6S474, D12ATA63, D4S2408, D6S1043, D19S433, D14S1434, CSF1PO, D10S1248, D18S51, D1S1677, D22S1045, D2S1776, D3S4529, FGA, Penta D, Penta E, TH01 and TPOX. The sequence of each allele was aligned to the reference sequence GRCh37 (hg19) and formatted according to the guidance of the International Society for Forensic Genetics. A subset of 221 samples was evaluated for testing concordance with allele calls derived from CE-based analysis using PowerPlex Fusion 6C, and there was 99.95% allele concordance. Twenty-five out of 31 auSTR loci showed an increased number of alleles due to repeat region sequence variation and/or single nucleotide polymorphisms (SNP) residing in the flanking regions. A total of 18 loci showed increased observed heterozygosity due to sequence variation; the loci exhibiting the greatest increase were: D13S317 (12% points), D5S818 (10% points), D8S1179 (7% points), D3S1358 (7% points), and D21S11 (6% points). The combined match probability decreased from 2.022E-24 (length-based data) to 1.042E-27 (sequence-based data) for the 20 CODIS core STR loci. The combined match probability (sequence-based data) for the 31 STR loci studied was 4.777E-40. The combined typical paternity index increased from 1.118E + 12 to 8.179E + 13 using length and sequence-based data, respectively. This Spanish population study performed in the framework of the EU-funded DNASEQEX project is expected to provide STR sequence-based allele frequencies for forensic casework and support implementation of massively parallel sequencing (MPS) technology in forensic laboratories.     

GHEP-ISFG collaborative simulated exercise for DVI/MPI: Lessons learned about large-scale profile database comparisons

The GHEP-ISFG Working Group has recognized the importance of assisting DNA laboratories to gain expertise in handling DVI or missing persons identification (MPI) projects which involve the need for large-scale genetic profile comparisons. Eleven laboratories participated in a DNA matching exercise to identify victims from a hypothetical conflict with 193 missing persons. The post mortem database was comprised of 87 skeletal remain profiles from a secondary mass grave displaying a minimal number of 58 individuals with evidence of commingling. The reference database was represented by 286 family reference profiles with diverse pedigrees. The goal of the exercise was to correctly discover re-associations and family matches. The results of direct matching for commingled remains re-associations were correct and fully concordant among all laboratories. However, the kinship analysis for missing persons identifications showed variable results among the participants. There was a group of laboratories with correct, concordant results but nearly half of the others showed discrepant results exhibiting likelihood ratio differences of several degrees of magnitude in some cases. Three main errors were detected: (a) some laboratories did not use the complete reference family genetic data to report the match with the remains, (b) the identity and/or non-identity hypotheses were sometimes wrongly expressed in the likelihood ratio calculations, and (c) many laboratories did not properly evaluate the prior odds for the event. The results suggest that large-scale profile comparisons for DVI or MPI is a challenge for forensic genetics laboratories and the statistical treatment of DNA matching and the Bayesian framework should be better standardized among laboratories.     

Sialendoscopy in the old patients: A new tool or a revolution?

Pathologies of the salivary glands can be divided into neoplastic, which affect mostly parenchyma, and non neoplastic, which are mainly ductal, cited in Myers and Ferris (2007) [1]. Ductal diseases consist in Sialadenitis that can be acute, due to a stone, or chronic, due to a stricture. One of the factors that contribute to sialadenitis is hyposalivation and altered composition of saliva, given in Triantafyllou (1992) [2]. Xerostomia affects the elderly in 20 to 39% of cases, according to various studies (Astor et al. (1999) [3], Locker (1993) [4], Gilbert et al. (1993) [5]). Main causes in the old patient are medications side effects, cited in Navazesh et al. (1996) [6], irradiation cited in Dreizen et al. (1976) [7], Sjögren's syndrome cited in Kaarela et Mutru (1982) [8], probable atrophy of the gland and ducts due to aging, and salivary stones. Obstructive inflammatory pathologies of salivary glands, caused mainly by sialolithiasis and strictures affect the general population as well as the elderly. However, no specific study has described yet its prevalence in the elderly population. But as xerostomia is probably associated with chronic sialadenitis, and as it is quite frequent in the old population, we can assume that ductal pathologies must be far underestimated in the geriatric population. The classical treatment for obstructive sialadenitis is the removal of the gland which is often difficult to consider in old patients because of the general anesthesia, and morbidity of the surgery (longer hospital stay, risk for facial nerve, complications related to external surgery). Sialendoscopy is one of the new innovations introduced in the last few years in the field of Otolaryngology, head and neck surgery for the diagnosis and treatment of acute and chronic sialadenitis, cited in Marchal et al. (1999) [9]. Its main advantage in the elderly population is that it can be performed in most cases as an ambulatory, outpatient procedure under local anesthesia.