Variant interpretation in molecular autopsy: a useful dilemma.

Sudden cardiac death (SCD) in adolescents and young adults may be the first manifestation of an inherited arrhythmic syndrome. Thus identification of a genetic origin in sudden death cases deemed inconclusive after a comprehensive autopsy and may help to reduce the risk of lethal episodes in the remaining family. Using next-generation sequencing (NGS), a large number of variants of unknown significance (VUS) are detected. In the majority of cases, there is insufficient evidence of pathogenicity, representing a huge dilemma in current genetic investigations. Misinterpretation of such variants may lead to inaccurate genetic diagnoses and/or the adoption of unnecessary and/or inappropriate therapeutic approaches. In our study, we applied current (ACMG) recommendations for variant classification in post-mortem genetic screening of a cohort of 56 SCD victims. We identified a total 53 rare protein-altering variants (MAF < 0.2%) classified as VUS or worse. Twelve percent of the cases exhibited a clinically actionable variant (pathogenic, likely pathogenic or VUS - potentially pathogenic) that would warrant cascade genetic screening in relatives. Most of the variants detected by means of the post-mortem genetic investigations were VUS. Thus, genetic testing by itself might be fairly meaningless without supporting background data. This data reinforces the need for an experienced multidisciplinary team for obtaining reliable and accountable interpretations of variant significance for elucidating potential causes for SCDs in the young. This enables the early identification of relatives at risk or excludes family members as genetic carriers. Also, development of adequate forensic guidelines to enable appropriate interpretation of rare genetic variants is fundamental.

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool.

We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.

Progress in the implementation of massively parallel sequencing for forensic genetics: results of a European-wide survey among professional users.

A European-wide online survey was conducted to generate an overview on the state-of-the-art using massively parallel sequencing (MPS) platforms for forensic DNA analysis and DNA phenotyping among forensic practitioners in Europe. The survey was part of the dissemination activities of the "VISible Attributes through GEnomics - VISAGE" Horizon 2020 funded European research project [30], in preparation of a series of educational training activities. A total of 105 replies from 32 European countries representing participants from police, governmental, academic, and private laboratories providing professional services in the field of forensic genetics were included in the final analysis. Of these, 73% already own an MPS platform or are planning to acquire one within the next 1-2 years. One-third of the participants have already carried out MPS-based STR sequencing, identity, or ancestry SNP typing. A total of 23-40% of participants are planning to explore all FDP applications showing the overall very high interest in using MPS for the whole range of forensic MPS markers and applications. About 50% of the participants have previously gathered experience using forensic DNA phenotyping (FDP) markers based on conventional (i.e., not MPS-based) DNA typing methods. A total of 55% of the participants have attended training on the general use of MPS technology, but 36% have received no training whatsoever. Accordingly, 90% have expressed high or medium interest to attend training on the analysis and interpretation of DNA phenotyping data for predicting appearance, ancestry, and age. The results of our survey will provide valuable information for organizing relevant training workshops on all aspects of MPS-based DNA phenotyping for the forensic genetics scientific community.

Monitoring transcellular fluid shifts during episodes of intradialytic hypotension using bioimpedance spectroscopy.

BACKGROUND: Transcellular fluid shifts during dialysis treatment could be related to the frequency and severity of intradialytic hypotension (IDH). We investigated that (i) in addition to ultrafiltration, extracellular fluid (ECF) is further depleted by transcellular fluid shifts and (ii) changes in intracellular fluid (ICF), which have been overlooked so far, or if they were considered, are not understood, might be due to these fluid shifts. METHODS: Thirty-six patients were categorized as haemodynamically stable, asymptomatic IDH or unstable (symptomatic IDH) according to their changes in systolic blood pressure and associated clinical symptoms. Their intradialytic changes in body fluids were studied using bioimpedance spectroscopy measurements and compared among groups. RESULTS: For IDH-prone patients, data showed a rapid drop in ECF that was more than expected from the ultrafiltration rate (UFR) profile and was associated with a significant increase in ICF (P = 0.001). Study of accumulative loss profiles of ECF revealed a loss in ECF up to 300 ml, more than that predicted from UFR for unstable patients. CONCLUSIONS: The considerable discrepancy between the expected and measured loss in ECF might provide evidence of transcellular fluid shifts possibly induced by changes in plasma osmolarity due to haemodialysis. Moreover, the results suggest a pattern of fluid removal in IDH-prone patients that significantly differs from that in haemodynamically stable patients.

Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA.

Forensic DNA phenotyping is gaining interest as the number of applications increases within the forensic genetics community. The possibility of providing investigative leads in addition to conventional DNA profiling for human identification provides new insights into otherwise "cold" police investigations. The ability of reporting on the bio-geographical ancestry (BGA), appearance characteristics and age based on DNA obtained from a crime scene sample of an unknown donor makes the exploration of such markers and the development of new methods meaningful for criminal investigations. The VISible Attributes through GEnomics (VISAGE) Consortium aims to disseminate and broaden the use of predictive markers and develop fully optimized and validated prototypes for forensic casework implementation. Here, the first VISAGE appearance and ancestry tool development, performance and validation is reported. A total of 153 SNPs (96.84 % assay conversion rate) were successfully incorporated into a single multiplex reaction using the AmpliSeq™ design pipeline, and applied for massively parallel sequencing with the Ion S5 platform. A collaborative effort involving six VISAGE laboratory partners was devised to perform all validation tests. An extensive validation plan was carefully organized to explore the assay's overall performance with optimum and low-input samples, as well as with challenging and casework mock samples. In addition, forensic validation studies such as concordance and mixture tests recurring to the Coriell sample set with known genotypes were performed. Finally, inhibitor tolerance and specificity were also evaluated. Results showed a robust, highly sensitive assay with good overall concordance between laboratories.

Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA.

Human head hair shape, commonly classified as straight, wavy, curly or frizzy, is an attractive target for Forensic DNA Phenotyping and other applications of human appearance prediction from DNA such as in paleogenetics. The genetic knowledge underlying head hair shape variation was recently improved by the outcome of a series of genome-wide association and replication studies in a total of 26,964 subjects, highlighting 12 loci of which 8 were novel and introducing a prediction model for Europeans based on 14 SNPs. In the present study, we evaluated the capacity of DNA-based head hair shape prediction by investigating an extended set of candidate SNP predictors and by using an independent set of samples for model validation. Prediction model building was carried out in 9674 subjects (6068 from Europe, 2899 from Asia and 707 of admixed European and Asian ancestries), used previously, by considering a novel list of 90 candidate SNPs. For model validation, genotype and phenotype data were newly collected in 2415 independent subjects (2138 Europeans and 277 non-Europeans) by applying two targeted massively parallel sequencing platforms, Ion Torrent PGM and MiSeq, or the MassARRAY platform. A binomial model was developed to predict straight vs. non-straight hair based on 32 SNPs from 26 genetic loci we identified as significantly contributing to the model. This model achieved prediction accuracies, expressed as AUC, of 0.664 in Europeans and 0.789 in non-Europeans; the statistically significant difference was explained mostly by the effect of one EDAR SNP in non-Europeans. Considering sex and age, in addition to the SNPs, slightly and insignificantly increased the prediction accuracies (AUC of 0.680 and 0.800, respectively). Based on the sample size and candidate DNA markers investigated, this study provides the most robust, validated, and accurate statistical prediction models and SNP predictor marker sets currently available for predicting head hair shape from DNA, providing the next step towards broadening Forensic DNA Phenotyping beyond pigmentation traits.

Increased cerebral water content in hemodialysis patients.

Little information is available on the impact of hemodialysis on cerebral water homeostasis and its distribution in chronic kidney disease. We used a neuropsychological test battery, structural magnetic resonance imaging (MRI) and a novel technique for quantitative measurement of localized water content using 3T MRI to investigate ten hemodialysis patients (HD) on a dialysis-free day and after hemodialysis (2.4±2.2 hours), and a matched healthy control group with the same time interval. Neuropsychological testing revealed mainly attentional and executive cognitive dysfunction in HD. Voxel-based-morphometry showed only marginal alterations in the right inferior medial temporal lobe white matter in HD compared to controls. Marked increases in global brain water content were found in the white matter, specifically in parietal areas, in HD patients compared to controls. Although the global water content in the gray matter did not differ between the two groups, regional increases of brain water content in particular in parieto-temporal gray matter areas were observed in HD patients. No relevant brain hydration changes were revealed before and after hemodialysis. Whereas longer duration of dialysis vintage was associated with increased water content in parieto-temporal-occipital regions, lower intradialytic weight changes were negatively correlated with brain water content in these areas in HD patients. Worse cognitive performance on an attention task correlated with increased hydration in frontal white matter. In conclusion, long-term HD is associated with altered brain tissue water homeostasis mainly in parietal white matter regions, whereas the attentional domain in the cognitive dysfunction profile in HD could be linked to increased frontal white matter water content.

The Montreal Cognitive Assessment (MoCA) - a sensitive screening instrument for detecting cognitive impairment in chronic hemodialysis patients.

BACKGROUND: Chronic kidney disease (CKD) patients undergoing hemodialysis (HD) therapy have an increased risk of developing cognitive impairment and dementia, which are known relevant factors in disease prognosis and therapeutic success, but still lack adequate screening in clinical routine. We evaluated the Montreal Cognitive Assessment (MoCA) for suitability in assessing cognitive performance in HD patients in comparison to the commonly used Mini-Mental State Examination (MMSE) and a detailed neuropsychological test battery, used as gold standard. METHODS: 43 HD patients and 42 healthy controls with an average age of 58 years, were assessed with the MoCA, the MMSE and a detailed neuropsychological test battery, covering the domains of memory, attention, language, visuospatial and executive functions. Composite scores were created for comparison of cognitive domains and test results were analyzed using Spearman's correlation and linear regression. Cognitive dysfunction was defined using z-score values and predictive values were calculated. Sensitivity and specificity of the MoCA were determined using receiver operating characteristic (ROC) analysis. RESULTS: HD patients performed worse in all cognitive domains, especially in memory recall and executive functions. The MoCA correlated well with the detailed test battery and identified patients with cognitive impairment with a sensitivity of 76.7% and specificity of 78.6% for a cut-off value of ≤24 out of 30 points. In the detailed assessment executive functions accounted significantly for performance in the MoCA. The MMSE only discriminated weakly between groups. CONCLUSIONS: The MoCA represents a suitable cognitive screening tool for hemodialysis patients, demonstrating good sensitivity and specificity levels, and covering executive functions, which appear to play an important role in cognitive performance of HD patients.

Temporal control over the initiation of cell motility by a regulator of G-protein signaling.

The control over the acquisition of cell motility is central for a variety of biological processes in development, homeostasis, and disease. An attractive in vivo model for investigating the regulation of migration initiation is that of primordial germ cells (PGCs) in zebrafish embryos. In this study, we show that, following PGC specification, the cells can polarize but do not migrate before the time chemokine-encoded directional cues are established. We found that the regulator of G-protein signaling 14a protein, whose RNA is a newly identified germ plasm component, regulates the temporal relations between the appearance of the guidance molecules and the acquisition of cellular motility by regulating E-cadherin levels.

Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour.

The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising laboratory and judged; 96% of the eye colour phenotypes were inferred correctly across 100 samples and 19 laboratories. The high success rates in genotyping and eye colour phenotyping clearly demonstrate the reproducibility and the robustness of the IrisPlex assay as well as the accuracy of the IrisPlex model to predict blue and brown eye colour from DNA. Additionally, this study demonstrates the ease with which the IrisPlex system is implementable and applicable across forensic laboratories around the world with varying pre-existing experiences.

Usefulness of bioimpedance spectroscopy for detection of hypotensive episode during dialysis.

Using statistical methods, this study investigates whether bioimpedance spectroscopy (BIS) and plasma electrolytes can be used to identify risk of intradialytic hypotension (IDH) based on information obtained during the first half of the dialysis treatment only. Data obtained from 40 patients included information on blood pressure, parameters defined from BIS, plasma electrolytes, and relevant clinical data. Patients were divided into three groups based on their intradialytic decrease in systolic blood pressure (SysBP) and associated symptoms and interventions: (1) Stable SysBP, (2) Asymptomatic unstable SysBP, and (3) symptomatic unstable SysBP. Retrospective analysis showed a significant reduction in extracellular fluid of 0.64 ± 0.62 L and potassium (K) concentration of 0.24 ± 1.67 mM in parallel with a decrease in SysBP of ≥25 mm Hg/hr. Data analysis using mixed-model procedure revealed that unstable patients compared with stable patients were characterized by higher extracellular resistance (p = 0.014) and K concentration (p = 0.009). Discriminant analysis using relative changes in extracellular resistance, potassium, and pH resulted in correct identification of 85% of the patients at risk. This study indicates that combining BIS and plasma electrolytes analysis may be a promising method to provide more accurate monitoring of IDH.

Clinical predictors of individual cognitive fluctuations in patients undergoing hemodialysis.

BACKGROUND: Cognitive impairment in hemodialysis (HD) patients is frequent and mediated by several factors. It is unclear which patients are more susceptible to cognitive variations around the dialysis cycle and which clinical factors may play a mediator role. We aimed to answer these issues by investigating intraindividual changes within the dialysis cycle. STUDY DESIGN: Cross-sectional observational study with repeated measures. SETTING & PARTICIPANTS: 47 HD patients and 40 controls without kidney disease, both without history of neurologic disease. PREDICTORS: Dialysis vintage, disease duration, vascular risk factors, comorbidity index score, intradialytic weight change, frequency of hypotensive episodes, and biochemical levels (hemoglobin, leukocytes, urea, creatinine, sodium, and potassium). Covariates included demographics (age, education, and sex). OUTCOMES & MEASUREMENTS: Significant individual deterioration in attention and executive functions (phasic and intrinsic alertness, Stroop test, and Trail Making Test) after dialysis, as measured by a regression-based reliable change method. Regression models were used to identify clinical predictors of individual cognitive decline after dialysis. RESULTS: After dialysis, patients primarily showed prolonged reaction times and psychomotor slowing. However, individual-based analyses revealed that fluctuations in attention and executive functions were present in only a minority of patients. Significant individual fluctuations on particular attention and executive tasks were associated moderately with intradialytic hypotensive episodes, as well as with psychoactive medication, and were predicted weakly by blood leukocyte count, sodium level, dialysis vintage, and volume. LIMITATIONS: Small sample size; patient group younger and healthier than the overall HD population, limiting generalizability. CONCLUSIONS: Only a minority of patients exhibit significant individual cognitive fluctuations, predominantly showing deterioration after dialysis in attention and executive functions. Susceptibility to such fluctuations was predicted in part by both HD-dependent and -independent factors.

Alternate-form reliability of the Montreal cognitive assessment screening test in a clinical setting.

AIMS: The Montreal Cognitive Assessment (MoCA) has gained recognition for its validity in detecting cognitive impairment in several clinical populations. For serial assessments, alternate forms are needed to overcome possible practice effects. Our objective was to investigate the reliability of two German MoCA alternate forms for longitudinal assessment applications. METHODS: The original and one of two alternate forms of the MoCA were administered within a 60-min interval of a clinical interview in a counterbalanced order to 100 healthy elderly controls, 30 patients with mild cognitive impairment (MCI) and 30 patients with Alzheimer's disease (AD). The diagnosis of the majority of patients was supported by in vivo AD pathology biomarkers. RESULTS: There was a strong correlation between the alternate forms and the original MoCA in all groups, but particularly in the clinical samples. Total mean scores did not differ significantly between the MoCA versions, even taking into account the presentation order. As in previous studies, age and education influenced performance in the MoCA. The same pattern of group differences (controls > MCI > AD) was observed for each of the versions. CONCLUSION: All three forms can be reliably and interchangeably used in serial cognitive assessment, confirming the MoCA's applicability in research and clinical longitudinal approaches.