Strengthening the reporting of genetic risk prediction studies: the GRIPS statement

The rapid and continuing progress in gene discovery for complex diseases is fueling interest in the potential application of genetic risk models for clinical and public health practice. The number of studies assessing the predictive ability is steadily increasing, but the quality and completeness of reporting varies. A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies, building on the principles established by previous reporting guidelines. These recommendations aim to enhance the transparency of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct, or analysis. A detailed Explanation and Elaboration document is published on the EJHG website.     

The STARD statement for reporting studies of diagnostic accuracy: explanation and elaboration. The Standards for Reporting of Diagnostic Accuracy Group

The quality of reporting of studies of diagnostic accuracy is less than optimal. Complete and accurate reporting is necessary to enable readers to assess the potential for bias in a study and to evaluate the generalisability of the results. A group of scientists and editors has developed the STARD (Standards for Reporting of Diagnostic Accuracy) statement to improve the quality of reporting of studies of diagnostic accuracy. The statement consists of a checklist of 25 items and flow diagram that authors can use to ensure that all relevant information is present. This explanatory document aims to facilitate the use, understanding and dissemination of the checklist. The document contains a clarification of the meaning, rationale and optimal use of each item on the checklist, as well as a short summary of the available evidence on bias and applicability. The STARD statement, checklist, flowchart, and this explanation and elaboration document should be useful resources to improve the reporting of diagnostic accuracy studies. Complete and informative reporting can only lead to better decisions in health care.     

Personalized risk prediction for type 2 diabetes: the potential of genetic risk scores

PurposeUsing effect estimates from genome-wide association studies (GWAS), we identified a genetic risk score (GRS) that has the strongest association with type 2 diabetes (T2D) status in a population-based cohort and investigated its potential for prospective T2D risk assessment.MethodsBy varying the number of single-nucleotide polymorphisms (SNPs) and their respective weights, alternative versions of GRS can be computed. They were tested in 1,181 T2D cases and 9,092 controls of the Estonian Biobank cohort. The best-fitting GRS was chosen for the subsequent analysis of incident T2D (386 cases).ResultsThe best fit was provided by a novel doubly weighted GRS that captures the effect of 1,000 SNPs. The hazard for incident T2D was 3.45 times (95% CI: 2.31–5.17) higher in the highest GRS quintile compared with the lowest quintile, after adjusting for body mass index and other known predictors. Adding GRS to the prediction model for 5-year T2D risk resulted in continuous net reclassification improvement of 0.324 (95% CI: 0.211–0.444). In addition, a significant effect of the GRS on all-cause and cardiovascular mortality was observed.ConclusionThe proposed GRS would improve the accuracy of T2D risk prediction when added to the currently used set of predictors.Genet Med 19 3, 322–329.     

Recommendations for reporting results of diagnostic genetic testing (biochemical,cytogenetic and molecular genetic)

Genetic test results can have considerable importance for patients, their parents and more remote family members. Clinical therapy and surveillance, reproductive decisions and genetic diagnostics in family members, including prenatal diagnosis, are based on these results. The genetic test report should therefore provide a clear, concise, accurate, fully interpretative and authoritative answer to the clinical question. The need for harmonizing reporting practice of genetic tests has been recognised by the External Quality Assessment (EQA), providers and laboratories. The ESHG Genetic Services Quality Committee has produced reporting guidelines for the genetic disciplines (biochemical, cytogenetic and molecular genetic). These guidelines give assistance on report content, including the interpretation of results. Selected examples of genetic test reports for all three disciplines are provided in an annexe.Diagnostic genetic testing is an extremely rapidly expanding area encompassing a broad range of laboratory investigations to analyse chromosomes (from classical karyotype to molecular cytogenetics), nucleic acids (DNA, RNA), proteins and metabolites used to detect heritable or somatic mutations, genotypes or phenotypes related to disease and health. Genetic testing requires particular consideration in that it is usually performed only once in a patient''s lifetime, and the results may have considerable importance for lifetime decisions not only for the individuals being tested but also for children and family. Interpreting and reporting variation in germline chromosomes, DNA sequences or their products is a heavy clinical responsibility for prediction of susceptibility to disease, patient diagnosis, prognosis, counselling, treatment or family planning. Providing a set of reporting frameworks that can be customised for different testing contexts but share some common principles could be beneficial to the practice of a number of laboratories, including non-OECD members and/or laboratories that do not participate in External Quality Assessments (EQA), and to laboratories with blurred boundaries between research and genetic testing services.Although several guidelines already exist for reporting the results of genetic testing,^1,2,3 these focus on molecular genetic testing and do not cover the other two branches of laboratory genetics, namely biochemical genetics and cytogenetics. Based on recent surveys of EQA results presented by some European EQA providers and the request from genetic laboratories for comprehensive reporting guidelines, it was considered that a unifying attempt to harmonise the reporting practice of genetic tests in Europe and neighbouring countries would be welcome.     

BOADICEA: a comprehensive breast cancer risk prediction model incorporating genetic and nongenetic risk factors

PurposeBreast cancer (BC) risk prediction allows systematic identification of individuals at highest and lowest risk. We extend the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk model to incorporate the effects of polygenic risk scores (PRS) and other risk factors (RFs).MethodsBOADICEA incorporates the effects of truncating variants inBRCA1, BRCA2, PALB2, CHEK2, and ATM; a PRS based on 313 single-nucleotide polymorphisms (SNPs) explaining 20% of BC polygenic variance; a residual polygenic component accounting for other genetic/familial effects; known lifestyle/hormonal/reproductive RFs; and mammographic density, while allowing for missing information.ResultsAmong all factors considered, the predicted UK BC risk distribution is widest for the PRS, followed by mammographic density. The highest BC risk stratification is achieved when all genetic and lifestyle/hormonal/reproductive/anthropomorphic factors are considered jointly. With all factors, the predicted lifetime risks for women in the UK population vary from 2.8% for the 1st percentile to 30.6% for the 99th percentile, with14.7% of women predicted to have a lifetime risk of ≥17–<30% (moderate risk according to National Institute for Health and Care Excellence [NICE] guidelines) and 1.1% a lifetime risk of ≥30% (high risk).ConclusionThis comprehensive model should enable high levels of BC risk stratification in the general population and women with family history, and facilitate individualized, informed decision-making on prevention therapies and screening.     

Evaluating the uncertainty of risk prediction in genetic counseling: a Bayesian approach

A general method to obtain the exact point estimate and the measure of uncertainty of recurrence risks for genetic counseling is present. This method, which follows Bayesian estimation theory, can be applied without restrictions of sample size, class of risk function, or parameter dimension. As an illustration, the recurrence risks for isolated cases in two autosomal dominant disorders with incomplete penetrance (mandibulofacial and fontonasal dyostoses) are estimated.     

Development of the Anatomical Quality Assurance (AQUA) Checklist: Guidelines for reporting original anatomical studies

The rise of evidence‐based anatomy has emphasized the need for original anatomical studies with high clarity, transparency, and comprehensiveness in reporting. Currently, inconsistencies in the quality and reporting of such studies have placed limits on accurate reliability and impact assessment. Our aim was to develop a checklist of reporting items that should be addressed by authors of original anatomical studies. The study steering committee formulated a preliminary conceptual design and began to generate items on the basis of a literature review and expert opinion. This led to the development of a preliminary checklist. The validity of this checklist was assessed by a Delphi procedure, and feedback from the Delphi panelists, who were experts in the area of anatomical research, was used to improve it. The Delphi procedure involved 12 experts in anatomical research. It comprised two rounds, after which unanimous consensus was reached regarding the items to be included in the checklist. The steering committee agreed to name the checklist AQUA. The preliminary AQUA Checklist consisted of 26 items divided into eight sections. Following round 1, some of the items underwent major revision and three new ones were introduced. The checklist was revised only for minor language inaccuracies after round 2. The final version of the AQUA Checklist consisted of the initial eight sections with a total of 29 items. The steering committee hopes the AQUA Checklist will improve the quality and reporting of anatomical studies. Clin. Anat. 30:14–20, 2017. © 2016 Wiley Periodicals, Inc.     

Hardy-Weinberg equilibrium in genetic association studies: an empirical evaluation of reporting, deviations, and power

We evaluated the testing and reporting of Hardy-Weinberg equilibrium (HWE) in recent genetic association studies, detected how frequently HWE was violated and estimated the power for HWE testing in this literature. Genetic association studies published in 2002 in Nature Genetics, American Journal of Human Genetics, and American Journal of Medical Genetics were assessed. Data were analyzed on 239 biallelic associations using 154 distinct genotype distribution data sets where HWE could be tested. Any information on HWE was given only for 150 (62.8%) associations (92 (59.7%) data sets). Reanalysis of the data showed significant deviation from HWE in the disease-free controls of 20 associations (13 data sets), but only four of them (two data sets) were admitted in the published articles. Another four deviations (in two data sets) were observed in the combined sample of cases and controls of studies where both cases and controls were diseased, and none were reported in the papers. In all six tested multiallelic associations (six data sets), there was violation of HWE, but this was not admitted in the published articles. Power calculations showed that most studies conforming to HWE simply were largely underpowered to detect HWE deviation; for example, power to detect an inbreeding of magnitude F=0.10 exceeded 80% in only 11 (7%) of the data sets being tested. This empirical evidence suggests that, even in high profile genetics journals, testing and reporting for HWE is often neglected and deviations are rarely admitted in the published reports. Moreover, power is limited for HWE testing in most current genetic association studies.     

Hemophilia A: genetic prediction and linkage studies in all available families in Finland

RFLP studies were done in 82 (75%) of all known hemophilia A families in the Finnish population (approximately 5 million). Two intragenic RFLPs (Bc1I/F8A, XbaI/p482.6) and two extragenic markers (TaqI/St14, Bg1II/DX13) were used. Among 263 females at risk, carriership could be evaluated with an intragenic marker in 47% and with an extragenic marker in 26%. In 27% of the females, carriership could be neither excluded nor confirmed; 68% of these females were relatives of an isolated patient. Eight recombinations between the factor VIII gene (F8C) and DXS52 (lod 25.02 at theta max 0.06), eight recombinations between F8C and DXS15 (lod 21.91 at theta max 0.05), and two recombinations between DXS52 and DXS15 (lod 33.56 at theta max 0.01) were found. Using multipoint linkage analysis, the most likely order of loci supported by the data was: F8C-DXS15-DXS52-DXS134. RFLP segregation analysis provides a highly useful method of carrier detection and prenatal diagnosis of hemophilia A, but its limitations must be carefully taken into account.     

Derivation of point of departure (PoD) estimates in genetic toxicology studies and their potential applications in risk assessment

Genetic toxicology data have traditionally been employed for qualitative, rather than quantitative evaluations of hazard. As a continuation of our earlier report that analyzed ethyl methanesulfonate (EMS) and methyl methanesulfonate (MMS) dose–response data (Gollapudi et al., 2013), here we present analyses of 1‐ethyl‐1‐nitrosourea (ENU) and 1‐methyl‐1‐nitrosourea (MNU) dose–response data and additional approaches for the determination of genetic toxicity point‐of‐departure (PoD) metrics. We previously described methods to determine the no‐observed‐genotoxic‐effect‐level (NOGEL), the breakpoint‐dose (BPD; previously named Td), and the benchmark dose (BMD₁₀) for genetic toxicity endpoints. In this study we employed those methods, along with a new approach, to determine the non‐linear slope‐transition‐dose (STD), and alternative methods to determine the BPD and BMD, for the analyses of nine ENU and 22 MNU datasets across a range of in vitro and in vivo endpoints. The NOGEL, BMDL₁₀ and BMDL_1SD PoD metrics could be readily calculated for most gene mutation and chromosomal damage studies; however, BPDs and STDs could not always be derived due to data limitations and constraints of the underlying statistical methods. The BMDL₁₀ values were often lower than the other PoDs, and the distribution of BMDL₁₀ values produced the lowest median PoD. Our observations indicate that, among the methods investigated in this study, the BMD approach is the preferred PoD for quantitatively describing genetic toxicology data. Once genetic toxicology PoDs are calculated via this approach, they can be used to derive reference doses and margin of exposure values that may be useful for evaluating human risk and regulatory decision making. Environ. Mol. Mutagen. 55:609–623, 2014. © 2014 The Authors. Environmental and Molecular Mutagenesis Published by Wiley Periodicals, Inc.     

Interaction of genetic risk and adoptive parent communication deviance: longitudinal prediction of adoptee psychiatric disorders

BACKGROUND: In the Finnish Adoptive Family Study of Schizophrenia, adoptee thinking disorders have been shown to be a joint effect of genetic liability for schizophrenia spectrum disorders and adoptive rearing-parent communication patterns. However, longitudinal predictions of clinical psychiatric disorders of the adoptees have not been reported. METHOD: Adoptees (n = 109) who had no DSM-III-R disorder at initial assessment (median age 18 years) were selected from the total sample of the Finnish Adoption Study of Schizophrenia. They were defined as at high versus low genetic risk based upon the lifetime diagnoses of their biological, adopting-away mothers - schizophrenia spectrum disorder versus no spectrum disorder. At initial assessment, adoptive rearing parents were independently evaluated from tape-recorded Rorschach protocols scored as manifesting either high or low Communication Deviance (CD), a composite index of communication patterns that distract and befuddle listeners. Adoptees were independently re-diagnosed after a median interval of 14 years and followed-up from national registers for an additional 7 years. RESULTS: The main effects of genetic liability (G) and CD of the adoptive parents (E), each taken separately, predicted significantly for psychiatric disorders of the adoptees as adults. However, when G, E, and their joint interaction effect were entered into the same logistic model, only the interaction effect was significant. The sample included seven adoptees with schizophrenia spectrum disorders, but a separate analysis to predict them was non-significant. CONCLUSION: Genetic liability for schizophrenia spectrum disorder and an adoptive family rearing variable interact, predicting longitudinally and significantly to broadly defined adoptee psychiatric disorder.     

Human papillomavirus reporting: minimizing patient and laboratory risk

Risk management efforts in the cytology laboratory must address the gap between what can be achieved with medical history's most effective cancer screening test, the Papanicolaou (Pap) test, and even higher entrenched public expectations. Data from the Atypical Squamous Cells of Undetermined Significance (ASCUS)/Low-Grade Squamous Intraepithelial Lesion Triage Study (ALTS) now provide level I clinical evidence from a large, randomized, controlled, multicenter clinical trial that reflex human papillomavirus (HPV) DNA testing of ASCUS cases is generally the preferred method for initial assessment of the most prevalent category of abnormal Pap interpretation. The proposed combination of HPV DNA testing with cytologic Pap testing, the DNA Pap test, further shows the potential to nearly eliminate false-negative screening results, based on sensitivity and negative predictive values reported in available studies. Human papillomavirus DNA testing also appears to represent a significant enhancement for detection of endocervical adenocarcinomas, which are difficult to detect and prevent. Human papillomavirus DNA testing, when used in conjunction with cervical cytology, can significantly reduce risk to both the patient and the laboratory.     

NADPH oxidase-mediated oxidative stress: genetic studies of the p22(phox) gene in hypertension

Increased vascular production of reactive oxygen species, especially superoxide anion, significantly contributes to the oxidative stress associated with hypertension. An enhanced superoxide production causes an increased inactivation of nitric oxide that diminishes nitric oxide bioavailability, thus contributing to endothelial dysfunction and hypertrophy of vascular cells. It has been shown that NADPH oxidases play a major role as the most important sources of superoxide anion in phagocytic and vascular cells. Several experimental observations have described an enhanced superoxide generation as a result of NADPH oxidase activation in hypertension. Although these enzymes respond to stimuli such as vasoactive factors, growth factors, and cytokines, recent data suggest a significant role of the genetic background in the modulation of the expression of its different components. Several polymorphisms have been identified in the promoter and in the coding region of CYBA, the gene that encodes the essential subunit of the NADPH oxidase p22phox, some of which seem to influence significantly the activity of these enzymes in the context of cardiovascular diseases. Among CYBA polymorphisms, genetic investigations have provided a novel marker, the -930(A/G) polymorphism, which determines the genetic susceptibility of hypertensive patients to oxidative stress.     

Exceptions to the rule: Case studies in the prediction of pathogenicity for genetic variants in hereditary cancer genes

Based on current consensus guidelines and standard practice, many genetic variants detected in clinical testing are classified as disease causing based on their predicted impact on the normal expression or function of the gene in the absence of additional data. However, our laboratory has identified a subset of such variants in hereditary cancer genes for which compelling contradictory evidence emerged after the initial evaluation following the first observation of the variant. Three representative examples of variants in BRCA1, BRCA2 and MSH2 that are predicted to disrupt splicing, prematurely truncate the protein, or remove the start codon were evaluated for pathogenicity by analyzing clinical data with multiple classification algorithms. Available clinical data for all three variants contradicts the expected pathogenic classification. These variants illustrate potential pitfalls associated with standard approaches to variant classification as well as the challenges associated with monitoring data, updating classifications, and reporting potentially contradictory interpretations to the clinicians responsible for translating test outcomes to appropriate clinical action. It is important to address these challenges now as the model for clinical testing moves toward the use of large multi‐gene panels and whole exome/genome analysis, which will dramatically increase the number of genetic variants identified.     

EEG correlates (event-related desynchronization) of emotional face elaboration: a temporal analysis

An EEG frequency band analysis was conducted, in order to explore the significance of brain oscillations (delta, theta, alpha and beta) for emotional face comprehension during different post-stimulus time intervals (50-150; 150-250; 250-350; and 350-450 ms). The study was conducted on twenty adults who looked at emotional (happy, sad, angry, fearful) or neutral faces. The results showed that motivational significance of the stimulus can modulate the power synchronization (event-related desynchronization (ERD) decrease) within the frequency band of delta and theta. We propose that delta and theta respond to variations in processing stage of emotional face: whereas, delta reflects updating of the stimulus, theta responds to the emotional significance of face. The findings revealed that emotional discrimination by theta is observable mainly within 150-250 time interval and that it is more distributed on anterior regions, whereas delta is maximally synchronized within 250-350 interval and more posteriorly distributed for all the stimulus type. Finally, a right-hemisphere dominance was found for theta during emotional face comprehension.