Guidelines For Clinical Interpretation Research Articles

Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes.

Over the last 5 years, RNA sequencing (RNA-seq) has been established and is increasingly applied as an effective approach complementary to DNA sequencing in molecular diagnostics. Currently, three RNA phenotypes, aberrant expression, aberrant splicing, and allelic imbalance, are considered to provide information about pathogenic variants. By providing a high-throughput, transcriptome-wide functional readout on variants causing aberrant RNA phenotypes, RNA-seq has increased diagnostic rates by about 15% over whole-exome sequencing. This breakthrough encouraged the development of computational tools and pipelines aiming to streamline RNA-seq analysis for implementation in clinical diagnostics. Although a number of studies showed the added value of RNA-seq for the molecular diagnosis of individuals with Mendelian disorders, there is no formal consensus on assessing variant pathogenicity strength based on RNA phenotypes. Taking RNA-seq as a functional assay for genetic variants, we evaluated the value of statistical significance and effect size of RNA phenotypes as evidence for the strength of variant pathogenicity. This was determined by the analysis of 394 pathogenic variants, of which 198 were associated with aberrant RNA phenotypes and 723 benign variants. Overall, this study seeks to establish recommendations for integrating functional RNA-seq data into the the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines classification system.

Insights into the intracardiac electrogram from analytical and numerical modelling

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): FWO-Flanders, KU Leuven internal starting grant Introduction and Purpose Cardiac electrograms (EGMs) are one of the most important recordings obtained during electroanatomical voltage mapping and lie at the basis for planning most clinical electrophysiological interventions. Despite its widespread use, the relation of EGM shape and amplitude to the underlying excitation patterns and properties of cardiac tissue is not completely understood. Recent clinical studies [1] have provided important new guidelines on the relation between EGM amplitudes and the thickness of myocardial walls. The aim of this study is to quantify the effect of the wall thickness on EGM amplitudes and duration using analytical and in-silico approaches. Methods We study bipolar EGMs both in-silico and analytically in a homogeneous slab of cardiac tissue (70 x 70 x L mm), where L = 2, 5, or 10 mm, with parallel fiber direction. Simulations were performed using the cardiac electrophysiology simulator openCARP [2]. Cardiac cells were described by the ten Tusscher-Panfilov 2006 model (TP06) [4] with epicardial tissue parameters. A plane wave propagating along the fiber direction was initiated. The extracellular voltage at 147 points arranged in a hemisphere around a point was measured to study the effect of bipolar electrode orientation (see Fig. 1A [3]). In addition, we developed an analytical approach to obtain an EGM, using an equivalent dipole representation of the depolarization wavefront and analytical evaluation of the corresponding integrals. Results Fig. 1B and 1C show the dependency of the EGM properties on the electrode orientation, as represented by the angles α (incidence angle) and β (angle between electrode and propagation direction) [3]. Solid lines represent data from a state-of-the-art numerical methodology, the dashed lines show our analytical estimations. Both the peak-to-peak amplitude and EGM width are well approximated by our theory for all orientations of the electrodes. Fig. 2 shows how the EGM is influenced by the myocardial wall thickness L. Both the amplitude and the duration are in good agreement with our theory. We observe that the amplitude as well as the width increase with the slab thickness, confirming the result in [1] but also delivering an accurate analytical expression for this change. It may thus allow to discriminate effects of thickness and other factors affecting the EGMs, such as substrate abnormalities, for example. Conclusion We developed an analytical approach which can correctly describe the amplitude, duration, and shape of the depolarization part of the EGM. Our theory agrees with the previous in-silico and clinical studies on the influence of catheter orientation [3,5], and wall thickness [1,3]. Subsequent work in this direction is expected to provide better guidelines for clinical interpretation of EGMs, accounting for the effects of the thickness of myocardial wall in the characterization of the substrate of cardiac arrhythmias.

The genetic architecture of pediatric cardiomyopathy

To understand the genetic contribution to primary pediatric cardiomyopathy, we performed exome sequencing in a large cohort of 528 children with cardiomyopathy. Using clinical interpretation guidelines and targeting genes implicated in cardiomyopathy, we identified a genetic cause in 32% of affected individuals. Cardiomyopathy sub-phenotypes differed by ancestry, age at diagnosis, and family history. Infants < 1 year were less likely to have a molecular diagnosis (p < 0.001). Using a discovery set of 1,703 candidate genes and informatic tools, we identified rare and damaging variants in 56% of affected individuals. We see an excess burden of damaging variants in affected individuals as compared to two independent control sets, 1000 Genomes Project (p < 0.001) and SPARK parental controls (p < 1× 10-16). Cardiomyopathy variant burden remained enriched when stratified by ancestry, variant type, and sub-phenotype, emphasizing the importance of understanding the contribution of these factors to genetic architecture. Enrichment in this discovery candidate gene set suggests multigenic mechanisms underlie sub-phenotype-specific causes and presentations of cardiomyopathy. These results identify important information about the genetic architecture of pediatric cardiomyopathy and support recommendations for clinical genetic testing in children while illustrating differences in genetic architecture by age, ancestry, and sub-phenotype and providing rationale for larger studies to investigate multigenic contributions.

Genetic Causes of Cardiomyopathy in Children: First Results From the Pediatric Cardiomyopathy Genes Study.

BackgroundPediatric cardiomyopathy is a genetically heterogeneous disease with substantial morbidity and mortality. Current guidelines recommend genetic testing in children with hypertrophic, dilated, or restrictive cardiomyopathy, but practice variations exist. Robust data on clinical testing practices and diagnostic yield in children are lacking. This study aimed to identify the genetic causes of cardiomyopathy in children and to investigate clinical genetic testing practices.Methods and ResultsChildren with familial or idiopathic cardiomyopathy were enrolled from 14 institutions in North America. Probands underwent exome sequencing. Rare sequence variants in 37 known cardiomyopathy genes were assessed for pathogenicity using consensus clinical interpretation guidelines. Of the 152 enrolled probands, 41% had a family history of cardiomyopathy. Of 81 (53%) who had undergone clinical genetic testing for cardiomyopathy before enrollment, 39 (48%) had a positive result. Genetic testing rates varied from 0% to 97% between sites. A positive family history and hypertrophic cardiomyopathy subtype were associated with increased likelihood of genetic testing (P=0.005 and P=0.03, respectively). A molecular cause was identified in an additional 21% of the 63 children who did not undergo clinical testing, with positive results identified in both familial and idiopathic cases and across all phenotypic subtypes.ConclusionsA definitive molecular genetic diagnosis can be made in a substantial proportion of children for whom the cause and heritable nature of their cardiomyopathy was previously unknown. Practice variations in genetic testing are great and should be reduced. Improvements can be made in comprehensive cardiac screening and predictive genetic testing in first‐degree relatives. Overall, our results support use of routine genetic testing in cases of both familial and idiopathic cardiomyopathy.RegistrationURL: https://www.clinicaltrials.gov; Unique identifier: NCT01873963.

A Cohort Study of the Temporal Stability of ImPACT Scores Among NCAA Division I Collegiate Athletes: Clinical Implications of Test-Retest Reliability for Enhancing Student Athlete Safety.

In this study we examined the temporal stability of the Immediate Post-Concussion Assessment and Cognitive Test (ImPACT) within NCAA Division I athletes across various timepoints using an exhaustive series of statistical models. Within a cohort design, 48 athletes completed repeated baseline ImPACT assessments at various timepoints. Intraclass correlation coefficients (ICC) were calculated using a two-way mixed effects model with absolute agreement. Four ImPACT composite scores (Verbal Memory, Visual Memory, Visual Motor Speed, and Reaction Time) demonstrated moderate reliability (ICC=0.51-0.66) across the span of a typical Division I athlete's career, which is below previous reliability recommendations (0.90) for measures used in individual decision-making. No evidence of fixed bias was detected within Verbal Memory, Visual Motor Speed, or Reaction Time composite scores, and minimal detectable change values exceeded the limits of agreement. The demonstrated temporal stability of the ImPACT falls below the published recommendations, and as such, fails to provide robust support for the NCAA's recommendation to obtain a single preparticipation cognitive baseline for use in sports-related concussion management throughout an athlete's career. Clinical interpretation guidelines are provided for clinicians who utilize baseline ImPACT scores for later performance comparisons.

Abstract 5707: A standard operating procedure for the interpretation of oncogenicity/pathogenicity of somatic mutations

Abstract Somatic variants in cancer-relevant genes are interpreted from multiple partially overlapping perspectives. When considered in discovery and translational research endeavors, it is important to determine if a particular variant observed in a gene of interest is oncogenic/pathogenic or not, as such knowledge provides the foundation on which targeted cancer treatment research is based. In contrast, clinical applications are dominated by diagnostic, prognostic, or therapeutic interpretations which in part also depends on underlying variant oncogenicity/pathogenicity. The Association for Molecular Pathology, the American Society of Clinical Oncology, and the College of American Pathologists (AMP/ASCO/CAP) have published structured somatic variant clinical interpretation guidelines which specifically address diagnostic, prognostic, and therapeutic implications. These guidelines have been well-received by the oncology community. Many variant knowledgebases, clinical laboratories/centers have adopted or are in the process of adopting these guidelines. The AMP/ASCO/CAP guidelines also describe different data types which are used to determine oncogenicity/pathogenicity of a variant, such as: population frequency, functional data, computational predictions, segregation, and somatic frequency. A second collaborative effort created the European Society for Medical Oncology (ESMO) Scale for Clinical Actionability of molecular Targets to provide a harmonized vocabulary that provides an evidence-based ranking system of molecular targets that supports their value as clinical targets. However, neither of these clinical guideline systems provide systematic and comprehensive procedures for aggregating population frequency, functional data, computational predictions, segregation, and somatic frequency to consistently interpret variant oncogenicity/pathogenicity, as has been published in the ACMG/AMP guidelines for interpretation of pathogenicity of germline variants. In order to address this unmet need for somatic variant oncogenicity/pathogenicity interpretation procedures, the Variant Interpretation for Cancer Consortium (VICC, a GA4GH driver project) Knowledge Curation and Interpretation Standards (KCIS) working group (WG) has developed a Standard Operating Procedure (SOP) with contributions from members of ClinGen Somatic Clinical Domain WG, and ClinGen Somatic/Germline variant curation WG using an approach similar to the ACMG/AMP germline pathogenicity guidelines to categorize evidence of oncogenicity/pathogenicity as very strong, strong, moderate or supporting. This SOP enables consistent and comprehensive assessment of oncogenicity/pathogenicity of somatic variants and latest version of an SOP can be found at https://cancervariants.org/wg/kcis/. Citation Format: Peter Horak, Malachi Griffith, Arpad Danos, Beth A. Pitel, Subha Madhavan, Xuelu Liu, Jennifer Lee, Gordana Raca, Shirley Li, Alex H. Wagner, Shashikant Kulkarni, Obi L. Griffith, Debyani Chakravarty, Dmitriy Sonkin. A standard operating procedure for the interpretation of oncogenicity/pathogenicity of somatic mutations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5707.

Sudden infant death as the most severe phenotype caused by genetic modulation in a family with atrial fibrillation

AimsTo assess the functional impact of two combined KCNH2 variants involved in atrial fibrillation, syncope and sudden infant death syndrome. Methods and resultsGenetic testing of a 4-month old SIDS victim identified a rare missense heterozygous in KCNH2 variant (V483I) and a missense homozygous polymorphism (K897T) which is often described as a genetic modifier. Electrophysiological characterisation of heterologous HERG channels representing two different KCNH2 genotypes within the family, showed significant differences in both voltage and time dependence of activation and inactivation with a global gain-of-function effect of mutant versus wild type channels and, also, differences between both types of recombinant channels. ConclusionsThe rare variant V483I in combination with K897T produces a gain-of-function effect that represents a pathological substrate for atrial fibrillation, syncope and sudden infant death syndrome events in this family. Ascertaining the genotype-phenotype correlation of genetic variants is imperative for the correct assessment of genetic testing and counselling. Translational perspectiveAccording to the current guidelines for clinical interpretation of sequence variants, functional studies are an essential tool for the ascertainment of variant pathogenicity. They are especially relevant in the context of sudden infant death syndrome and sudden cardiac death, where individuals cannot be clinically evaluated. The patch-clamp technique is a gold-standard for analysis of the biophysical mechanisms of ion channels.

The landscape of epilepsy-related GATOR1 variants

PurposeTo define the phenotypic and mutational spectrum of epilepsies related to DEPDC5, NPRL2 and NPRL3 genes encoding the GATOR1 complex, a negative regulator of the mTORC1 pathway MethodsWe analyzed clinical and genetic data of 73 novel probands (familial and sporadic) with epilepsy-related variants in GATOR1-encoding genes and proposed new guidelines for clinical interpretation of GATOR1 variants. ResultsThe GATOR1 seizure phenotype consisted mostly in focal seizures (e.g., hypermotor or frontal lobe seizures in 50%), with a mean age at onset of 4.4 years, often sleep-related and drug-resistant (54%), and associated with focal cortical dysplasia (20%). Infantile spasms were reported in 10% of the probands. Sudden unexpected death in epilepsy (SUDEP) occurred in 10% of the families. Novel classification framework of all 140 epilepsy-related GATOR1 variants (including the variants of this study) revealed that 68% are loss-of-function pathogenic, 14% are likely pathogenic, 15% are variants of uncertain significance and 3% are likely benign. ConclusionOur data emphasize the increasingly important role of GATOR1 genes in the pathogenesis of focal epilepsies (>180 probands to date). The GATOR1 phenotypic spectrum ranges from sporadic early-onset epilepsies with cognitive impairment comorbidities to familial focal epilepsies, and SUDEP.

Test-Retest Reliability and Interpretation of Common Concussion Assessment Tools: Findings from the NCAA-DoD CARE Consortium

BackgroundConcussion diagnosis is typically made through clinical examination and supported by performance on clinical assessment tools. Performance on commonly implemented and emerging assessment tools is known to vary between administrations, in the absence of concussion.ObjectiveTo evaluate the test-retest reliability of commonly implemented and emerging concussion assessment tools across a large nationally representative sample of student-athletes.MethodsParticipants (n = 4874) from the Concussion Assessment, Research, and Education Consortium completed annual baseline assessments on two or three occasions. Each assessment included measures of self-reported concussion symptoms, motor control, brief and extended neurocognitive function, reaction time, oculomotor/oculovestibular function, and quality of life. Consistency between years 1 and 2 and 1 and 3 were estimated using intraclass correlation coefficients or Kappa and effect sizes (Cohen’s d). Clinical interpretation guidelines were also generated using confidence intervals to account for non-normally distributed data.ResultsReliability for the self-reported concussion symptoms, motor control, and brief and extended neurocognitive assessments from year 1 to 2 ranged from 0.30 to 0.72 while effect sizes ranged from 0.01 to 0.28 (i.e., small). The reliability for these same measures ranged from 0.34 to 0.66 for the year 1–3 interval with effect sizes ranging from 0.05 to 0.42 (i.e., small to less than medium). The year 1–2 reliability for the reaction time, oculomotor/oculovestibular function, and quality-of-life measures ranged from 0.28 to 0.74 with effect sizes from 0.01 to 0.38 (i.e., small to less than medium effects).ConclusionsThis investigation noted less than optimal reliability for most common and emerging concussion assessment tools. Despite this finding, their use is still necessitated by the absence of a gold standard diagnostic measure, with the ultimate goal of developing more refined and sound tools for clinical use. Clinical interpretation guidelines are provided for the clinician to apply with a degree of certainty in application.

Increasing Antibiotic Resistance in Shigella spp. from Infected New York City Residents, New York, USA.

Approximately 20% of Shigella isolates tested in New York City, New York, USA, during 2013–2015 displayed decreased azithromycin susceptibility. Case-patients were older and more frequently male and HIV infected than those with azithromycin-susceptible Shigella infection; 90% identified as men who have sex with men. Clinical interpretation guidelines for azithromycin resistance and outcome studies are needed.

The sensitivity and specificity of clinical measures of sport concussion: three tests are better than one

ContextA battery of clinical measures of neurocognition, balance and symptoms has been recommended for the management of sport concussion (SC) but is based on variable evidence.ObjectiveTo examine the sensitivity and...

Fetal state assessment using fuzzy analysis of fetal heart rate signals—Agreement with the neonatal outcome

Fetal monitoring is based on analysis of fetal heart rate signal. Visual interpretation is difficult so computer-aided systems for quantitative analysis are commonly used. The clinical interpretation guidelines provided by FIGO (Fédération Internationale de Gynécologie et d’Obstétrique) were used to develop the weighted fuzzy scoring system for qualitative assessment of the fetal state. In this work, agreement of the fuzzy classification system with the neonatal outcome assessment was analyzed. Various datasets were evaluated, depending on interpretation method of the signals which were recorded from patients. The obtained results confirmed possibility of the efficient fetal state assessment using the fuzzy inference method proposed.

A multi-centre international quality control study comparing mRNA splicing assay protocols and reporting practices from the ENIGMA consortium

Classification of intronic and predicted missense changes in the breast cancer susceptibility genes BRCA1 and BRCA2 remains a significant challenge for management of patients carrying these variants. Defective mRNA splicing is established as a pathway to disease, and mRNA analysis of unclassified variants has been shown to assist in classification and genetic counselling. However the interpretation of splicing assay results can be difficult, particularly for those variants that give rise to aberrations in a background of naturally occurring isoforms. The ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) consortium was set up to facilitate research and improve research methods used to classify rare variants in the BRCA1 and BRCA2 (and potentially other) breast cancer predisposition genes. ENIGMA has established a Splicing Working Group, with stated purpose to pool the expertise of different active research groups to conduct large-scale studies that improve the clinical classification of likely spliceogenic variants. An initial project of the Splicing Working Group is to assess the consistency of protocols and results obtained across the multiple participating laboratories from Australia, Europe, UK and the USA. A comparison of mRNA assay protocols in use across 21 labs has identified differences in source material for RNA assays (cultured and uncultured lymphocytes, lymphoblastoid cell lines (LCLs) or constructs), differential use of nonsense-mediated decay inhibitors, and numerous differences in mRNA extraction, DNase treatment and cDNA synthesis methods. A second phase of the project is now underway to determine the impact of the splicing assay methods routinely used by these laboratories on assay data and clinical interpretation of a panel of variants. LCLs were selected from the kConFab repository from carriers of a variant associated with single major aberrant mRNA transcript absent in controls (n=4); carriers of a variant associated with a complicated aberrant mRNA splicing profile involving multiple transcripts including naturally occurring isoforms (n=5); female cancer-free controls (n=11). LCLs have already been distributed to 15 of 20 participating sites, and mRNA assays are underway. Preliminary results indicate that major aberrations associated with several variants mirror results previously observed for mRNA from uncultured lymphocytes. In addition, there is evidence for notable differences in expression of some isoforms compared to results previously observed for RNA from uncultured lymphocytes . This collaborative effort will provide information to inform optimal standardised mRNA splicing assay methodology, and to improve guidelines for clinical interpretation of assay results.

The minnesota multiphasic personality inventory and chronic pain: A conceptual analysis of a long-standing but complicated relationship

The Minnesota Multiphasic Personality Disorder (MMPI) and its successor, the MMPI-2, have a long-standing tradition in the assessment of patients with chronic pain. With the introduction of more narrowly defined and factor-analyzed pain inventories, however, the utility of the MMPI-2 for pain assessment has been brought into question. In this review, the relevant literature is carefully scrutinized from a conceptual and historical perspective. It is concluded that many of the (recent) criticisms are largely ungrounded. Rather than the test itself being at fault or of little utility in the field of pain assessment, it has simply been applied inappropriately (i.e., for determination of pain etiology or underlying personality structure “explaining” the chronic pain). In conclusion, it is suggested that the application of the MMPI-2 in the assessment of patients with chronic pain should correspond more closely to the original aims and psychometric properties of the tool—that is, for screening and the generation of hypotheses regarding comorbid psychopathology and personality features having the potential to complicate the treatment process. Guidelines for clinical interpretation of MMPI-2 profiles with regard to chronic pain are provided.

Further Validation of the Adolescent Form of the SASSI

ABSTRACT The Substance Abuse Subtle Screening Inventory (Adolescent Form) is designed to detect chemical dependence in youth 12 to 18. The author reports accuracy rates of between 80 and 90% compared to clinical diagnoses. In addition, guidelines for clinical interpretation of the subscales are widely used although no empirical validation has been done. This research investigated the validity of the instrument in two studies. Results showed that the SASSI effectively discriminated between an at-risk high school group and clients of a residential treatment center. However, agreement of SASSI classification with clinical diagnosis was only 62%, and Kappa coefficient confirmed the lack of strong agreement. Predictive validity of the clinical subscales was also examined. The Defensiveness (DEF) subscale was found to be a poor indicator of a diagnosis of depressive disorder, and the Correctional (COR) subscale score was not associated with a clinical diagnosis of conduct disorder or oppositional defiant disorder. The hypothesis that a SASSI “rule of thumb” could be used to predict a diagnosis of chemical abuse was not supported. Gender and ethnic differences were also analyzed.