Genetic testing and counselling has become a fundamental part of the diagnostic work-up and risk stratification in ion channel diseases. The diagnostic yield varies among the different entities. For the most common diseases, there is a class I recommendation for the initiation of genetic testing and counseling. The German law for genetic diagnostics defines all steps of the pathway in detail. In clinical practice, coordination of the different levels of clinical guidance and genetic diagnostics and testing poses a logistic challenge. Involving human geneticists in the procedure is mandatory. For predictive genetic testing, human genetic counseling is mandatory before initiation of the testing and after obtaining the results. As far as causality of genetic variants for the arrhythmic phenotypes is concerned, repeated curations are undertaken to avoid misinterpretation and overdiagnosis.
UNASSIGNED: Die molekulargenetische Untersuchung ist mittlerweile elementarer Bestandteil der Diagnostik bei Verdacht auf angeborene Ursachen für maligne Arrhythmien, Kardiomyopathien oder den plötzlichen Herztod. Die Ergiebigkeit der molekulargenetischen Untersuchung variiert zwischen den einzelnen Erkrankungen. Für die wichtigsten Ionenkanalerkrankungen und Kardiomyopathien besteht mittlerweile eine Klasse-I-Indikation zur Durchführung einer genetischen Testung. Das Gendiagnostikgesetz (GenDG) regelt die Zulassungen und Zuständigkeiten für die verschiedenen Schritte der Untersuchung (von der Veranlassung der Untersuchung bis zur humangenetischen Beratung und Befundmitteilung). Im klinischen Alltag stellt die Koordination der verschiedenen Beteiligten eine gewisse Herausforderung dar. Die Hinzuziehung von Humangenetikspezialisten mit fachspezifischer Kenntnis kardiologischer Erkrankungen ist unbedingt notwendig. Für die sog. „prädiktive genetische Untersuchung“ ist sowohl bei der Veranlassung der Untersuchung als auch bei der erforderlichen humangenetischen Beratung vor und nach der Untersuchung humangenetische Facharztkompetenz bzw. die Zusatzqualifikation für die fachgebundene humangenetische Beratung unerlässlich. In Bezug auf die zuverlässige Beurteilung einer genetischen Variante wird in regelmäßigen Abständen die Kausalität zwischen genetischer Veränderung und Phänotyp überprüft. Dies führt in einigen Fällen, insbesondere bei Varianten mit unklarer Signifikanz (VUS; ACMG [American College of Medical Genetics and Genomics] Klasse 3) zur Neubewertung der Pathogenität einzelner Varianten.

Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is a relatively common inborn error of metabolism, but due to difficulty in accurately predicting affected status through newborn screening, molecular confirmation of the causative variants by sequencing of the ACADVL gene is necessary. Although the ACMG/AMP guidelines have helped standardize variant classification, ACADVL variant classification remains disparate due to a phenotype that can be nonspecific, the possibility of variants that produce late-onset disease, and relatively high carrier frequency, amongst other challenges. Therefore, an ACADVL-specific variant curation expert panel (VCEP) was created to facilitate the specification of the ACMG/AMP guidelines for VLCADD. We expect these guidelines to help streamline, increase concordance, and expedite the classification of ACADVL variants.

The American College of Medical Genetics and Genomics (ACMG)-recommended five variant classification categories (pathogenic, likely pathogenic, uncertain significance, likely benign, and benign) have been widely used in medical genetics. However, these guidelines are fundamentally constrained in practice owing to their focus upon Mendelian disease genes and their dichotomous classification of variants as being either causal or not. Herein, we attempt to expand the ACMG guidelines into a general variant classification framework that takes into account not only the continuum of clinical phenotypes, but also the continuum of the variants\' genetic effects, and the different pathological roles of the implicated genes.
As a disease model, we employed chronic pancreatitis (CP), which manifests clinically as a spectrum from monogenic to multifactorial. Bearing in mind that any general conceptual proposal should be based upon sound data, we focused our analysis on the four most extensively studied CP genes, PRSS1, CFTR, SPINK1 and CTRC. Based upon several cross-gene and cross-variant comparisons, we first assigned the different genes to two distinct categories in terms of disease causation: CP-causing (PRSS1 and SPINK1) and CP-predisposing (CFTR and CTRC). We then employed two new classificatory categories, \"predisposing\" and \"likely predisposing\", to replace ACMG\'s \"pathogenic\" and \"likely pathogenic\" categories in the context of CP-predisposing genes, thereby classifying all pathologically relevant variants in these genes as \"predisposing\". In the case of CP-causing genes, the two new classificatory categories served to extend the five ACMG categories whilst two thresholds (allele frequency and functional) were introduced to discriminate \"pathogenic\" from \"predisposing\" variants.
Employing CP as a disease model, we expand ACMG guidelines into a five-category classification system (predisposing, likely predisposing, uncertain significance, likely benign, and benign) and a seven-category classification system (pathogenic, likely pathogenic, predisposing, likely predisposing, uncertain significance, likely benign, and benign) in the context of disease-predisposing and disease-causing genes, respectively. Taken together, the two systems constitute a general variant classification framework that, in principle, should span the entire spectrum of variants in any disease-related gene. The maximal compliance of our five-category and seven-category classification systems with the ACMG guidelines ought to facilitate their practical application.

Amyotrophic lateral sclerosis (ALS) is the most common type of motor neuron disease whose causes are unclear. The first ALS gene associated with the autosomal dominant form of the disease was SOD1. This gene has a high rate of rare variants, and an appropriate classification is essential for a correct ALS diagnosis. In this study, we re-evaluated the classification of all previously reported SOD1 variants (n = 202) from ALSoD, project MinE, and in-house databases by applying the ACMG-AMP criteria to ALS. New bioinformatics analysis, frequency rating, and a thorough search for functional studies were performed. We also proposed adjusting criteria strength describing how to apply them to SOD1 variants. Most of the previously reported variants have been reclassified as likely pathogenic and pathogenic based on the modified weight of the PS3 criterion, highlighting how in vivo or in vitro functional studies are determining their interpretation and classification. Furthermore, this study reveals the concordance and discordance of annotations between open databases, indicating the need for expert review to adapt the study of variants to a specific disease. Indeed, in complex diseases, such as ALS, the oligogenic inheritance, the presence of genes that act as risk factors and the reduced penetration must be considered. Overall, the diagnosis of ALS remains clinical, and improving variant classification could support genetic data as diagnostic criteria.

Fungi are an essential component of any ecosystem, but they can also cause mild and severe plant diseases. Plant diseases are caused by a wide array of fungal groups that affect a diverse range of hosts with different tissue specificities. Fungi were previously named based only on morphology and, in many cases, host association, which has led to superfluous species names and synonyms. Morphology-based identification represents an important method for genus level identification and molecular data are important to accurately identify species. Accurate identification of fungal pathogens is vital as the scientific name links the knowledge concerning a species including the biology, host range, distribution, and potential risk of the pathogen, which are vital for effective control measures. Thus, in the modern era, a polyphasic approach is recommended when identifying fungal pathogens. It is also important to determine if the organism is capable of causing host damage, which usually relies on the application of Koch\'s postulates for fungal plant pathogens. The importance and the challenges of applying Koch\'s postulates are discussed. Bradford Hill criteria, which are generally used in establishing the cause of human disease, are briefly introduced. We provide guidelines for pathogenicity testing based on the implementation of modified Koch\'s postulates incorporating biological gradient, consistency, and plausibility criteria from Bradford Hill. We provide a set of protocols for fungal pathogenicity testing along with a severity score guide, which takes into consideration the depth of lesions. The application of a standard protocol for fungal pathogenicity testing and disease assessment in plants will enable inter-studies comparison, thus improving accuracy. When introducing novel plant pathogenic fungal species without proving the taxon is the causal agent using Koch\'s postulates, we advise the use of the term associated with the \"disease symptoms\" of \"the host plant\". Where possible, details of disease symptoms should be clearly articulated.

OBJECTIVE: Discordant variant classifications among public databases is one of the well-documented limitations when interpreting the pathogenicity of variants. The aim of this study is to investigate the level of germline variant misannotation from the Human Gene Mutation Database (HGMD) and the annotation concordance between databases.
METHODS: We used a total of 188,106 classified variants (disease-causing mutations [n = 179,454] and polymorphisms [n = 8652]) in 6466 genes from the HGMD. All variants were reanalyzed based on the American College of Medical Genetics and Genomics (ACMG) guidelines and compared to ClinVar database variants.
RESULTS: When variants were classified based on the ACMG guidelines, misclassification was observed in 3.47% (2289/65,896) of variants. The overall concordance between HGMD and ClinVar was 97.62% (52,499/53,780) of variants studied.
CONCLUSIONS: Variants in databases must be used with caution when variant pathogenicity is interpreted. This study reveals the frequency of misannotation of the HGMD variants and annotation concordance between databases in depth.

Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.