Commercially available industry-relevant software in the education of genome variant curation

BACKGROUND Genome analytics is a drastically expanding field, and there is an increasing demand for individuals with the necessary skillset to analyse the genome data that is being generated. A new Masters by coursework was developed to train individuals in genome analytics. Institutions analysing genomes commonly utilise in-house analysis tools, but increasingly commercial software packages that integrate AI are being considered in the research and diagnostic space (De La Vega et al., 2021). AIMS Evaluate the effectiveness of commercially available software as a tool for teaching variant analysis, classification and curation, enabling the analysis of real-world case examples for the teaching, training and assessment of students in the field of diagnostic genome analysis.   Assess students’ perspectives on work readiness after using commercially available tools in the educational environment. DESIGN AND METHODS Students were exposed to the use and limitations of a commercial software package for Human genome curation during two core units of the course. This software was used as part of both in-class training and in their assessment case studies. Students were invited to voluntarily complete an online survey including qualitative and quantitative components featuring Likert scale questions, both pre and post exposure to the software. Paired data from 23 individuals (73% response rate), most aged between 18 and 25, were recorded and anonymised prior to analysis. Qualitative data were thematically coded blind by two individuals independently using emergent coding (Charmaz, 2008). RESULTS AND CONCLUSIONS This project indicates that after the completion of the units that integrated commercially available industry software, we measured increased student confidence (increase in percentage reporting fairly confident or higher) in joining the genetic analysis workforce (significant change from 37% to 70%) and in completing job-specific tasks (significant increase in 7 out of 9 tasks of between 28% to 39%). The aspects of their studies the students valued in relation to these changes and their perception of the usefulness of integration of the commercial software were elucidated from qualitative theming, and can inform others looking to integrate commercially available software within their tertiary degree. REFERENCES Charmaz, K. (2008).  Grounded theory as an emergent method. In S. N. Hesse-Biber & P. Leavy (Eds.), Handbook of emergent methods. (pp. 155-170). The Guilford Press.  De La Vega, F.M., Chowdhury, S., Moore, B., Frise, E., McCarthy, J., Hernandez, E.J., Wong, T., James, K., Guidugli, L., Agrawal, P.B., Genetti, C.A., Brownstein, C.A., Beggs, A.H., Löscher, B.S., Franke, A., Boone, B., Levy, S.E., Õunap, K., Pajusalu, S., … Kingsmore, S.F. (2021). Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. Genome Med, 13(1), 153. https://doi.org/10.1186/s13073-021-00965-

Molecular Inconsistencies in a Fragile X Male with Early Onset Ataxia

Mosaicism for FMR1 premutation (PM: 55–199 CGG)/full mutation (FM: >200 CGG) alleles or the presence of unmethylated FM (UFM) have been associated with a less severe fragile X syndrome (FXS) phenotype and fragile X associated tremor/ataxia syndrome (FXTAS)—a late onset neurodegenerative disorder. We describe a 38 year old male carrying a 100% methylated FM detected with Southern blot (SB), which is consistent with complete silencing of FMR1 and a diagnosis of fragile X syndrome. However, his formal cognitive scores were not at the most severe end of the FXS phenotype and he displayed tremor and ataxic gait. With the association of UFM with FXTAS, we speculated that his ataxia might be related to an undetected proportion of UFM alleles. Such UFM alleles were confirmed by more sensitive PCR based methylation testing showing FM methylation between 60% and 70% in blood, buccal, and saliva samples and real-time PCR analysis showing incomplete silencing of FMR1. While he did not meet diagnostic criteria for FXTAS based on MRI findings, the underlying cause of his ataxia may be related to UFM alleles not detected by SB, and follow-up clinical and molecular assessment are justified if his symptoms worsen

EMQN:Recommendations for genetic testing in inherited cardiomyopathies and arrhythmias

Inherited cardiomyopathies and arrhythmias (ICAs) are a prevalent and clinically heterogeneous group of genetic disorders that are associated with increased risk of sudden cardiac death and heart failure. Making a genetic diagnosis can inform the management of patients and their at-risk relatives and, as such, molecular genetic testing is now considered an integral component of the clinical care pathway. However, ICAs are characterised by high genetic and allelic heterogeneity, incomplete / age-related penetrance, and variable expressivity. Therefore, despite our improved understanding of the genetic basis of these conditions, and significant technological advances over the past two decades, identifying and recognising the causative genotype remains challenging. As clinical genetic testing for ICAs becomes more widely available, it is increasingly important for clinical laboratories to consolidate existing knowledge and experience to inform and improve future practice. These recommendations have been compiled to help clinical laboratories navigate the challenges of ICAs and thereby facilitate best practice and consistency in genetic test provision for this group of disorders. General recommendations on internal and external quality control, referral, analysis, result interpretation, and reporting are described. Also included are appendices that provide specific information pertinent to genetic testing for hypertrophic, dilated, and arrhythmogenic right ventricular cardiomyopathies, long QT syndrome, Brugada syndrome, and catecholaminergic polymorphic ventricular tachycardia.</p

New polymorphic DNA marker close to the fragile site FRAXA

Abstract DNA from a human-hamster hybrid cell line, 908-K1B17, containing a small terminal portion of the long arm of the human X chromosome as well as the pericentric region of 19q was used as starting material for the isolation of an X-chromosome-specific DNA segment, RN1 (DXS369), which identifies a XmnI RFLP. Linkage analysis in fragile X families resulted in a maximum lod score of 15.3 at a recombination fraction of 0.05 between RN1 and fra(X). Analysis of recombinations around the fra(X) locus assigned RN1 proximal to fra(X) and distal to DXS105. Analysis of the marker content of hybrid cell line 908K1B17 suggests the localization of RN1 between DXS98 and fra(X). Heterozygosity of DXS369 is approximately 50%, which extends the diagnostic potential of RFLP analysis in fragile X families significantly

DNA content of a functioning chicken kinetochore

© The Author(s) 2014. In order to understand the three-dimensional structure of the functional kinetochore in vertebrates, we require a complete list and stoichiometry for the protein components of the kinetochore, which can be provided by genetic and proteomic experiments. We also need to know how the chromatin-containing CENP-A, which makes up the structural foundation for the kinetochore, is folded, and how much of that DNA is involved in assembling the kinetochore. In this MS, we demonstrate that functioning metaphase kinetochores in chicken DT40 cells contain roughly 50 kb of DNA, an amount that corresponds extremely closely to the length of chromosomal DNA associated with CENP-A in ChIP-seq experiments. Thus, during kinetochore assembly, CENP-A chromatin is compacted into the inner kinetochore plate without including significant amounts of flanking pericentromeric heterochromatin. © 2014 The Author(s).Wellcome Trust [grant number 073915]; Wellcome Trust Centre for Cell Biology (core grant numbers 077707 and 092076); Darwin Trust of Edinburg