Risk categorization for oversight of laboratory-developed tests for inherited conditions

Clinical-genetic analysis of selected genes involved in the development of the human skeleton in 128 Czech patients with suspected congenital skeletal abnormalities

BACKGROUND

Congenital skeletal abnormalities are a heterogeneous group of diseases most commonly associated with small or disproportionate growth, cranial and facial dysmorphisms, delayed bone maturation, etc. Nonetheless, no detailed genotype-phenotype correlation in patients with specific genetic variants is readily available. Ergo, this study focuses on the analysis of patient phenotypes with candidate variants in genes involved in bone growth as detected by molecular genetic analysis.

METHODS

In this study we used molecular genetic methods to analyse the ACAN, COL2A1, FGFR3, IGFALS, IGF1, IGF1R, GHR, NPR2, STAT5B and SHOX genes in 128 Czech children with suspected congenital skeletal abnormalities. Pathogenic variants and variants of unclear clinical significance were identified and we compared their frequency in this study cohort to the European non-Finnish population. Furthermore, a prediction tool was utilised to determine their possible impact on the final protein. All clinical patient data was obtained during pre-test genetic counselling.

RESULTS

Pathogenic variants were identified in the FGFR3, GHR, COL2A1 and SHOX genes in a total of six patients. Furthermore, we identified 23 variants with unclear clinical significance and high allelic frequency in this cohort of patients with skeletal abnormalities. Five of them have not yet been reported in the scientific literature.

CONCLUSION

Congenital skeletal abnormalities may lead to a number of musculoskeletal, neurological, cardiovascular problems. Knowledge of specific pathogenic variants may help us in therapeutic procedures.

Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)

Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.

Reliability and Validity of Proposed Risk Stratification Methods for Laboratory Developed Tests

OBJECTIVES

To determine whether different laboratory developed test (LDT) risk stratification proposals would assign differing levels of risk to selected LDTs as a measure of the validity of those proposals, and whether there would be differing interrater agreement rates as a measure of the reliability of those proposals.

METHODS

A total of 4 reviewers applied 6 proposals for risk stratification of 4 LDTs. Interrater agreement was calculated as a measure of the reliability of the proposals. Also, a consensus risk categorization and concordance rate for each LDT was developed as a measure of the validity of the proposals.

RESULTS

Interrater agreement rates (reliability) ranged from 38% to 100%, and concordance rates (validity) ranged from 20% to 100%.

CONCLUSIONS

A spectrum of reliability and validity was observed depending on the policy used and the LDT categorized. Before implementation or legislation of risk-stratification methods, large evaluations of reliability and validity should be conducted on any proposed method.

Standards and guidelines for canine clinical genetic testing laboratories

This publication represents a proposed approach to quality standards and guidelines for canine clinical genetic testing laboratories. Currently, there are no guidelines for laboratories performing clinical testing on dogs. Thus, there is no consensus set of protocols that set the minimal standards of quality among these laboratories, potentially causing variable results between laboratories, inconsistencies in reporting, and the inability to share information that could impact testing among organizations. A minimal standard for quality in testing is needed as breeders use the information from genetic testing to make breeding choices and irreversible decisions regarding spay, neuter or euthanasia. Incorrect results can have significant impact on the health of the dogs being tested and on their subsequent progeny. Because of the potentially serious consequences of an incorrect result or incorrect interpretation, results should be reviewed by and reported by individuals who meet a minimum standard of qualifications. Quality guidelines for canine genetic testing laboratories should include not only the analytical phase, but also the preanalytical and postanalytical phases, as this document attempts to address.

Improved standards for prenatal diagnosis of citrullinemia

Citrullinemia type I is a urea cycle disorder caused by autosomal recessive mutations in argininosuccinate synthetase 1 (ASS1). In the classical form of this disease, symptoms manifest during the neonatal period as progressive lethargy, poor feeding, and central nervous system depression secondary to hyperammonemia. In pregnancies involving two carrier parents, prenatal diagnosis is important for both reproductive decisions and advanced preparation for neonatal care. The current gold standard for prenatal diagnosis has been the citrulline incorporation assay in addition to DNA mutation analysis. Herein, we review our experience with prenatal diagnosis of citrullinemia type I over the span of 11 years in 41 at-risk pregnancies. During this time, we identified 15 affected fetuses using a combination of molecular and biochemical testing. Given the established limitations of both the citrulline incorporation assay as well DNA mutation analysis, we probed our data to assess the value of amniotic fluid amino acid levels in prenatal diagnosis. Previous publications have proposed using the amniotic fluid ratio of citrulline/(arginine+ornithine) in prenatal diagnosis; however, we noted that amniotic fluid arginine levels were normal in our cohort and hypothesized that the amniotic fluid citrulline/ornithine ratio may be superior. Indeed, our analyses revealed that the ratio of amniotic fluid citrulline/ornithine alone correctly distinguished affected from unaffected fetuses in all cases. During the establishment of a normal reference range we discovered significant elevations in amniotic fluid citrulline levels in at-risk pregnancies compared to the normal population even when the fetus was unaffected. This highlights the importance of using amniotic fluid from carrier mothers when setting up a normal reference range. Finally, we report our experience as one of the first centers to adopt Sanger sequencing for prospective prenatal diagnosis of citrullinemia. While this is clearly a useful tool in many cases, we encountered families for whom molecular analysis uncovered variants of unknown clinical significance or no mutation at all. Based upon these new findings, we recommend a combinatorial approach involving ASS1 sequencing and amniotic fluid citrulline/ornithine for the prenatal diagnosis of citrullinemia type I.

Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge

Massively parallel sequencing has become a powerful tool for the clinical management of patients with applications in diagnosis, guidance of treatment, prediction of drug response, and carrier screening. A considerable challenge for the clinical implementation of these technologies is the management of the vast amount of sequence data generated, in particular the annotation and clinical interpretation of genomic variants. Here, we describe annotation steps that can be automated and common strategies employed for variant prioritization. The definition of best practice standards for variant annotation and prioritization is still ongoing; at present, there is limited consensus regarding an optimal clinical sequencing pipeline. We provide considerations to help define these. For the first time, clinical genetics and genomics is not limited by our ability to sequence, but our ability to clinically interpret and use genomic information in health management. We argue that the development of standardized variant annotation and interpretation approaches and software tools implementing these warrants further support. As we gain a better understanding of the significance of genomic variation through research, patients will be able to benefit from the full scope that these technologies offer.