ACMG clinical laboratory standards for next-generation sequencing

Abstract

Next-generation sequencing technologies have been and continue to be deployed in clinical laboratories, enabling rapid transformations in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude, and continuous advances are being made. It is now feasible to analyze an individual's near-complete exome or genome to assist in the diagnosis of a wide array of clinical scenarios. Next-generation sequencing technologies are also facilitating further advances in therapeutic decision making and disease prediction for at-risk patients. However, with rapid advances come additional challenges involving the clinical validation and use of these constantly evolving technologies and platforms in clinical laboratories. To assist clinical laboratories with the validation of next-generation sequencing methods and platforms, the ongoing monitoring of next-generation sequencing testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics has developed the following professional standards and guidelines.

A novel 33‐Gene targeted resequencing panel provides accurate, clinical‐grade diagnosis and improves patient management for rare inherited anaemias

“…Validation of ORCP followed the 2013 ACMG guidelines (Rehm et al , 2013). Sensitivity and specificity : 44 unique variants identified by ORCP were confirmed by Sanger sequencing (one sequence variant previously identified by Sanger sequencing was not detected by ORCP using set filters).…”

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

“…These reports should also state whether MLPA or other methods have been performed to detect large rearrangements. Examples of effective NGS-based reports are included in the reference list 60,61 .…”

“…The International Agency for Research on Cancer (IARC) 62 has classified genetic variants into five categories (class 5: 'pathogenic'; class 4: 'likely pathogenic'; class 3: 'VUS'; class 2: 'likely not pathogenic'; and class 1: 'not pathogenic'), and this system has been adopted by most laboratories 61,63 . The five-category system is the most comprehensive classification system for molecular geneticists and research experts; however, the Study Group recognizes that a simplified classification in three categories only ('pathogenic' , 'VUS' and 'benign') can be considered for reports to physicians and for genetic counselling purposes, as this distinction is usually adequate for clinical decision-making.…”

“…Given the diversity of PPGL susceptibility genes and associated subphenotypes, the Study Group recommends that the referring physicians provide detailed phenotypic information to assist the laboratory in analysing and interpreting the results of testing. This information could help to prioritize variants for further consideration 61 . An example of this situation is the RET gene, in which the identification of an unquestionable pathogenic mutation has clear clinical implications (for example, thyroidectomy to prevent the development of the associated, highly penetrant medullary carcinoma of the thyroid).…”

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“…However, a large number of variants need interpretation and subsequent classification. Classification of the clinical significance of a genetic variant ranges from benign to pathogenic and, to ensure a consistent and standardized output, variant classification must follow international consensus‐based guidelines (Amendola et al , 2016; Rehm et al , 2013; Richards et al , 2015; Matthijs et al , 2016). …”