Adapting ACMG/AMP sequence variant classification guidelines for single-gene copy number variants

Abstract

The ability of a single technology, next-generation sequencing, to provide both sequence and copy number variant (CNV) results has driven the merger of clinical cytogenetics and molecular genetics. Consequently, the distinction between the definition of a sequence variant and a CNV is blurry. As the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) standards and guidelines for interpretation of sequence variants address CNV classification only sparingly, this study focused on adapting ACMG/AMP criteria for single-gene CNV interpretation.Methods: CNV-specific modifications of the 2015 ACMG/AMP criteria were developed and their utility was independently tested by three diagnostic laboratories. Each laboratory team interpreted the same 12 single-gene CNVs using three systems: (1) without ACMG/AMP guidance, (2) with ACMG/AMP criteria, and (3) with new modifications. A replication study of 12 different CNVs validated the modified criteria.Results: The adapted criteria system presented here showed improved concordance and usability for single-gene CNVs compared with using the ACMG/AMP interpretation guidelines focused on sequence variants. Conclusion:These single-gene CNV criteria modifications could be used as a supplement to the ACMG/AMP guidelines for sequence variants, allowing for a streamlined workflow and a step toward a uniform classification system for both sequence and copy number alterations.

Application of Next-Generation Sequencing for Genetic Diagnosis in Neonatal Intensive Care Units: Results of a Multicenter Study in China

“…Copy number variations (CNVs) and small variants were identified using VarScan 2 and Genome Analysis Toolkit (GATK) (4.0.10.1). Variants were interpreted and categorized according to the five-tier classification system recommended by the American College of Medical Genetics and Genomics (Richards et al, 2015;Brandt et al, 2020). Small variations were confirmed by Sanger sequencing.…”

Practical guide to genetic screening for inherited eye diseases

“…Variant pathogenicity interpretation has been standardised and classified using the five-class system (Class 5 Pathogenic; 4 Likely pathogenic; 3 Variant of unknown clinical significance; 2 Likely benign; and 1 Benign) for small nucleotide variants and small insertions/deletions (indels) 109 and this classification was also adapted for CNVs in single genes. 110,111 When no disease-causing variants are identified in known genes associated with inherited eye disorders, cases must be re-analysed for novel genes. High impact variants outside the panel can be uploaded to various data sharing platforms including GeneMatcher 112 with the aim of identifying supporting data for causality of novel gene variants in similarly affected individuals for a large collaborative network of researchers.…”

Spectrum of Genetic Variants Associated with Anterior Segment Dysgenesis in South Florida

“…Sanger sequencing was performed to confirm the variants, and when other family members were available only those that showed complete segregation with the phenotype in the entire family were considered pathogenic. We used the American College of Medical Genetics guidelines to interpret variant pathogenicity [15,16].…”