PPM - Interpretation and Reporting of Copy Number Variants Detected by CMA in Constitutional Testing-Checklist

Checklist

Pdf Summary

The document discusses a set of questions related to the interpretation and reporting of copy number variants (CNVs) detected by chromosomal microarray analysis (CMA) in constitutional testing. Some of the key points covered in the document are as follows:<br /><br />- The first question pertains to reviewing the patient's age, sex, and testing indication, which suggests that these factors may influence the interpretation and reporting process.<br />- The document highlights the importance of verifying the quality metrics and concentration of DNA used in the testing.<br />- It is important for the microarray data to pass all quality control (QC) metrics, indicating that the data meets the necessary standards for accurate analysis.<br />- The use of technical standards from organizations like ACMG/ClinGen for interpreting CNVs, categorizing them as benign, pathogenic, or of uncertain significance, is recommended.<br />- The ISCN 2020 guidelines are suggested for reporting CNVs, which provide a standardized notation system.<br />- The report should include cytogenetic location information, such as chromosome arm and band designations, to specify the genomic region affected by the CNV.<br />- Size and genomic coordinates, including the genome build used, should also be included in the report for accurate mapping of the CNV.<br />- The copy number state, such as single-copy gain or loss, should be clearly indicated in the report.<br />- All clinically significant genes within the CNV should be included for interpretation, as they may have implications for the patient's health.<br />- The report should provide a brief description of the methodology used, including specific details about the platform utilized for the CMA.<br />- It is important to address any limitations of the testing, such as the detection of balanced rearrangements.<br />- The criteria used to determine the reporting of a CNV should be described in the report, ensuring transparency in the decision-making process.<br />- The need for genetic counseling should be addressed in the report, providing guidance on the implications of the CNV for the patient and their family.<br />- If applicable, a recommendation for follow-up testing, including family studies, should be included in the report to further understand the inheritance pattern and potential implications of the CNV.<br /><br />These questions and guidelines serve as a comprehensive checklist for ensuring accurate interpretation and reporting of CNVs detected by CMA in constitutional testing.

Keywords

copy number variants

chromosomal microarray analysis

constitutional testing

interpretation

reporting

quality control

genomic region

copy number state

clinically significant genes

genetic counseling