Functions Walter Matreyek Pdf 24

Functions Walter Matreyek Pdf 24

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Given the variability of the phenotypes in clinical studies, it is critical to define what a “benign” variant is. Given that the current sensitivity and specificity of protein-based assays is not 100%, we recommend that a MAVE should be reported as a “benign” if the assay result implies that the variant would not cause a functional change, regardless of the phenotype reported in any of the clinical studies. As more functional data are generated for the same variant, a MAVE score may change to reflect the increasing consensus between the individual MAVEs and the composite score. A “benign” MAVE score is not perfect and would not preclude a variant from causality; rather, it indicates that a particular functional assay did not reveal a disruptive change in protein function. Thus, MAVEs may be most useful to triage variants with a clearly benign effect. In cases where the individual MAVE results are conflicting, a composite MAVE score or a change in the MAVE score should be carefully examined by the clinician and relatives of the patient. The detection of two or more MAVEs that predict a benign outcome as opposed to all MAVEs predicting a pathogenic outcome may be clinically useful. It is important to recognize that although MAF varies by population, most variants are rare and, therefore, are less likely to be benign [31, 32]. We therefore recommend that NGS platforms include at least one MAVE for all genes, and when applicable, a second MAVE that characterizes all protein-based functional assays for which data are available.

Reporting of rigor and reproducibility is a critical component of understanding the data generated by functional assays. The reporting of rigor and reproducibility should be a component of the experimental workflow of functional assays that can be clearly distinguished from the reporting of the results of the assays. Rigor and reproducibility are different from the results of the assays. There is no requirement that rigor and reproducibility be reported in experimental papers. In contrast, the reporting of the results of functional assays is a component of the results of the paper. Thus, rigor and reproducibility, unlike results, are not expected in the abstract, while results are. We recommend that the reporting of rigor and reproducibility should be highlighted in the experimental workflow section of the paper.

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