Supplementary Tables S1-S15 from <i>In Silico</i> Systems Biology Analysis of Variants of Uncertain Significance in Lynch Syndrome Supports the Prioritization of Functional Molecular Validation
Authors: Borras Ester , Chang Kyle , Pande Mala , Cuddy Amanda , Bosch Jennifer L. , Bannon Sarah A. , Mork Maureen E. , Rodriguez-Bigas Miguel A. , Taggart Melissa W. , Lynch Patrick M. , You Y. Nancy , Vilar Eduardo 
Published: April 2023

<p>S1. Variants of unknown significance detected in the MD Anderson cohort. S2. Clinical characteristics of the VUS carriers reported in Supplementary Table 1. Pathogenic mutations detected in the same patient carrying a VUS are presented in bold. S3. Clinical characteristics of carriers of variants reclassified as InSIGHT Class 1 and 5. These variants have been used for validation purposes. S4. Validation set of splicing variants obtained from the InSiGHT database that have been already reclassified as Class 1 and 5. S5. Classification at the RNA level using three bioinformatic in silico programs of all reported VUS. Results in gray indicate major alterations which are those that are predicted to destroy or create splicing sites or produce a SS score modification {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S6. Detailed results of in silico RNA bioinformatic prediction tools for those variants classified as affecting Splicing Sites or Inconclusive by In silico prediction tools. Results in gray indicate major alterations. For splice site predictions, major alterations are those that are predicted to destroy or create splicing sites or produce a SS score modification {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S7. Splicing validation set using three bioinformatic in silico programs of a set of splicing variants obtained from the InSIGHT database and that have been already re-classified as Class 1 and 5. Results in gray indicate major alterations, which are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when only one program predict pathogenicity. S8. Detailed in silico RNA bioinformatic prediction results for splicing variants already reclassified as class 5 used for validation of in silico tools. Variants presented here were predicted to be Aberrant or Inconclusive based on our RNA in silico approach. Results in gray indicate major alterations. For splice site prediction, major alternations are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S9. Classification at protein level of reported VUS using five bioinformatic in silico programs. Results in gray indicate major alterations. Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S10. Detailed results of in silico analysis at protein level. S11. Summary of the clinical characteristics and mRNA and protein in silico predictions of the identified MMR VUS. Raw data concerning these analyses is detailed in Supplementary Tables 1-6. S12. Classification at the RNA level using three bioinformatic in silico programs of Identified Variants reclasified as InSIGHT Class 1 and 5 from the MD Anderson database. These variants have been used for validation purposes. Results in gray indicate major alterations, which are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when only one program predict pathogenicity. S13. Detailed in silico RNA bioinformatic prediction results for variants reclassified as InSIGHT class 1 and 5 that obtained results of affecting splicing sites or Inconclusive. Results in gray indicate major alterations. For splice site prediction, major alternations are destroyed or created SS or score modifications {greater than or equal to}20%; Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S14. Classification at protein level using five bioinformatic in silico programs of variants reclassified as InSIGHT Class 1 and 5. These variants were used for validation purposes. Results in gray indicate major alterations. Predictions are interpreted as inconclusive when the same results are not obtained by all the programs used. S15. Summary of the clinical characteristics and mRNA and protein in silico analyses of variants reclassified as InSIGHT Class 1 and 5. These variants were used for valiadation purposes. Information concerning these variants is detailed in supplementary Tables 8-11.</p>