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Table 3 Diagnosis prediction for test-patients using PhenoVar

From: PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes

Patient identification number Number of variants ≤ 5% Phenovar ranking (phenotypic weight only) PhenoVar ranking (equal genotypic weight model) Phenovar ranking (disease-causing genotypic weight) Matched traits
1a 3631 11 1 1 2
2a 3848 1 1 1 3
3a 3842 >200 37 7 1
4a 3841 84 11 3 2
5a* 4353 26 2 1 2
6a* 3913 30 3 2 2
7a 3850 >200 131 22 1
8a* 3819 1 1 1 3
9a 4519 2 1 1 2
10a 3799 2 1 1 3
1b 3631 3 1 1 2
2b 3848 6 4 4 2
3b 3842 100 3 1 1
4b 3841 4 1 1 2
5b 4353 3 1 1 3
6b 3913 136 8 2 1
7b 3850 11 1 1 2
8b 3819 156 17 1 1
9b 4519 22 2 1 2
10b 3799 1 1 1 3
  1. The first column in this table lists the identification number assigned to each test-patient. The number of variants with global minor allele frequency (GMAF) of less than 5% present in the modified exome assigned to each patient is highlighted in the second column. The next three columns denote the position of the correct diagnosis for each patient, as ranked by Phenovar using some of its different options: first solely based on the selected phenotypic traits of the respective patient (third column); next, by integrating the phenotypic traits and variants present in the exome of the patient: while assigning the same weight to all variants (fourth column); and finally, by assigning a higher weight to mutations known or predicted to cause disease (fifth column). The last column indicates how many of the traits selected by the medical geneticist “blinded” to the correct diagnoses matched any traits in Phenobase.
  2. *Mutation annotated incorrectly (please refer to discussion).