BMC Genomic Data

Table 2 Results of two-fold cross validations using simulated variants

From: Classification of genetic variants in genes associated with Lynch syndrome using a clinical history weighting algorithm

		Fold A		Fold B
MLH1		Variant type		Variant type
		Pathogenic	Benign	Pathogenic	Benign
HWA Call	Pathogenic	24880	60	24836	35
	Benign	176	49748	166	49765
	No Call	444	692	498	700
Total Trials		25500	50500	25500	50500
PPV		0.9962		0.9978
NPV		0.9978		0.9979
MSH2		Variant Type		Variant Type
		Pathogenic	Benign	Pathogenic	Benign
HWA Call	Pathogenic	24775	12	24262	14
	Benign	111	50329	164	50243
	No Call	614	159	1074	243
Total Trials		25500	50500	25500	50500
PPV		0.9988		0.9986
NPV		0.9991		0.9987
MSH6		Variant Type		Variant Type
		Pathogenic	Benign	Pathogenic	Benign
HWA Call	Pathogenic	23787	9	24014	25
	Benign	180	50262	88	49754
	No Call	1533	229	1398	721
Total Trials		25500	50500	25500	50500
PPV		0.9987		0.9965
NPV		0.9990		0.9995

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ISSN: 2730-6844

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