Fig. 2: Exome-wide analysis of germline variant discovery in the presence and absence of additional genomics datasets. | Genetics in Medicine

Fig. 2: Exome-wide analysis of germline variant discovery in the presence and absence of additional genomics datasets.

From: Evaluating the molecular diagnostic yield of joint genotyping–based approach for detecting rare germline pathogenic and putative loss-of-function variants

Fig. 2

a, b Confusion matrices of the final quality classification status of the germline variants detected in the testicular and breast cancer cohorts, respectively, between the first and second computational runs. c, d Manhattan plots of the p-values for the germline variants, filtered by GATK-JG in both computational runs, to be absent by chance in a randomly selected 239 individuals from the European ancestry. A total of 184,827 variants had a p value < 1.76e−07 (depicted in c by the horizontal dotted red line) in the testicular cancer cohort and 116,078 variants had a p value < 2.04e−07 (depicted in d by the horizontal dotted red line) in the breast cancer cohort, suggesting a non-random under detection effect of the GATK-JG for common variants across coding regions.

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