Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases

Table 3 The results of applying filtering steps over all the variant files (including those with no relevant variant detected)

Panel	Input	Functional sites	Public Pop. DBs	SGP Pop. DB	Quality	Zygosity
Cardiovascular	746	338	76	26	9	2
Deafness	828	257	63	50	17	6
Dermatology	1113	271	71	41	17	5
Dysmorphology/Dysplasia	1529	369	80	43	15	2
Endocrinology	1129	326	61	42	19	5
Gastroenterology	362	190	60	20	6	1
Hematology	1474	324	79	39	18	3
Inborn Errors of Metabolism	1955	571	94	54	24	4
Neurology	2885	718	158	87	29	4
PID	633	309	111	22	6	1
Pulmonology	723	230	74	39	21	3
Renal	507	132	35	21	7	1
Vision	906	341	75	51	17	3
Total (averages)	1138	337	80	41	16	3

The table entries are the average number of variants per panel after applying the respective filter in the column title. The column titled ‘Input’ is the input without applying any filter. The column titled ‘Functional sites’ is for the step of filtering intronic, UTR, synonymous variants. The column titled ‘Public Pop. DBs’ is for the step of filtering variants based on the 1000 Genomes Project database. The column titled ‘SGP Pop. DBs’ is for the step of filtering variants based on the in-house database. The column titled ‘Quality’ is for the step of filtering based on the quality criteria. The column titled ‘Zygosity’ is for the step of excluding non-homozygous variants

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