Genome-wide linkage and exome analyses identify variants of HMCN1for splenic epidermoid cyst

BMC Medical Genetics

Table 1 Number of variants obtained using different filters in a family of splenic epidermoid cyst

Criteria for variants filtering	AFFECTED				NOT AFFECTED		UNCONFIRMED*
Criteria for variants filtering	III:2	IV:3	IV:4	II:2	III:1	II:1	II:3	II:5
Total (Exonic, Splicing)	22903	23110	22925	22686	22705	23389	22900	22748
SNVs (NS, SC)	10735	10836	10679	10576	10641	10939	10630	10576
Not in dbSNP or 1000 Genomes	630	625	606	606	576	687	648	664
Within linkage region
Chr. 1: 181,329,185-211,652,186 bp	8	6	8	9	8	6	7	6
Chr. 14: 36,888,531-58,397,917 bp	5	4	2	2	3	3	4	2
Shared by all AFFECTED	2 (CNTN2 & DDHD1)	2	2	2	-	-	1 (DDHD1)	1
INDELs (FS, non-FS)	218	222	224	232	231	226	232	235
Not in dbSNP or 1000 Genomes	23	25	26	23	19	31	32	25
Within linkage region
Chr. 1: 181,329,185-211,652,186	0	0	0	0	0	1	0	0
Chr. 14: 36,888,531-58,397,917	0	0	0	0	0	0	0	0
Rare variants
Total (NS, SC, FS, Non-FS)	352	360	350	335	337	352	336	367
Within linkage region
Chr. 1: 181,329,185-211,652,186	3	5	5	6	4	5	8	11
Chr. 14: 36,888,531-58,397,917	0	0	0	0	0	0	0	0
Shared by all AFFECTED	1 (HMCN1)	1	1	1	-	-	-	-

Exonic and splicing site variants were filtered based on being single nucleotide variants (SNVs) including non-synonymous (NS) and stop codon (SC) variants, while insertion/deletion (INDELs) including frame-shift (FS) and non-frame-shift (non-FS) variants. Novel variants were those not reported in dbSNP database (dbSNP 137) and rare variants (up to 2%) filter is based on the Japanese allele frequencies data from 1000 Genomes database. *Those family members were set as UNCONFIRMED because their affection status was based on clinical examination of the spleen.

ISSN: 1471-2350