Identification of novel sarcoma risk genes using a two-stage genome wide DNA sequencing strategy in cancer cluster families and population case and control cohorts

Table 3 Summary of SOLAR association and segregation analysis by variant category

avSNP147	Chr^a	Position	Gene	AA change/ Reg. Feature^b	Family #	Cancer Outcome	p-value^c	Q-value^d	Variant Type	SIFT^e	PolyPhen-2	Family MAF^f	MAF 1 K ^g
Rare Private Variants
–	8	145,773,319	ARHGAP39	G1151A	3	Age at onset of cancer	0.01	1.00	NS	Deleterious	Deleterious	0.079	–
						Any Cancer	0.02	1.00
Known Private Rare Variants
rs191227556	16	4,606,552	C16orf96	T62C TF^h Binding + DNase Footprint + DNase Peak	2	Age at onset of cancer	0.01	1.00	NS/ REG	Deleterious	Deleterious	0.105	0.0002
						Any Cancer	0.01	1.00
rs139741319	7	20,721,130	ABCB5	TF binding + matched TF motif + DNase peak	2	Age at onset of cancer	0.01	1.00	REG	–	–	0.105	0.0008
						Any Cancer	0.01	1.00
rs139213019	1	40,929,077	ZFP69B	C1421G	3	Age at onset of cancer	0.01	1.00	NS	Deleterious	Deleterious	0.079	0.0016
						Any Cancer	0.02	1.00
rs116741007	4	1,348,920	UVSSA	G1063A	3	Age at onset of cancer	0.01	1.00	NS	Deleterious	Deleterious	0.079	0..0040
						Any Cancer	0.02	1.00
rs200706119	16	66,503,705	BEAN1	C226A	3	Age at onset of cancer	0.01	1.00	NS	Tolerated	–	0.079	0.0050
rs139373762	1	45,224,937	KIF2C	TF Binding + DNase Footprint + DNase Peak	3	Age at onset of cancer	0.01	1.00	REG	–	–	0.079	0.0012
Candidate Gene Variants
rs45614840	16	334,543	PDIA2	C356G	2	Age at onset of cancer	0.01	1.00	NS	Deleterious	Deleterious	0.105	0.05
						Any Cancer	0.01	1.00

^aChr Chromosome; ^bAmino Acid Change or Regulatory Feature of the Observed Variants; ^cUncorrected p-value; ^dBonferroni corrected p-value for multiple testing (α = 0.05); ^eSIFT Sorting Intolerant from Tolerant. ^fMinor Allele Frequency in Family; ^gMAF 1000G: Minor Allele Frequencies from the 1000 Genomes Database; ^hTF Transcription Factor

ISSN: 1471-2350