Whole genome sequencing for the investigation of canine mammary tumor inheritance - an initial assessment of high-risk breast cancer genes reveal BRCA2 and STK11 variants potentially associated with risk in purebred dogs

Huskey, Anna L. W.; Goebel, Katie; Lloveras-Fuentes, Carlos; McNeely, Isaac; Merner, Nancy D.

doi:10.1186/s40575-020-00084-w

Canine Medicine and Genetics

Table 3 Summary of canine coding variants found within orthologs of human breast cancer susceptibility genes

From: Whole genome sequencing for the investigation of canine mammary tumor inheritance - an initial assessment of high-risk breast cancer genes reveal BRCA2 and STK11 variants potentially associated with risk in purebred dogs

Gene	RS ID Number	Variant Name	Protein Name	Variant Type	Polyphen Score	MAF in EVA Control Cohort (%)	MAF in CMT cases Cohort (%)	P-values (Total CMT Cases versus EVA Controls)	Initially Reported - CMT Heritability Study (Reference #)
BRCA1: ENSCAFT00000043953.1	rs397509570**	c.G3075A**	p.S1025S**	synonymous	NA	49.3	46.4	0.8465	Borge et al. 2011 [46]
BRCA2: ENSCAFT00000010309.3	rs23250374	c.A428G	p.H143R	missense	BENIGN	25.7	42.9	0.0749	Yoshikawa et al. 2008 [47]
	rs850935038**	c.T1158G**	p.C386W**	missense	BENIGN	20.6	42.9	0.0095	Yoshikawa et al. 2008 [47]
	rs851104585**	c.C2144A**	p.P715Q**	missense	BENIGN	0	0	1	–
	rs852009320**	c.C2154A**	p.S718S**	synonymous	NA	0	0	1	–
	rs851813778**	c.C2183T**	p.A728V**	missense	BENIGN	0	0	1	–
	rs851048998**	c.A2222G**	p.N741S**	missense	BENIGN	0	0	1	–
	rs23244160	c.A2401C	p.K801Q	missense	POSSIBLY DAMAGING	31.2	14.3	0.0868	Borge et al. 2011 [46]
	rs8676219	c.A4304G	p.K1435R	missense	BENIGN	25.9	42.9	0.0758	Yoshikawa et al. 2008 [47]
	rs397511123	c.6918_6920delGTT	p.L2307del	In frame deletion	NA	31.2	14.3	0.0868	Borge et al. 2011 [46]
	rs23255542	c.C6930T	p.F2310F	synonymous	NA	28.9	42.9	0.1359	Yoshikawa et al. 2008 [47]
	rs853007536**	c.9995_9996insAAA**	p.M3332delinsIK**	indel	NA	20.9	42.9	0.0162	Yoshikawa et al. 2005 [48]
CDH1: ENSCAFT00000032333.3	rs852509306	c.387_389delCCA	p.129delH	In frame deletion	NA	18.9	17.9	1	Borge et al. 2011 [46]
	rs397512866	c.C945T	p.S315S	synonymous	NA	12.3	14.3	0.7659	Borge et al. 2011 [46]
	rs851557759	c.A2448G	p.E816E	synonymous	NA	8.6	3.6	0.7187	–
PTEN: ENSCAFT00000024821.3	rs397513087	c.C909T	p.L303L	synonymous	NA	3.7	7.1	0.2970	Borge et al. 2011 [46]
STK11: ENSCAFT00000031055.3	–	c.C109T^	p.P37S^	missense	UNKNOWN	0	3.6	0.0654	–
	–	c.A286G^	p.M96V^	missense	BENIGN	0	10.7	0.0003	–
	–	c.T293C^	p.F98S^	missense	BENIGN	0	10.7	0.0003	–
TP53: ENSCAFT00000026465.3	no mutations were found

** Major allele corresponds to the alternate allele, not the reference allele (based on EVA control data)
^ P-values for these variants were generated following the assumption that 200 of the control dogs were successfully sequenced in this location, and no mutations were identified

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ISSN: 2662-9380

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