. 2017 May 11;133(3):469–476. doi: 10.1007/s11060-017-2459-z

Table 1.

Mutation profile of the eight successfully sequenced BM samples

Patient	Sample ID	Gene	Codon change	Variant frequency (%)	Amino acid change	COSMIC ID	Consequence	Confirmational BRCA-analysis
1	N32-08	BRCA1	c.5450C>A	6.6	p.Ser1817Ter		Stop gained
		GPC3	c.359G>A	42.9	p.Arg120His		Missense variant
		PRF1	c.272C>T	11.8	p.Ala91Val		Missense variant
		SMAD4	c.906G>T	6.8	p.Trp302Cys	COSM1389045	Missense variant (splice region)
		TP53	c.829T>G	62.9	p.Cys277Gly	COSM45074	Missense variant
2	N93-95	BRCA1	c.3018_3021delTTCA	86.4	p.His1006GlnfsTer17		Frameshift variant (truncation)
		CHEK2	c.1246A>G	13.1	p.Lys416Glu		Missense variant
		NBN	c.1870C>T	8.4	p.Arg624Cys	COSM1102335	Missense variant
		RB1	c.2104C>A	70.4	p.Gln702Lys	COSM76180	Missense variant (splice region)
		TP53	c.376-2A>G	80.1	Splice mutation	COSM45672	Splice acceptor variant
3	N423-99	CHEK2	c.1246A>G	12.6	p.Lys416Glu		Missense variant
		FH	c.1384C>G	9.7	p.His462Asp		Missense variant
		KIT	c.2540C>T	6.4	p.Thr847Met	COSM1212555	Missense variant
4	N459-08	BRCA1	c.672_4096del^a	99.9	Deletion		Gross deletion	√
		NF1	c.1154G>A	9.8	p.Arg385His	COSM133082	Missense variant
		TP53	c.797G>T	91.8	p.Gly266Val	COSM10958	Missense variant
5	N714-02	ALK	c.2763C>G	20	p.Phe921Leu		Missense variant
		BRCA1	c.2679_2682delGAAA	66	p.Lys893AsnfsTer106		Frameshift variant (truncation)	√
		HNF1A	c.79A>C	50	p.Ile27Leu	COSM430522	Missense variant
6	N926-06	ATM	c.5557G>A	48.3	p.Asp1853Asn	COSM41596	Missense variant
		BRCA1	c.5329dupC	67.6	p.Gln1777ProfsTer74		Frameshift variant (elongation)	√
		MET	c.3029C>T	37.9	p.Thr1010Ile	COSM707	Missense variant
		NBN	c.633T>A	65	p.Asp211Glu		Missense variant
		RUNX1	c.508 + 1G>A	28.6	Splice mutation	COSM24722	Splice donor variant
		SUFU	c.1128G>C	27.8	p.Glu376Asp		Missense variant
		TP53	c.743G>A	23.8	p.Arg248Gln	COSM10662	Missense variant
7	N1210-00	ATM	c.5188C>T	8.3	p.Arg1730Ter	COSM172204	Stop gained
		BRCA2	c.3846_3847delTG	76	p.Val1283LysfsTer2		Frameshift variant (truncation)	√
		EPCAM	c.421A>G	41	p.Thr141Ala		Missense variant
		FANCG	c.890C>T	93.9	p.Thr297Ile	COSM150601	Missense variant
		PTCH1	c.1322G>T	7.1	p.Arg441Leu	COSM95099	Missense variant
		RB1	c.1666C>T	10.6	p.Arg556Ter	COSM888	Stop gained
		TP53	c.797G>A	79	p.Gly266Glu	COSM10867	Missense variant
8	N1250-00	ATM	c.3161C>G	55	p.Pro1054Arg	COSM21827	Missense variant
		BRCA2	c.5946delT	68.2	p.Ser1982ArgfsTer22	COSM26515	Frameshift variant (truncation)
		CDKN2A	c.442G>A	48.2	p.Ala148Thr		Missense variant
		TP53	c.428_429dupTG	71	p.Gln144CysfsTer27		Frameshift variant (elongation)

^a100% loss of heterozygosity of c.4039A>G (Exon 11b) was found in BM compared to heterozygous normal tissue