Cytology material is equivalent to tumor tissue in determining mutations of BRCA 1/2 genes in patients with tubo-ovarian high grade serous carcinoma

Gornjec, Andreja; Novakovic, Srdjan; Stegel, Vida; Hocevar, Marko; Pohar Marinsek, Ziva; Gazic, Barbara; Krajc, Mateja; Skof, Erik

doi:10.1186/s12885-019-5535-2

Table 3 BRCA mutations in cytological samples. All patients were previously tested for germline mutations from DNA extracted from the peripheral blood samples

From: Cytology material is equivalent to tumor tissue in determining mutations of BRCA 1/2 genes in patients with tubo-ovarian high grade serous carcinoma

Sample No.	% of TC in the sample	Gene	Mutation	AF in CS	Germline vs. somatic mutation ^i,j	Classification	BIC^b	HGMD^c	UMD^d	LOVD^e	ClinVar^f
Sample No.	% of TC in the sample	Gene	HGVS c.DNA^a HGVS protein^a	AF in CS	Germline vs. somatic mutation ^i,j	Classification	BIC^b	HGMD^c	UMD^d	LOVD^e	ClinVar^f
1	70–80%	BRCA1	c.844_850dupT CATTAC ^h p.(Gln284Leufs*5)	41%	germline	pathogenic	CI	DM	C	AfF	P
2	90%	BRCA1	c.116G > A ^h p.(Cys39Tyr)	97%	germline	pathogenic	UV	DM	/	AfF	P
3	70%	BRCA1	deletion of exons 4–9^g c.(134 + 1_135–1)_(670 + 1_671–1)del p.?	85%	germline	pathogenic	/	DM	/	/	/
4	80%	BRCA1	c.1543G > T ^h p.(Glu515*)	83%	somatic	pathogenic	/	/	/	/	P
5	10%	BRCA1	c.3018_3021delTTCA ^h p.(His1006Glnfs*17)	48%	germline	pathogenic	CI	DM	C	/	P
6	30%	BRCA1	c.1687C > T ^h p.(Gln563*)	53%	germline	pathogenic	CI	DM	C	AfF	P
7	90%	BRCA1	c.850C > T ^h p.(Gln284*)	94%	germline	pathogenic	/	DM	/	/	P
8	70–60%	BRCA1	deletion of exons 4–9^g c.(134 + 1_135–1)_(670 + 1_671–1)del p.?	80%	germline	pathogenic	/	DM	/	/	/
9	30–40%	BRCA2	c.4139_4140dupTT ^h p.(Lys1381Leufs*8)	55%	germline	pathogenic	/	DM	/	/	P
10	80%	BRCA1	c.843_846delCTCA ^h p.(Ser282Tyrfs*15)	93%	Germline	pathogenic	CI	DM	C	AfF	P
11	60%	BRCA1	c.843_846delCTCA ^h p.(Ser282Tyrfs*15)	84%	germline	pathogenic	CI	DM	C	AfF	P
12	> 95%	BRCA2	deletion of exons 22–27^g c.(8754 + 1_8755–1)_(*1_?)del p.?	80%	somatic	pathogenic	/	DM	/	/	/
13	50%	BRCA1	c.843_846delCTCA ^h p.(Ser282Tyrfs*15)	81%	germline	pathogenic	CI	DM	C	AfF	P
14	1–3%	BRCA1	c.1687C > T ^h p.(Gln563*)	51%	germline	pathogenic	CI	DM	C	AfF	P
15	< 10%	BRCA1	c.3436_3439delTGTT ^h p.(Cys1146Leufs*8)	43%	germline	pathogenic	/	DM	C	/	P
16	20%	BRCA1	c.844_850dupTCATTAC ^h p.(Gln284Leufs*5)	46%	germline	pathogenic	CI	DM	C	AfF	P
17	40%	BRCA1	c.4065_4068delTCAA ^h p.(Asn1355Lysfs*10)	54%	germline	pathogenic	CI	DM	/	UV	P

^aThe description of nucleotide sequence variations is in accordance with HGVS nomenclature. DNA variants are numerated according to NCBI reference sequence NM_007294.3 for BRCA1 and NM_000059.3 for BRCA2. First nucleotide of start codon ATG is numerated as 1
^b https://research.nhgri.nih.gov/bic/
^c https://portal.biobase-international.com/
^dhttp://www.umd.be/BRCA1/ and http://www.umd.be/brca2/
^ehttps://lovd.nl/BRCA1 and https://lovd.nl/BRCA2
^f https://www.ncbi.nlm.nih.gov/clinvar/
^gAll large deletions were confirmed by MLPA analysis in cytological and tumor sample
^hAll SNV as well as indel were confirmed by Sanger sequencing in blood samples in case of germline mutations, and in cytological and tumor samples in case of somatic mutation
ⁱMutations were defined as germline, when they were detected in patients blood sample with mutation allele frequencies > 45%
^jMutations were defined as somatic, when detected in FFPE tumor samples and CF samples and not detected in patients blood sample
TC-tumor cells, AF-allele frequency in the sample, CS-cytological sample, P-pathogenic, CI-clinically important, DM-disease causing mutation, C-casual, AfF-affects function, UV-unknown

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ISSN: 1471-2407

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