Cancer Treatment and Transnational Researches in China

Genetic evaluation of BRCA1 associated A complex genes with triple-negative breast cancer susceptibility in Chinese women Hong Ling M.D. Ph.D. Associate Professor Session code: SPO-8 Department of Breast Surgery, Fudan University Shanghai Cancer Center Disclosure of interest: No Introduction Breast Cancer

Highly heterogeneous disease

Molecular Subtypes: Luminal A, Luminal B, HER2 type & Triple-Negative Breast Cancer (TNBC)

BRCA1 or BRCA2 nucleic acid variant

BRCA1/2 mutation mostly happen in TNBC Introduction BRCA1 Associate Complexes Introduction BRCA1 Associate A Complex

Abraxas 4q21.23

Rap80 5q35.2

Brcc36 Xq28

BRE 2p23.2

BABAM1/NBA1 19p13.11 Introduction Single Nucleotide Polymorphisms, SNP

• SNP of BRCA1 associate A complex

• rs8170, rs3745185, rs10406920 --- NBA1 rs11891642 --- BRE

• No Chinese data

Methods Two-Step study

Step I: ---Examine common genetic variants of the BRCA1-A complex genes in patients with TNBC ---Identify the TNBC specific SNPs

Step II: ---Verify these SNPs in non-TNBC patients

Methods Two-Step study

Step I Step II

- 414 TNBC vs 354 controls - 652 non-TNBC vs 890 controls - Polymorphism selection - rs7250266, rs2278256 - Screen for variants - Genotyping - Identified - Velidation rs7250266, rs2278256

Methods Polymorphism Selection

• Functional regions (exons, intron-exon boundaries, promoter region and 3’ UTR) MAF>0.05

• tagSNP: Tagger Pairwise r2>0.8, MAF>0.05

• hot SNP

Exclusion: Hardy–Weinberg equilibrium (HWE): P < 0.05 call rate <0.95 Methods Polymorphism Selection

Abraxas rs77519137, rs13125836, rs72931487, rs12642536, rs17352824 BRCC36 rs895745, rs4898413, rs5945286, rs5945300 Rap80 rs12422, rs3733876, rs11739147, rs365132, rs13360277, rs353465, rs17078658, rs17078630, rs13167812 NBA1 rs2278256, rs3745185, rs10406920, rs8170, rs7250266, rs144376330, rs10403581 BRE rs6547829, rs12464240, rs17709034, rs6721349, rs58720304, rs12478271, rs10173507, rs6737313, rs6710214, rs10209126, rs11891642, rs10189899

Results MAF – NBA1

rs number Position Protein Change Minor Reference MAF Allele Allele Case Control P value

rs2278256 Promoter G A 0.32 0.36 0.06

rs3745185 Intron A G 0.13 0.11 0.21

rs10406920 Intron T C <0.01 0.00 NA

rs8170 Exon synonymous T C 0.00 0.00 NA

rs7250266 Promoter G C 0.14 0.19 <0.01

rs144376330 Exon synonymous T C 0.01 0.01 0.88

rs10403581 Intron C A 0.27 0.28 0.49 rs number Position Minor Reference MAF Allele Allele Results Case Control P

MAF – BRCC36, Rap80 rs895745 Intron A G 0.19 0.22 0.28

rs4898413 Intron T A 0.19 0.22 0.29

rs5945286 Intron T C 0.06 0.06 0.96 rs number Positio Protein Minor Reference MAF n Change Allele Allele Case rs5945300Control IntronP value G A 0.18 0.21 0.17 rs12422 3'UTR G T 0.00 0.00 NA rs3733876 Exon Missense A G 0.17 0.15 0.28 rs11739147 Intron C T 0.36 0.35 0.82 rs365132 Exon synonymous G T 0.47 0.49 0.82 rs13360277 Exon Missense G A 0.02 0.01 0.30 rs353465 Intron C T 0.36 0.35 0.80 rs17078658 Intron G T 0.11 0.10 0.45 rs17078630 Intron T C 0.00 0.00 NA rs13167812 Exon Missense A G 0.00 0.00 NA Results rs number Position Minor Allele Reference MAF MAF – BRE, Abraxas Allele Case Control P value

rs6547829 Intron T C 0.17 0.16 0.72 rs number Position Protein Minor Reference MAF Change Allele rs12464240Allele Intron T C 0.44 0.45 0.94 Case Control P value rs17709034 Intron T C 0.00 0.00 NA rs77519137 3'UTR G A 0.00 <0.01 NA rs6721349 Intron T C <0.01 <0.01 0.94 rs13125836 Exon Missense T rs58720304C 0.003'UTR 0.00C NA T 0.38 0.36 0.58 rs72931487 3' near gene G rs12478271A 0.00Intron 0.00T NA C 0.01 0.01 0.58 rs12642536 Exon Missense C rs10173507T 0.32Intron 0.33C 0.45 T 0.30 0.30 0.96 rs6737313 Intron G A 0.44 0.45 0.74 rs17352824 Intron G A 0.32 0.34 0.35 rs6710214 Intron G A 0.27 0.29 0.54

rs10209126 Intron T C 0.36 0.34 0.62

rs11891642 Intron T C <0.01 <0.01 0.86

rs10189899 Intron A G 0.35 0.33 0.25 Results Genotyping – NBA1 SNP Genotyp Codominant Dominant model Recessive

e OR (95% CI) P OR (95% CI) P OR (95% CI) P rs2278256 AA reference 0.16 reference 0.06 reference 0.29 AG 0.78 (0.58-1.06) 0.76 (0.57-1.02) 0.79 (0.51-1.22) GG 0.70 (0.44-1.11) rs3745185 GG reference 0.36 reference 0.17 reference 1.00 AG 1.29 (0.91-1.84) 1.27 (0.90-1.79) 1.00 (0.33-3.01) AA 1.06 (0.35-3.18) rs7250266 CC reference 0.03 reference 0.01 reference 0.11 GC 0.70 (0.51-0.97) 0.67 (0.49-0.92) 0.52 (0.23-1.17) GG 0.48 (0.21-1.07) rs10403581 AA reference 0.70 reference 0.70 reference 0.40 CA 0.98 (0.73-1.34) 0.95 (0.71-1.26) 0.81 (0.49-1.33) CC 0.80 (0.48-1.34) Results Genotyping – BRCC36, RAP80, Abraxas

SNP Genotype Codominant Dominant model CodominantRecessive Dominant model Recessive SNP Genotype OR (95% CI) P OR (95% CI) P OROR (95%(95% CI)CI) PP OR (95% CI) P OR (95% CI) P rs3733876 GG reference 0.52 reference 0.25 reference 0.79 rs895745 GG reference 0.44 reference reference AG 1.20 (0.87-1.67) 1.20 (0.88-1.65) 1.12 (0.49-2.59) AG SNP0.92 (0.68-Genotype Codominant0.89 (0.66 -1.19) 0.42Dominant 0.64 (0.31 model-1.34) 0.24Recessive

1.25) AA 1.18 (0.51-2.73) OR (95% CI) P OR (95% CI) P OR (95% CI) P AA 0.63 (0.30- rs11739147 TT reference 0 .43 reference 0.43 reference 0.45 1.32) rs12642536 TT reference TC reference1.18 (0.87 -1.59) reference1.12 (0.84 -1.50) 0.84 (0.53-1.32) rs4898413 AA reference 0.45 reference 0.44 reference 0.24 CT 0.95 (0.70-1.28) CC0.72 0.920.92 (0.69 (0.57-1.23)-1.49) 0.58 0.84 (0.53 -1.33) 0.46 AT 0.93 (0.68- 0.89 (0.66-1.19) 0.65 (0.31-1.35) rs365132 TT reference 0.19 reference 0.95 reference 0.09 1.26) CC 0.82 (0.50-1.33) TT 0.63 (0.30- GT 1.12 (0.80-1.58) 1.01 (0.73-1.40) 0.75 (0.53-1.05) rs173528241.32) AA reference reference reference GG 0.80 (0.53-1.21) rs5945286 CC reference 0.07 reference 0.68 reference NA

AG 0.93rs353465 (0.69-1.26) TT0.61 0.90reference (0.68-1.20) 0.47 0.420.82 reference(0.51-1.29) 0.39 0.41 reference 0.46 TC 1.18 (0.76- 1.10 (0.71-1.69) NA GG 0.79 (0.48-1.28) 1.84) TC 1.18 (0.87-1.60) 1.13 (0.85-1.51) 0.84 (0.54-1.33) TT NA CC 0.92 (0.57-1.50) rs5945300 AA reference 0.15 rs17078658reference TT 0.36 referencereference 0.06 reference reference GT 1.18 (0.82-1.69) 0.66 1.17 (0.82-1.66) 0.39 0.86 (0.17-4.29) 0.85 GA 0.93 (0.68- 0.87 (0.65-1.17) 0.44 (0.19-1.06) 1.26) GG 0.89 (0.18-4.44)

SNP Genotype Codominant Dominant model Recessive OR (95% CI) P OR (95% CI) P OR (95% CI) P

Results rs6737313 AA reference reference reference

Genotyping – BRE AG 0.99 (0.72-1.38) 0.93 0.97 (0.71-1.33) 0.87 0.93 (0.65-1.34) 0.70 SNP Genotype Codominant Dominant modelGG 0.93Recessive (0.61-1.40) OR (95% CI) P rs6710214OR (95% CI) AA P referenceOR (95% CI) P reference reference rs6547829 CC reference reference AG 0.83reference (0.62- 1.12) 0.44 0.86 (0.65-1.15) 0.31 1.13 (0.66-1.92) 0.66

CT 1.26 (0.92-1.73) 0.07 1.17 (0.86-1.59)GG 0.33 1.040.38 (0.60 (0.13-1.80)-1.10) 0.06

TT 0.41 (0.14-1.18) rs10209126 CC reference reference reference rs12464240 CC reference reference TC 0.85reference (0.62- 1.15) 0.12 0.93 (0.70-1.24) 0.63 1.50 (0.95-2.35) 0.08

CT 0.99 (0.71-1.37) 1.00 0.99 (0.73-1.35)TT 0.94 1.371.00 (0.85 (0.75-2.21)-1.32) 0.98 TT 0.98 (0.65-1.48) rs10189899 GG reference reference reference rs58720304 TT reference reference reference GA 1.07 (0.79-1.45) 0.46 1.12 (0.84-1.49) 0.45 1.32 (0.82-2.11) 0.25 CT 0.94 (0.70-1.28) 0.48 1.00 (0.75-1.34) 1.00 1.29 (0.83-2.00) 0.25 AA 1.37 (0.83-2.25) CC 1.25 (0.78-2.00) rs10173507 TT reference reference reference CT 0.91 (0.68-1.23) 0.73 0.94 (0.71-1.25) 0.66 1.14 (0.68-1.91) 0.61 CC 1.09 (0.64-1.86) Results Linkage Disequilibrium (LD) – BRE, BRCC36 Results Linkage Disequilibrium (LD) – Rap80, Abraxas

Results Linkage Disequilibrium (LD) – NBA1

Results Haplotype – BRCC36, Rap80, Abraxas, BRE

SNPs Frequency OR 95%CI P SNPs rs6547 rs1246 rs5872 rs1247 Frequencyrs1017350 rs6737OR rs67102195%CI P rs10189 829 4240 0304 8271 7 313 4 rs10209126 899 rs895745 rs4898413 rs5945286C C rs5945300T C T A A C G 0.282 1.00 C C C C T A A C A 0.178 1.31 0.91 - 1.88 0.15 SNPs Frequency OR 95%CI P G A C C T A T C 0.744C G 1.00 G T G 0.159 1.17 0.81 - 1.70 0.40 T T rs3733876T C rs11739147T Grs365132 A rs13360277T Grs353465 0.042 rs170786581.10 0.58 - 2.09 0.78 A T C G 0.188 0.87 0.67-1.13 0.28 C T C C C G G T A 0.036 0.93 0.44 - 1.94 0.84 0.375 1.00 G A T C T G A T C T 0.049C GG 1.09 G 0.68A-1.75 C 0.72 GT 0.031 T 1.00 0.50 - 1.98 1.00 C C C C T A A C G 0.023 0.80 0.3520.35 - 1.84 0.611.15 0.90-1.46 0.27 A SNPs T T GFrequency A COR 0.014 95%CIT 0.77 0.32P A-1.84 0.55 C T T T C C T G A C A 0.023 0.88 0.39 - 1.97 0.75

A T T A T T 0.158 1.28 0.95-1.72 0.10 A rs12642536T rs17352824C T T A C C rareT G A T A 0.022 1.39 0.57 - 3.42 0.47 0.105 1.29 0.90-1.85 0.17 G T A A C T T G0.672 G T C T1.00 rareC GG A A C GT 0.021 G 0.54 0.21 - 1.40 0.21 C C T C T A A T G 0.017 2.17 rare0.76 - 6.13 0.15 G C A G T G0.323 G T0.92 rare 0.74 T- 1.14 0.42G T T C T C C C G G T G 0.016 1.36 0.51 - 3.62 0.54 T G rare rare A A C C C G G T C C rareT AG A A C AC 0.014 T 2.20 0.63 - 7.70 0.22 rare A C T A T T T Arare G T C C rareT GT A A C GC 0.013 T 1.50 0.44 - 5.11 0.52 rare T T T C T G A T A G T T A T G rare

A T G A T T rare Results Haplotype – NBA1

SNPs Frequency OR 95%CI P

rs7250266 rs2278256 rs1443763 rs1040358 rs3745185 30 1 C A C A G 0.528 1.00 C G C A G 0.172 0.99 0.75 - 1.32 0.97 G G C C G 0.149 0.75 0.56-0.99 0.04 C A C C A 0.122 1.14 0.83 - 1.57 0.41 G G C A G 0.015 0.34 0.14 - 0.85 0.02 C A T A G 0.012 1.00 0.38-2.58 0.99 G A C C G rare C G C C G rare C G C C A rare Results Step II - rs7250266, rs2278256 non-TNBC breast cancer vs. control

MAF: 0.18 vs 0.19 (P=0.85)

Genotype • GC: OR= 0.94, 95% CI: 0.75-1.18 • GG: OR= 1.09, 95% CI: 0.64-1.86 P = 0.81 • GC+GG: OR = 0.96, 95% CI 0.77-1.19 P = 0.71

Conclusions

• The mutation carrier of rs7250266 had a lower chance of developing TNBC than wild type carrier in Chinese women.

• rs7250266 is a TNBC-specific SNP.

• The results are different between Chinese and Caucasian.

• Further function investigation is needed.

Thank you!