Novel Insights into Breast Cancer Genetic Variance through RNA Sequencing
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1 Insights into Breast Cancer Genetic Variance through RNA Sequencing SUPPLEMENTARY DATA Anelia Horvath, 1,2* Suresh Babu Pakala, 2* Prakriti Mudvari, 1* Sirigiri Divijendra Natha Reddy, 2 Kazufumi Ohshiro, 2 Sandra Casimiro, 3 Ricardo Pires, 3 Suzanne A. W. Fuqua 4, Masakazu Toi, 5 Luis Costa, 3 Sujit Nair, 2 Saraswati Sukumar, 6 & Rakesh Kumar 1,2# 1 McCormick Genomic and Proteomics Center, 2 Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, District of Columbia 20037, USA; 3 Institute of Molecular Medicine and, Hospital de Santa Maria CHLN, Lisbon, Portugal; 4 Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA; 5 Department of of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan; 6 Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD 21231, USA *Equal contribution #Correspondence: bcmrxk@gwu.edu 1 Manuscript Information Figures: 5 Tables: 4 Supplementary Information Figures: 1 Tables: 4
2 Supplementary Figure 1. Top affected molecular networks were cell death and survival, cellular development, and cellular growth and proliferation, and the top affected canonical pathway was estrogen receptor signaling
3 Supplementary Table 1. SNPs and INDELs identified across 17 Breast Cancer Samples. Sample Variant Total (prior to filtering) (prior to filtering) Known + Filtered Known + Filtered (genic) Known + Filtered (Exonic) TNBC Non-TNBC HER-2 Positive Summary SUM AVE UNIQUE SNPs Genes Indels Genes SNP Genes Indels Genes SNPs Genes Indels Genes SNPs Genes Indels Genes SNPs Genes Indels Genes
4 Supplementary Table 2. Overlap between the variations found by our study and the publically available genome wide association studies (GWAS) genelist #rsid Sample QUAL INFO accepted_hits.baccession functiongvsscorephastcconsscoregeafr EUR AS genomesesp none rs DP=2;VDB=0.0156;AF1=1;AC1=2;DP4=0,0,2,0;MQ=20;FQ=-33 1/1:32,6,0:4 none intergenic unknown PBX1 rs DP=8;VDB=0.0300;AF1=1;AC1=2;DP4=0,1,5,2;MQ=20;FQ=-31;PV4=0.37,0.0014,1,1 1/1:86,4,0:7 NM_ intron unknown PBX1 rs DP=8;VDB=0.0453;AF1=0.4999;AC1=1;DP4=3,1,2,1;MQ=20;FQ=9.38;PV4=1,0.0005,1,1 0/1:36,0,50:37 NM_ intron unknown PBX1 rs DP=14;VDB=0.0453;AF1=0.5;AC1=1;DP4=4,3,4,1;MQ=20;FQ=22;PV4=0.58,0.0057,1,1 0/1:49,0,77:52 NM_ intron unknown PBX1 rs DP=6;VDB=0.0640;AF1=1;AC1=2;DP4=0,0,2,4;MQ=20;FQ=-45 1/1:90,18,0:33 NM_ intron unknown RNF146 rs DP=8;VDB=0.0527;AF1=1;AC1=2;DP4=0,0,2,6;MQ=20;FQ=-51 1/1:116,24,0:45 NM_ intron unknown RNF146 rs DP=2;VDB=0.0673;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33 1/1:40,6,0:8 NM_ intron unknown RNF146 rs DP=5;VDB=0.0673;AF1=1;AC1=2;DP4=0,0,3,2;MQ=20;FQ=-42 1/1:85,15,0:27 NM_ intron unknown RNF146 rs DP=2;VDB=0.0640;AF1=1;AC1=2;DP4=0,0,2,0;MQ=20;FQ=-33 1/1:36,6,0:6 NM_ intron unknown FGFR2 rs DP=4;VDB=0.0453;AF1=1;AC1=2;DP4=0,0,2,2;MQ=20;FQ=-39 1/1:73,12,0:21 NM_ intron unknown FGFR2 rs DP=9;VDB=0.0591;AF1=1;AC1=2;DP4=0,0,6,3;MQ=20;FQ=-54 1/1:123,27,0:51 NM_ intron unknown FGFR2 rs DP=4;VDB=0.0668;AF1=1;AC1=2;DP4=0,0,2,1;MQ=20;FQ=-36 1/1:56,9,0:15 NM_ intron unknown FGFR2 rs DP=5;VDB=0.0661;AF1=1;AC1=2;DP4=0,0,3,2;MQ=20;FQ=-42 1/1:85,15,0:27 NM_ intron unknown LSP1 rs DP=2;VDB=0.0527;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33 1/1:40,6,0:8 NM_ intron unknown LSP1 rs DP=2;VDB=0.0591;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33 1/1:40,6,0:8 NM_ intron unknown none rs DP=12;VDB=0.0300;AF1=1;AC1=2;DP4=0,1,4,5;MQ=20;FQ=-37;PV4=1,7.7e-07,1,0.3 1/1:114,10,0:17 none intergenic unknown none rs DP=6;VDB=0.0232;AF1=1;AC1=2;DP4=0,0,2,4;MQ=20;FQ=-45 1/1:98,18,0:33 none intergenic unknown none rs DP=2;VDB=0.0167;AF1=1;AC1=2;DP4=0,0,0,2;MQ=20;FQ=-33 1/1:36,6,0:6 none intergenic unknown none rs DP=4;VDB=0.0029;AF1=0.543;AC1=1;DP4=1,0,1,2;MQ=20;FQ=-19;PV4=1,0.013,1,1 0/1:45,0,8:11 none intergenic unknown ZMIZ1 rs DP=2;VDB=0.0233;AF1=1;AC1=2;DP4=0,0,2,0;MQ=20;FQ=-33 1/1:36,6,0:6 NM_ intron unknown ZMIZ1 rs DP=4;VDB=0.0542;AF1=1;AC1=2;DP4=0,0,2,1;MQ=20;FQ=-36 1/1:56,9,0:15 NM_ intron unknown BABAM1 rs DP=34;VDB=0.0673;AF1=1;AC1=2;DP4=3,2,26,3;MQ=20;FQ=-35;PV4=0.15,0.0003,1,0.19 1/1:78,8,0:14 NM_ coding-syno A=2226/G=10096 BABAM1 rs DP=30;VDB=0.0673;AF1=1;AC1=2;DP4=0,0,21,7;MQ=20;FQ=-111 1/1:167,84,0:99 NM_ coding-syno A=2226/G=10096 BABAM1 rs DP=22;VDB=0.0376;AF1=0.5;AC1=1;DP4=10,2,8,2;MQ=20;FQ=48.5;PV4=1, ,1, /1:76,0,85:78 NM_ coding-syno A=2226/G=10096 SLC4A7 rs DP=19;VDB=0.0591;AF1=1;AC1=2;DP4=1,1,5,12;MQ=20;FQ=-44;PV4=1,1.2e-07,1,1 1/1:128,17,0:31 NM_ utr unknown SLC4A7 rs DP=6;VDB=0.0527;AF1=1;AC1=2;DP4=0,0,3,3;MQ=20;FQ=-45 1/1:98,18,0:33 NM_ utr SLC4A7 rs DP=7;VDB=0.0368;AF1=0.4998;AC1=1;DP4=2,2,2,1;MQ=20;FQ=5.45;PV4=1, ,1,0.2 0/1:31,0,53:30 NM_ utr unknown SLC4A7 rs DP=13;VDB=0.0640;AF1=1;AC1=2;DP4=0,1,7,3;MQ=20;FQ=-40;PV4=0.36,9.7e-07,1,1 1/1:111,13,0:23 NM_ utr unknown SLC4A7 rs DP=9;VDB=0.0376;AF1=0.5003;AC1=1;DP4=2,1,4,2;MQ=20;FQ=4.77;PV4=1, ,1,0.34 0/1:68,0,30:33 NM_ utr unknown SLC4A7 rs DP=4;VDB=0.0268;AF1=1;AC1=2;DP4=0,0,3,1;MQ=20;FQ=-39 1/1:64,12,0:21 NM_ utr
5 Supplementary Table 3. Number of novel SNPs and INDELs after filtering; the within gene located variants and protein altering variant numbers are also shown, together with the affected genes number Samples TNBC Non-TNBC HER-2 Positive Summary Variants SUM AVE UNIQ (Total) SNPs Indels SNPs (Within Genes) Genes Indels Genes Total* Nonsense Missense (Exonic) Splice Site Genes Indels Genes *Total number SNPs includes synonymous
6 Supplementary Table 4. variants showing allele preferential expression Gene Sample Subtype CHR POS REF ALT QUAL Function GVS AA PROT PPH CONS Phas Cons GERP# Ref reads # Var reads AGRN 78 TNBC G A 131 coding-synonymous none 1517/2046unknown AP2A1 83 TNBC 19 5E+07 G T,A 25.1 splice-3 none NA unknown ARHGAP18 90 TNBC 6 1.3E+08 C T 78.1 missense ALA,THR 382/ ATM 66 Non-TNBC E+08 T G 98 splice-5 none NA unknown BRK1 48 Non-TNBC 3 1E+07 A G 27.3 splice-3 none NA unknown BTBD18 26 HER E+07 C T 116 missense GLU,LYS 564/ CACNA1C 66 Non-TNBC T C 89.4 splice-5 none NA unknown CASC3 56 HER E+07 G A 53.1 missense ALA,THR 670/ CASP3 26 HER E+08 A T 90.2 splice-5 none NA unknown CD44 42 Non-TNBC E+07 A C 24.2 splice-3 none NA unknown CHD3 48 Non-TNBC G T 89.4 coding-synonymous none 1463/1967unknown CHD4 69 TNBC C T 89.1 splice-5 none NA unknown CHGB 66 Non-TNBC G C 28.5 splice-5 none NA unknown COL16A1 49 Non-TNBC 1 3.2E+07 A T,C 26.5 splice-5 none NA unknown CP 42 Non-TNBC 3 1.5E+08 C G 49.5 splice-5 none NA unknown CYC1 26 HER E+08 T G 127 coding-synonymous none 207/326 unknown DBI 83 TNBC 2 1.2E+08 T G 28.1 splice-5 none NA unknown DDX52 56 HER E+07 T A 87.2 missense ILE,PHE 463/ DHX8 76 TNBC E+07 G A 45.5 coding-synonymous none 902/1221 unknown DIP2A 78 TNBC E+07 T A 40.2 missense SER,THR 1096/ DPM1 69 TNBC 20 5E+07 A T 101 splice-5 none NA unknown DRAP1 48 Non-TNBC E+07 A C 66.1 splice-3 none NA unknown DSG1 26 HER E+07 G A 53.1 missense VAL,ILE 808/ EFCAB4A 49 Non-TNBC G C 78.1 missense ARG,PRO 193/ EIF3H 48 Non-TNBC 8 1.2E+08 C G 113 coding-synonymous none 173/353 unknown ENO1 42 Non-TNBC G A 124 coding-synonymous none 123/435 unknown EXOC2 42 Non-TNBC A G 86 coding-synonymous none 567/925 unknown FASN 53 HER2 17 8E+07 G A 93.8 coding-synonymous none 294/2512 unknown FBN1 65 Non-TNBC E+07 T A 28.5 splice-3 none NA unknown FBXO21 42 Non-TNBC E+08 A C 52.1 splice-5 none NA unknown FLNB 42 Non-TNBC 3 5.8E+07 A C 56.1 splice-3 none NA unknown GOLGA4 78 TNBC 3 3.7E+07 G A 130 missense VAL,ILE 887/ HCFC2 90 TNBC 12 1E+08 G C 40.1 missense LYS,ASN 787/ HDAC1 42 Non-TNBC 1 3.3E+07 T G 42.3 splice-5 none NA unknown HDDC2 42 Non-TNBC 6 1.3E+08 G C 112 missense LEU,VAL 117/ HDLBP 90 TNBC 2 2.4E+08 G A 156 coding-synonymous none 1018/1269unknown IBTK 49 Non-TNBC 6 8.3E+07 C T 64 splice-5 none NA unknown ILF3 42 Non-TNBC E+07 T G 25.2 splice-5 none NA unknown INPP4A 83 TNBC 2 9.9E+07 A G 53.1 splice-3 none NA unknown ITPR1 71 Non-TNBC T C 55.5 coding-synonymous none 117/2696 unknown KDM2A 78 TNBC E+07 T G 132 splice-5 none NA unknown LMF2 90 TNBC E+07 G A 59.5 missense PRO,LEU 632/ LOC Non-TNBC E+07 T C 118 coding-synonymous none 70/190 unknown LOC Non-TNBC E+07 T A 77 coding-synonymous none 91/190 unknown LOC Non-TNBC E+07 C G 45.5 missense GLN,HIS 97/190 unknown LRRC42 42 Non-TNBC 1 5.4E+07 G A 25.5 splice-5 none NA unknown LYZ 42 Non-TNBC 12 7E+07 T G 29.1 splice-5 none NA unknown MAGED1 90 TNBC X 5.2E+07 G C 105 missense GLY,ALA 87/ MARS 26 HER E+07 C T 129 missense THR,ILE 217/ MCM6 49 Non-TNBC 2 1.4E+08 A T,C 42.1 splice-5 none NA unknown MCTS1 48 Non-TNBC X 1.2E+08 G T 72.5 splice-3 none NA unknown MLH1 76 TNBC 3 3.7E+07 A T 60.1 splice-3 none NA unknown MTAP 53 HER E+07 A G 47.1 missense LYS,ARG 71/ MTIF2 26 HER E+07 G A 113 missense HIS,TYR 678/ MYO1B 76 TNBC 2 1.9E+08 G A 90 coding-synonymous none 210/1079 unknown
7 Supplementary Table 4 (cont). variants showing allele preferential expression Gene Sample Subtype CHR POS REF ALT QUAL Function GVS AA PROT PPH CONS Phas Cons GERP# Ref reads # Var reads MYOF 56 HER E+07 A G 109 splice-5 none NA unknown MYT1 90 TNBC E+07 T A 31.5 coding-synonymous none 836/1122 unknown NCAPD3 26 HER E+08 A C 137 missense LEU,TRP 1087/ NOP58 78 TNBC 2 2E+08 G A 38.2 splice-5 none NA unknown NOTCH3 48 Non-TNBC E+07 T C 25.5 splice-3 none NA unknown NR2F6 50 TNBC E+07 G A 148 coding-synonymous none 170/405 unknown NR3C1 42 Non-TNBC 5 1.4E+08 A G 19.2 splice-5 none NA unknown PFKL 83 TNBC E+07 C T 116 coding-synonymous none 532/781 unknown PKM 42 Non-TNBC E+07 G C 106 missense PRO,ALA 477/ PKN2 50 TNBC 1 8.9E+07 A G 31.5 splice-3 none NA unknown PLOD1 78 TNBC 1 1.2E+07 G A 25.3 splice-5 none NA unknown PPA1 42 Non-TNBC E+07 C T 67.1 splice-5 none NA unknown PPP2CB 83 HER E+07 C T 60.1 splice-5 none NA unknown PPP4C 42 Non-TNBC 16 3E+07 G C 36.1 splice-5 none NA unknown PRKDC 26 HER E+07 C T 36.5 splice-3 none NA unknown PTPRA 56 HER G T 78.1 splice-3 none NA unknown PTPRS 26 HER A G 89.4 splice-5 none NA unknown RBBP4 53 HER E+07 G A 66.1 coding-synonymous none 26/426 unknown RDX 42 Non-TNBC E+08 A T,G 103 splice-5 none NA unknown RFC4 83 TNBC 3 1.9E+08 T A 46.3 splice-3 none NA unknown RGPD3 53 HER E+08 A G 84 missense-near-splice MET,THR 586/ RNF40 42 Non-TNBC E+07 G C 46.3 splice-5 none NA unknown RNF41 26 HER E+07 C T 146 coding-synonymous-nenone 166/318 unknown RRP7A 42 Non-TNBC E+07 A T 34.2 splice-5 none NA unknown SCNN1A 42 Non-TNBC G A 62.1 coding-synonymous none 483/729 unknown SERPINA3 69 TNBC E+07 T A 222 missense SER,THR 302/ SHARPIN 42 Non-TNBC 8 1.5E+08 C T 119 coding-synonymous-nenone 67/388 unknown SIPA1L2 78 TNBC 1 2.3E+08 C T 94 splice-5 none NA unknown SPHK1 26 HER E+07 C T 74.1 missense ARG,CYS 365/ SPTBN1 53 HER E+07 T C 82.1 coding-synonymous none 1547/2156unknown ST6GALNAC83 HER E+08 G A 40.2 missense ARG,CYS 198/ STRN3 42 Non-TNBC E+07 C T 57 splice-5 none NA unknown SUN2 26 HER E+07 C T 89.4 coding-synonymous none 718/718 unknown SYTL4 49 Non-TNBC X 1E+08 A T 106 splice-5 none NA unknown TFDP2 66 Non-TNBC 3 1.4E+08 C T 48.1 splice-5 none NA unknown TMEM Non-TNBC 2 2E+08 A C 73 splice-5 none NA unknown TNS3 83 HER E+07 C T 30.2 splice-5 none NA unknown TRAP1 26 HER G A 58.5 missense THR,ILE 328/ TRAPPC9 26 HER E+08 G A 128 coding-synonymous none 255/1247 unknown TRIM2 90 TNBC 4 1.5E+08 C G 126 missense SER,CYS 522/ TRIP12 66 Non-TNBC 2 2.3E+08 T A 30.5 splice-3 none NA unknown TSPAN5 78 TNBC 4 9.9E+07 A T 97 splice-5 none NA unknown TTBK2 26 HER E+07 A T 24.8 splice-5 none NA unknown UTP20 42 Non-TNBC 12 1E+08 A T 21.3 splice-3 none NA unknown VTI1B 42 Non-TNBC E+07 A C 66.1 splice-5 none NA unknown WARS 50 TNBC 14 1E+08 A C 46.3 splice-5 none NA unknown WDR47 49 Non-TNBC 1 1.1E+08 A G 34.2 splice-5 none NA unknown XYLT1 171 HER E+07 G A 66.1 missense SER,LEU 450/ YIF1B 69 TNBC E+07 G T 66.1 missense ASP,GLU 104/ ZC3H HER E+07 C T 115 splice-5 none NA unknown ZC3H15 42 Non-TNBC 2 1.9E+08 G A 50.1 splice-5 none NA unknown ZFYVE HER E+07 A G 53.1 splice-5 none NA unknown ZRANB2 66 Non-TNBC 1 7.2E+07 C T 122 splice-5 none NA unknown
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