Table S1. Demographics of patients and tumor characteristics.

Supplemental Tables for: A Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers Kim Hirshfield et al. Table S1. Demographics of patients and tumor characteristics. Total number patients, N 100 Gender Male 37 Female 63 Race Caucasian 76 African American 13 Hispanic 8 Asian 3 Mean age (range), years 56.5 (3.7-81.3) Stage at study entry (AJCC TNM) M1 91 M0 9 Mean time from testing to death or current date, days 129 Mean number of therapies prior to genomic testing (range) b 2.5 (0-9) Tumor Type a Breast Triple Negative Ductal, ER+/HER2- Lobular Phyllodes Upper GI (esophageal, GE junction, gastric) 5 Pancreatic 10 Hepatobiliary 4 Colorectal 9 GU (renal, urothelial, prostate, bladder) 8 Gynecologic (ovary, endometrial, cervix, fallopian tube) 16 Sarcoma/GIST 10 Thyroid 5 Neuroendocrine 4 Thoracic (NSCLC, mesothelioma) 3 Skin (melanoma, squamous, basalosquamous) 4 CUP (epithelial) 3 Other 3 a two patients were removed from study and no data is available; b prior therapies included systemic therapy, excludingrai 131, given at time of recurrence or metastasis with the exception of a minority of patients where testing was performed after adjuvant therapy. CUP, cancer of unknown primary; NSCLC, nonsmall cell lung cancer; GIST, gastrointestinal stromal tumor; GI, gastrointestinal; GE, gastroesophageal; ER, estrogen receptor; GU genitourinary. 8 1 2 3

Supplemental Tables for: A Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers Kim Hirshfield et al. Patient number Table S2. Tumor subtypes and comprehensive genomic profile for individual specimens for each patient. Tumor type Specimen 1 Specimen 2 Number prior therapies 1 Pancreatic adenocarcinoma PIK3CA P104R; FBXW7 R479Q; BRCA2 V1862fs*1; KRAS G12D; ARID1A G277fs*123, Y551fs*68; TP53 N239D, T230A; CTCF G48fs*14, T204fs*26; SETD2 T1652fs*14; SPEN D1198fs*2 Duration on prior therapy c, months Duration on targeted therapy d, response 1 1.5 2 months with PI3K inhibitor; Could not be assessed 2 Pancreatic adenocarcinoma No specimen 2 1 n/a 3 Orbital alveolar PIK3CA Q546E, H1047R; MYCN 3 1 n/a rhabdomyosarcoma P44L; CSF1R V32G 4 Patient came off study No specimen 1 4 n/a 5a Ductal carcinoma breast, TNBC, platinum-sensitive 5b Ductal carcinoma breast, TNBC, platinum-resistant 6 GE junction adenocarcinoma 7 Colon, mucinous adenocarcinoma, signet cell BRCA1 E23fs*17; PIK3CA Q546R; RAF1 amp; ATXN7L1-RUNX1 fusion; TP53 R342P BRCA1 E23fs*17; PIK3CA Q546R; ATXN7L1-RUNX1 fusion; TP53 R342P; PTEN E314fs*9; JAK3 A1925; TNK R646C KRAS G13D; TP53 C176F; CDKN2A R58 TP53 C275Y; ZNF217 amp; AURKA amp; CCND2 amp; FGF6 amp; IGF1R R595H BRCA1 E23fs*17; PIK3CA Q546R; RAF1 amp; ATXN7L1-RUNX1 fusion; TP53 R342P; CDKN2A/B homozygous loss; ERBB2 amp; SMAD4 W99 3 1.5 5 months with oral etoposide; Both pre and post-testing were targeted therapy but role of tumor profiling was to identify reversion mutations n/a n/a n/a 4 2 n/a 4 2 n/a 8 Synovial cell cancer none b 3 1 n/a 9 GE junction CCND1 amp; CCND3 amp; CDK6 4 6 2 months with lapatinib;

adenocarcinoma amp; ERBB2 amp; FGF19 amp; could not be assessed FGF3 amp; FGF4 amp; NF1 N1154fs*4; TP53 R248Q 10 CUP epithelial origin, none 2 unknown n/a inguinal 11 Patient came off study No specimen 0 n/a n/a 12 RCC, unclassified type CDKN2A H83Y; MET H1094L 1 6 5 months with crizotinib (previously reported Ref 26) 13 RCC, unclassified type NF2 I280fs*16; CDKN2A W110* 5 2 n/a 14 Merkel Cell Carcinoma (neuroendocrine) 15 Urothelial carcinoma, transitional cell FGF10 amp; RICTOR amp 1 1 1 month with temsirolimus; could not be assessed ERBB2 S310F; CDKN2A/B homozygous loss; FGFR1 G818R; KMD6A Q555*; PIK3CA H1047R; TP53 E286Q 16 Endometrial APC E1577*; ARID1A Y308fs*85; PIK3R1 E555*; RB1 L797fs*13; TP53 R342fs*3 4 1 1 month with lapatinib; could not be assessed 4 unknown n/a 17 GIST BRAF V600E; MCL1 amp BRAF V600E; MCL1 amp 1 0.5 lost to follow-up 18 Anal cancer, squamous DNMT3A F755fs*1; PIK3CA amp; 1 lost to lost to follow-up TSC2 homozygous loss; SOX2 amp follow-up 19 Krukenberg tumor, upper GI source ARID1A G314fs*49; PTPN11 G60V; EGFR VIII 4 2 lost to follow-up; was prescribed afatinib 20 Pancreatic adenocarcinoma CDKN2A/B homozygous loss; KRAS G12D; STK11 splice site 465-1G>A; TP53 V157G 2 5 n/a 21 Thyroid, follicular none 3 3 n/a; Has had sustained responses to multiple serial TKIs despite no identified alteration 22 Ductal carcinoma breast, TNBC FGFR2 amp; MYC amp; PTEN homozygous loss; RB1 L523*; TP53 D41fs*2 23 Colon adenocarcinoma APC S837*, S1465fs*3; GNAS R201H; KRAS G13D; PIK3CA E545A; PTEN D24fs*17 3 P age 3 1 n/a 3 11 1 month; with PI3K inhibitor Discontinued treatment due to

24 GE junction adenocarcinoma 25 Ductal carcinoma breast, TNBC hematoma which could not be attributable to therapy No specimen 2 4 n/a BRCA2 N863fs*11, S1982fs*22; FLT3 N676K; KDM6A R519*; NOTCH1 M2318fs*34 0 n/a 22 months with PARP inhibitor (was targeted therapy based on subsequent profiling); stable disease 5 1 n/a; lost to follow-up 26 Prostate adenocarcinoma PTEN R15fs*17; TMPRSS2-ERG fusion 27 Colon adenocarcinoma KRAS Q61H; TP53 Y220H; APC 4 7 1 month regorafenib Q1429*, R876*; GATA3 splice; PBRM1 R1160; ATRX G1085 28 RCC, papillary NF2 K329fs*17; BAP1 D117fs*9 0 n/a n/a 29 Thyroid cancer, papillary BRAF V600E 0 n/a pending initiation on clinical trial with targeted therapy 30 Colon adenocarcinoma ALK R214H; CTNNB1 splice site 14-2delTTATA, L7fs*8; FGFR1 amp; TP53 R282W; ZNF703 amp 31 Ductal carcinoma breast, TNBC KRAS amp; TP53 S127F; NOTCH1 H2428fs*3; BAP1 homozygous loss; CCND2 amp; SPEN T156fs*5; FGF23 amp; FGF6 amp 5 5 3 month with crizotinib and stereotactic radiosurgery with brain metastases; progression of brain and abdominal metastases 9 4 n/a 32 Ovarian cancer, granulosa ATM W2638*; FOXL2 C134W 1 3 lost to follow-up cell tumor 33 Pancreatic adenocarcinoma No specimen 4 2 n/a 34 Pancreatic adenocarcinoma No specimen 1 2 n/a 35 Pancreatic adenocarcinoma KRAS G12D; TP53 Y236D; CDKN2A 2 3 n/a E88* 36 Melanoma CCDC91-BRAF fusion; EPHA3 D832N; IDH1 R132C; PTEN T277fs*21 1 2 n/a 4 P age

37 Carcinoid (neuroendocrine), Small Intestine EP300 P925T; FGFR4 D425N 4 1.5 23 months with sorafenib; resolution bulky mediastinal lymphadenopathy and stability retroperitoneal lymph nodes TP53 R213*; CCNE1 amp; KRAS 2 1 n/a 38 Esophageal adenocarcinoma amp 39 Pancreatic adenocarcinoma KRAS G12R; APC I1307K KRAS G12R; APC I1307K; STK11 P326fs*43; CDKN2A loss 40 Thyroid cancer, papillary ATR splice site 6552+1G>A; MEN1 S538fs*24; NRAS Q61R 41 Pancreatic adenocarcinoma CDKN2A/B homozygous loss; FGFR3 amp; KDR amp; NF1 T467fs*3; PDGFRA amp 4 2.5 n/a; pending evaluation for CDK4/6 inhibitor 0 n/a n/a 3 4 n/a 42 Mucoepidermoid TP53 E204*; RB1 loss 2 unknown n/a carcinoma maxillary sinus 43 GIST (GE junction) KIT L576_P577insPYDL 0 n/a 36 months and ongoing response with imatinib; NED with resolution of pleural effusion 44a Thyroid cancer, papillary BRAF V600E 2 5.5 3 months with vemurafenib; significant response with reduced number and size of innumerable lung nodules 44b Skin, squamous cell HRAS Q61L n/a n/a n/a carcinoma 45 Colon adenocarcinoma No specimen 3 3 n/a 46 Gallbladder BRCA2 Q373*; TP53 S94*; RB1 1 10 n/a; lost to follow-up Adenocarcinoma R455*; ARID2 G1296fs*5 47 Ampullary adenocarcinoma FLT1 R238C; ERBB2 S310F; NTRK1 1 1 n/a S477Y 48 Mesothelioma, epithelioid DNMT3A P904L; NF2 Q456fs*39 3 23 5 months with temsirolimus with stable 5 P age

49 Leiomyosarcoma PTEN homozygous loss; RB1 homozygous loss; NTRK1 rearrangement, intron 7; ATRX S1156fs*18 50 Endometrial carcinoma, papillary 51 Ductal carcinoma breast, disease, discontinued due to side effects 5 1 n/a CCNE1 amp 3 2 n/a TP53 W53*; BCL6 N73S 7 3 n/a ER+, PR-/Her2-52 Thyroid cancer, papillary BRAF V600E 2 1 Pending initiation of clinical trial with targeted therapy 53 Ductal carcinoma breast, TNBC 54 Ovarian cancer, papillary serous BRCA2 K3326* TP53 R273C; EMSY amp; JUN amp; MYCL1 amp; CRKL amp; ESR1 amp 55 Anaplastic oligodendroglioma IDH1 R132H; PIK3CA H1047R; SETD2 R2024* 56 Colon adenocarcinoma APC Q1429*, R805*; KRAS G12V; PTEN loss 57 Adenoid cystic carcinoma, tonsil BRCA2 K3326*; NOTCH2 Q1479fs*72; TP53 splice site 919+2T>G TP53 R273C; EMSY amp; JUN amp ; MYCL1 amp; MYC amp; CCNE1 amp; SRC amp 8 7 n/a 3 1 n/a none SETD2 Q1147* 1 2 months; ongoing response 2 1 7 months with ongoing response to everolimus 4 9 11 months with regorafenib; lost to followup n/a 58 Cholangiocarcinoma, NRAS Q61K; IDH1 R132G 2 lost to n/a intrahepatic follow-up 59 Pancreatic adenocarcinoma KRAS G12D; STK11 W308fs*8; APC I1307K; TP53 R249S; MCL1 amp 2 9 1 month with pemetrexed; unknown 60 Urothelial carcinoma, papillary/micropapillary 1 4 n/a 61 Urothelial carcinoma, micropapillary 6 P age CCND3 amp; FGF10 amp; MCL1 amp; MLL2 truncation exon 48; RB1 G617fs*36; RICTOR amp; RUNX1 R166Q; TP53 E258K, S215R AKT2 amp; CREBBP E1562*; FGF10 amp; FGFR1 amp; MSH6 S602*; 3 6 n/a

MYST3 amp; RB1 S215*; RICTOR amp; TP53 D281H; ZNF703 amp 62 Colon cancer, cecum KRAS G12V; SMAD4 S32fs*1 5 2 n/a 63 Ovarian cancer NF1 homozygous loss; TP53 R273H 64 Colon adenocarcinoma TP53 T253fs*11; APC R232*; ERBB2 amp 65 Colon adenocarcinoma KRAS G12V; TP53 R273C; APC E138fs*31, P1361fs*3, Q1378fs*1 66 RCC, solid tubular/papillary NF2 splice site 1574+2T>A; type CDKN2A/B homozygous loss; APC I1307K 67 Ductal carcinoma breast, PIK3CA E542K; PTEN A126T, TNBC M35V; TP53 C238Y 68 Carcinoid (neuroendocrine), CDKN1B G97fs*22; MEN1 E468*, mediastinum R420* 69 Mesothelioma, malignant, KDR N793S; NF2 homozygous loss; desmoplastic (sarcomatoid) 70 Endometrial carcinoma, endometrioid 71 Cervical cancer, HPVassociated 72 Ovarian cancer, papillary serous carcinoma 73 Ovarian cancer, NOS, undifferentiated 74 Endometrial adenocarcinoma, mixed serous papillary and endometrioid 7 P age CDKN2A/B homozygous loss PIK3CA H1047R; PTEN Y336*; ALK A1200V; ARID1A G276fs*87, N1253fs*13; PAK3 P53T; EP300 M1470fs*26; BCOR R1131L, P1587fs*53; CTCF T204fs*18; MAP3K1 N1079fs*2; MLL2 P4889fs*18 PIK3CA E545K, amp; RET V706M; SOX2 amp TP53 R280fs*26; MYC amp; MCL1 amp TP53 F212fs*3; MYC amp; NFKBIA amp MTOR E1799K; MCL1 amp; TP53 T155fs*15; ARID1A Q1473*; DNMT3A W330*; EMSY amp; PPP2R1A P179R; CTCF T317fs*91; MAP3K1 splice NF1 homozygous loss; TP53 R273H; ARID1A Q528* 1 5 n/a 4 4 1 month with regorafenib; could not be assessed; insurance denied trastuzumab 3 1 n/a 2 3 2 months with AKT inhibitor; progression of disease 3 1 n/a unknown unknown n/a 0 n/a n/a 1 3 7 months; no interval scans until progression of disease 5 8 n/a 4 3 n/a 8 4 n/a 2 6 n/a

75 CUP, adenocarcinoma, No specimen 2 1 n/a likely pancreatobiliary 76 Melanoma NRAS Q61K; ERBB4 A708T; PIK3CA 1 4 n/a E970K; GRIN2A S1425L; ATRX Q1385* 77 Ductal carcinoma breast, TP53 R175H 1 2 n/a TNBC 78 Invasive lobular carcinoma breast, ER/PR+, Her2- PIK3CA E545K; TP53 G108S; CDH1 S270fs*12 1 2 months with ongoing n/a 79 Chondrosarcoma, dedifferentiated, leiomyosarcomatous 80 GIST KIT V559A; PTEN splice site 209+1G>T; TSC1 V752fs*5; CDKN2A/B homozygous loss; CDKN2C homozygous loss; CDK12 N1439fs*53+; LRP1B homozygous loss response CDKN2A/B loss; IDH2 R172S 0 n/a n/a 0 n/a 2 months with regorafenib; could not be assessed 81 Hemangiopericytoma FGF6 V127M 0 n/a n/a 82 Cholangiocarcinoma KRAS G12D; MCL1 amp; IDH1 2 3 n/a R132H; NFKBIA amp ; JUN amp 83 Fallopian tube cancer TP53 K132Q 4 5 1 month with carboplatin; could not be assessed 84 CUP, adenocarcinoma none 0 n/a n/a 85 Non-small cell lung cancer STK11 homozygous loss; CDKN2A/B homozygous loss; TP53 C176F; KIT splice site 757-2_757-1AG>TT; SMARCA4 E1394*; MLL2 Q809fs*121 86 Phyllodes breast, malignant PIK3R1 Y150fs*22; ATM L608fs*6; CDKN2A/B homozygous loss 87 Phyllodes breast, malignant PIK3R1 K459del; PTEN homozygous loss; FGFR1 N546K; SETD2 N1303fs*7, S260fs*4; FLT3 Q115fs*17 1 lost to follow-up n/a n/a n/a n/a 3 1 1 month with pazopanib; could not be assessed 88 Phyllodes breast, borderline PTEN R233*; EGFR A289V, L62R; n/a n/a n/a 8 P age

malignant 89 Ovarian cancer, carcinosarcoma 90 Ovarian cancer, serous carcinoma SMARCA4 R1093Q; MED12 V41_P49del; SETD2 F573fs*5, R1322* TP53 C238Y; PIK3CA E545K; CDKN2A/B homozygous loss; BRCA2 T3033fs*12; MAP2K1 amp; MYC amp; SETD2 S332*; IGF1R amp TP53 R342*; PTEN homozygous loss; BRCA1 Q172fs*62; BRCA2 truncation exon 11 TP53 C238Y; PIK3CA E545K; CDKN2A/B homozygous loss; BRCA2 T3033fs*12; MYC amp; SETD2 S332*; CCND1 amp; MCL1 amp; FGF19 amp; FGF4 amp; FGF3 amp; C17orf39 amp 0 n/a n/a; patient died prior to initiation 4 n/a 1 month 91 Ewings sarcoma EWSR1-FLI1 fusion 4 n/a n/a 92 Skin, basalosquamous 1 lost to lost to follow-up carcinoma follow-up TP53 V274D; CDKN2A E88*; NOTCH1 splice site 2354-1G>A; NOTCH2 splice site 4005+1G>T; MYST3 amp ; MLL2 S186* 93 PNET CDKN2A homozygous loss 1 unknown n/a 94 Ovarian cancer, serous TP53 G244D; BRCA1 Q1240*; 5 n/a 4 months carcinoma LRP1B D3421fs*96 95 Uterine Sarcoma TP53 R282W; FBXW7 R465C; CDC73 rearrangement, exon 1; LRP1B deletion, exons 8-15; ZNF217 amp 1 6 n/a 96 Soft tissue rhabdomyosarcoma (NOS) 97 Breast Invasive Ductal carcinoma, ER+/HER2- none 2 13 n/a FGFR1 amp; MDM2 amp ; FANCA P1037fs*14; GATA3 S437fs*9+; ZNF703 amp 98a Pancreatic adenocarcinoma KRAS G12V; CDKN2A A21D; TP53 H193R; SMAD4 G86V 98b Follicular lymphoma KRAS G13D ; CDKN2A homozygous loss; BCL2 A131V, A4P, G47D, R129H; TNFAIP3 homozygous loss; MLL2 9 P age KRAS G12V; CDKN2A A21D; TP53 H193R; FGFR1 amp; MYST3 amp 6 2 24 months with everolimus; stable disease on reduced dose and ongoing response 1 3 n/a n/a n/a n/a

K1576fs*2, Q3942*; SOCS1 A3T; CREBBP C1408Y, R1173* 99 Invasive lobular carcinoma PIK3CA M1004I; CDH1 truncation, 9 3 n/a breast, ER/PR+/HER2- intron 9; ESR1 Y537S 100 Carcinoid none 0 n/a n/a equivocal, subclonal, a additional specimen from same patient; TNBC= triple negative breast cancer (ER-/PR-/HER2-); GI=gastrointestinal; TKIs=tyrosine kinase inhibitors; NED=no evidence of disease; Amp=amplification; ER=estrogen receptor; PR=progesterone receptor; PNET, Primitive neuroectoderm tumor HPV= human papilloma virus; NOS= not otherwise specified; IDC= invasive ductal carcinoma; CUP= cancer of unknown primary; GE= gastroesophageal; RCC= renal cell carcinoma; GIST= gastrointestinal stromal tumor. b Synovial cell cancer had no alterations by genomic profiling but displayed t(x;18) SYT SSX2 fusion detected by FISH only. c n/a= No therapy given prior to genomic profiling. d n/a= No targeted therapy given after genomic profiling. 10 P age

Table S3. Identified Genomic Alterations Grouped by Pathways. P53 RAS/RAF/MAPK PI3K/mTOR Fibroblast Growth Factor Receptor/ligand Cell Cycle DNA Repair Transcription factor/ regulator Epigenetic modifier Other RTKs TP53 MDM2 MDM4 KRAS NRAS HRAS BRAF RAF1 ARAF CRKL MAP3K1 MAP2K1 MAP2K2 MAP2K4 NF2 NF1 AKT1 AKT2 AKT3 mtor PIK3CA PIK3CG PIK3R1 PTEN RPTOR RICTOR TSC1 TSC2 FGFR1 FGFR2 FGFR3 FGFR4 FGF3 FGF4 FGF6 FGF10 FGF14 FGF19 FGF23 AURKA AURKB CDKN2A/B CDKN2A CDKN2B CDKN2C CDKN1B CCND1 CCND2 CCND3 CCNE CDK4 CDK6 CDK8 CDK12 CEBPA CHEK1 CHEK2 MED12 STAG2 ATM ATR BARD1 BLM BRCA1 BRCA2 BRIP1 FANCA FANCC FANCD2 FANCF FANCG FANCL MRE11A MUTYH PALB2 PRKDC RAD50 RAD51 ATRX CBFB CDC73 CIC CTCF EP300 ERG EWSR FOXL2 GATA1 GATA2 GATA3 IRF4 JUN MEF2B MITF MYC MYCN MYCL1 NKX2-1 RUNX1 SPEN SOX2 SOX10 WT1 ZNF217 ZNF703 ASXL1 BAP1 DNMT3A DOT1L EZH2 KDM6A KDM5C KDM5A MYST3 MLL2 SETD2 ALK ABL1 AXL BTK CSF1R DDR2 EPHA3 EPHA5 EPHB1 ERBB2 EGFR ERBB4 FLT1 FLT3 FLT4 IGF1R KIT MET NTRK1 NTRK2 NTRK3 PDGFRA PDGFRB RET SRC TGFBR2 11 P age

Immunity Apoptosis Hormone receptor/ regulator/ coactivator NFKB/JAK/STAT SWI/SNF Complex Intracellular Signaling Cascade Wnt/Catenin GPCR MISC Function CD79A CD79B CRLF2 IKZF1 IL7R KLHL6 MYD88 PAX5 PRDM1 TNFAIP3 BCL2 BCL2L2 BCL6 BCOR BCORL1 DAXX MCL1 SPOP AR CREBBP ESR1 HGF INHBA TSHR RARA IKBKE JAK1 JAK2 JAK3 NFKB1A STAT4 SOCS1 ARID1A ARID2 PBRM1 SMARC4A SMARCB1 CBL IRS2 PDK1 PRKAR1A SMAD4 CDH1 CTNNA1 CTNNB1 RNF43 WISP3 GNA11 GNA13 GNAQ GNAS GPR124 GRIN2A PAK3 SMO FBXW7 KEAP1 LRP1B MEN1 NFE2L2 NPM1 NUP93 SF3B1 TOP1 Cell Trafficking Rb Misc Receptor Angiogenesis Self-renewal Protein phosphatase Mismatch Repair Metabolism Unknown ARFRP1 XPO1 RB1 CARD11 MPL PTCH1 SUFU KDR VHL NOTCH1 NOTCH2 PTPN11 PPP2R1A APC FAM123B MSH2 MSH6 GSK3B IDH1 IDH2 STK11 C17orf39 EMSY FAM46C 12 P age

Table S4. Potential germline variants identified in tumor only genomic profiling. Gene protein cds position depth Allele Frequency purity APC I1307K 3920T>A chr5:112175211 1289 47 0.072 APC I1307K 3920T>A chr5:112175211 178 46 0.303 APC I1307K 3920T>A chr5:112175211 871 51 0.600 BCL6 N73S 218A>G chr3:187449662 754 62 0.194 CSF1R V32G 95T>G chr5:149460542 1222 47 0.939 EP300 P925T 2773C>A chr22:41546158 693 49 0.677 FGF6 V127M 379G>A chr12:4553370 507 49 0.200 FGFR4 D425N 1273G>A chr5:176520548 646 47 0.677 FLT1 R238C 712C>T chr13:29008057 1019 50 0.101 IGF1R R595H 1784G>A chr15:99456467 678 39 0.300 KDR N793S 2378A>G chr4:55964435 663 33 0.497 NTRK1 S477Y 1430C>A chr1:156845387 721 51 0.101 SMARCA4 R1093Q 3278G>A chr19:11138522 519 53 0.146 TP53 G108S 322G>A chr17:7579365 510 74 0.656 ARID1A N1253fs*13 3757_3766delAA CGGCGGGA chr1:27099877 383 45 0.461 ATM W2638* 7913G>A chr11:108203613 814 53 0.200 ATR splice 6552+1G>A chr3:142188178 330 48 0.301 BRCA1 E23fs*17 66_67delAG chr17:41276046 625 76 0.732 BRCA1 Q172fs*62 514_514delC chr17:41251824 614 70 0.568 BRCA1 Q1240* 3718C>T chr17:41243830 711 83 0.650 BRCA2 S1982fs*22 5945_5945delT chr13:32914436 1198 49 0.300 BRCA2 K3326* 9976A>T chr13:32972626 1033 22 0.401 CTNNB1 splice 14-2delTTATA chr3:41266010 643 28 0.254 FANCA P1037fs*14 3109_3136delCCT CTCGGCCACACCC CTTCCCAGGAGC chr16:89816240 369 23 0.454 MSH6 S602* 1805C>A chr2:48026927 1010 49 0.458 NCOR1 splice 3401-2A>G chr17:15983380 692 61 0.231 PIK3R1 E555* 1663G>T chr5:67591070 862 32 0.548 RB1 L797fs*13 2388_2388delC chr13:49039402 722 33 0.548 TSC1 V752fs*5 2253_2263delGG TTAGTCTGC chr9:135778119 382 95 0.908 13 P age