SUPPLEMENTARY INFORMATION. Exome Sequencing Reveals Frequent Inactivating Mutations in BAP1, ARID1A, and PBRM1 in Intrahepatic Cholangiocarcinomas
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1 SUPPLEMENTARY INFORMATION Exome Sequencing Reveals Frequent Inactivating Mutations in BAP1, ARID1A, and PBRM1 in Intrahepatic Cholangiocarcinomas Yuchen Jiao, Timothy M. Pawlik, Robert A. Anders, Florin M. Selaru, Mirte M. Streppel, Donald J. Lucas, Noushin Niknafs, Violeta Beleva Guthrie, Anirban Maitra, Pedram Argani, G. Johan A. Offerhaus, Juan Carlos Roa, Lewis R. Roberts, Gregory J. Gores, Irinel Popescu, Sorin T. Alexandrescu, Simona Dima, Matteo Fassan, Michele Simbolo, Andrea Mafficini, Paola Capelli, Rita T. Lawlor, Andrea Ruzzenente, Alfredo Guglielmi, Giampaolo Tortora, Filippo de Braud, Aldo Scarpa+, William Jarnagin, David Klimstra, Rachel Karchin, Victor E. Velculescu, Ralph H. Hruban, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, and Laura D. Wood
2 Supplementary Table 1A. Patient Characteristics of Intrahepatic Cholangiocarcinomas (Discovery Screen) n=32 (%) Age, median (range) 64 (35-84) Male gender 13 (40.6) Race** Source of sample White 28 (93.3) Black 2 (6.7) JHH 13 (40.6) MKSCC 12 (37.5) Mayo 5 (15.6) Bucharest 2 (6.3) Cirrhosis*** 1 (5.0) Size, median (range)* 6 (3-30) Bilobar involvement*** 6 (30.0) Nodes AJCC stage N0 29 (90.6) N1 3 (9.4) 1 13 (40.6) 2 12 (37.5) 3 0 (0) 4A 6 (18.8) 4B 1 (3.1) Liver resection^ < Hemihepatectomy 8 (42.1) Margins* Hemihepatectomy 8 (42.1) Extended Hepatectomy 3 (15.8) Vascular invasion R0 30 (96.8) R1 1 (3.2) None 20 (62.5) Microscopic 9 (28.1) Major 3 (9.4) Perineural invasion^^ 0 (0) Biliary invasion^ 4 (21.1) Satellite lesions*** 6 (30.0) Intrahepatic metastases^ 3 (15.8) Adjuvant therapy^^ 7 (38.9) *missing data for 1 sample; **missing data for 2 samples; ***missing data for 12 samples; ^missing data for 13 samples; ^^missing data for 14 samples
3 Supplementary Table 1B. Patient Characteristics of Gallbladder Carcinomas (Discovery Screen) n=9 (%) Age, median (range) 66 (44-81) Male gender 3 (33.3) Race White 7 (77.8) Other 2 (22.2) Source of sample JHH 5 (55.6) MSKCC 4 (44.4) Cirrhosis 0 (0) Size, median (range) 3.5 ( ) Hepatic involvement 5 (55.6) Nodes** N0 0 (0) N1 4 (57.1) N2 3 (42.9) AJCC stage 1 0 (0) 2 1 (11.1) 3 1 (11.1) 4 7 (77.8) Liver resection* None 1 (12.5) < Hemihepatectomy 5 (62.5) Hemihepatectomy 1 (12.5) Extended Hepatectomy 1 (12.5) Margins R0 4 (44.4) R1 1 (11.1) R2 4 (44.4) Vascular invasion None 5 (55.6) Microscopic 1 (11.1) Major 3 (33.3) Perineural invasion 5 (55.6) Biliary invasion 4 (44.4) Satellite lesions 2 (22.2) Differentiation Well 1 (11.1) Moderate 4 (44.4) Poor 4 (44.4) Adjuvant therapy 4 (44.4) *missing data from 1 sample; **missing data from 2 samples
4 Supplementary Table 2. Summary of Exome Sequencing Data for Intrahepatic Cholangiocarcinoma and Gallbladder Carcinoma CHOL01 CHOL02 CHOL04 CHOL06 CHOL07 CHOL08 CHOL09 CHOL11 Average Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Bases in target region 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 Bases sequenced (after quality filtering) 14,198,681,102 16,196,288,850 14,701,825,650 13,491,509,250 15,686,466,450 10,486,275,600 7,789,824,000 15,985,524,000 12,571,905,750 15,116,581,800 16,927,057,800 17,845,498,200 7,375,270,050 14,313,461,100 15,278,541,750 16,204,460,100 15,657,389,850 Bases mapped to genome 13,025,536,864 13,830,594,300 12,545,220,675 11,500,570,725 13,469,933,850 8,929,201,050 6,650,475,975 13,654,509,225 10,800,441,375 12,961,188,750 14,472,141,300 15,075,098,850 6,306,968,475 12,313,584,225 13,138,631,175 13,935,080,175 13,450,977,225 Bases mapped to targeted region 6,141,629,620 6,723,306,319 6,176,292,182 5,566,419,367 6,612,335,315 4,537,304,952 3,325,833,331 6,630,032,834 5,385,843,413 6,259,959,263 7,230,636,099 7,043,893,327 2,984,993,247 6,052,273,054 6,633,362,802 6,836,506,962 6,830,756,154 Average # of reads per targeted base Targeted bases with at least 10 reads (%) 91.1% 93.1% 93.3% 92.7% 93.6% 91.1% 91.5% 93.4% 93.3% 93.3% 93.6% 93.9% 90.1% 93.3% 93.4% 93.2% 93.4% Known SNPs identified in targeted region 18,418 18,538 18,661 18,082 18,291 18,249 18,474 18,655 18,759 18,548 18,590 20,672 20,510 18,455 18,470 18,657 18,752 CHOL12 CHOL13 CHOL14 CHOL15 CHOL18 CHOL19 CHOL20 CHOL24 Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 14,010,898,050 12,872,900,400 13,408,142,250 13,585,054,800 16,737,465,600 15,413,478,150 13,045,099,500 14,660,258,400 16,773,412,000 16,763,945,000 12,737,019,200 15,899,201,800 13,211,924,800 12,895,033,400 12,892,702,000 14,169,198,800 12,064,277,550 10,957,897,800 11,522,596,200 11,673,324,825 14,356,298,850 13,139,564,550 11,254,892,775 12,592,745,775 16,042,819,500 15,976,945,200 12,284,667,200 15,361,453,500 12,722,569,000 12,384,586,100 12,425,996,000 13,642,309,200 5,744,393,735 5,080,213,100 5,804,745,164 5,869,080,323 7,387,372,730 6,461,573,047 5,482,685,993 6,283,765,656 7,305,981,861 8,911,282,657 5,700,456,314 8,226,830,339 6,042,136,154 6,431,296,610 5,737,262,582 7,140,397, % 93.2% 92.2% 93.4% 92.7% 93.6% 92.2% 92.3% 91.1% 88.9% 89.9% 90.2% 89.5% 89.6% 90.5% 90.3% 18,749 18,864 18,374 18,539 18,592 18,841 18,685 18,772 19,107 18,923 18,207 18,260 18,174 18,183 18,449 18,446 CHOL25 CHOL26 CHOL27 CHOL28 CHOL35 CHOL37 CHOL40 CHOL42 Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 15,798,185,200 14,999,627,600 9,527,156,800 14,455,493,800 17,147,773,800 13,845,717,800 15,478,029,400 21,016,393,200 16,001,122,000 15,043,697,600 13,319,743,200 13,714,394,200 12,778,900,200 13,755,367,000 9,156,170,800 16,457,293,000 15,217,573,900 14,451,768,200 9,178,803,800 13,942,599,300 16,549,104,400 13,358,455,800 14,950,797,800 18,795,200,500 15,426,362,900 13,427,491,900 12,842,153,900 12,227,692,000 12,293,982,200 12,335,483,400 8,795,552,200 15,836,538,400 7,074,076,275 7,574,619,352 4,225,716,420 7,330,652,744 7,677,840,428 7,055,679,700 6,996,434,725 6,105,910,213 6,968,238,201 4,400,300,375 5,878,301,045 3,855,352,217 5,547,409,266 4,196,704,175 4,095,386,950 7,449,408, % 90.4% 89.1% 90.0% 90.7% 90.2% 90.0% 90.8% 90.6% 89.7% 89.0% 89.1% 89.2% 89.1% 88.7% 90.7% 18,178 18,158 18,127 18,182 18,131 18,087 18,080 18,525 18,280 18,492 18,143 18,475 17,916 18,344 17,738 18,155 CHOL44 CHOL47 CHOL48 CHOL49 CHOL50 CHOL52 CHOL53 CHOL54 Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 15,854,213,400 11,431,708,400 15,725,616,800 13,912,733,800 14,323,524,600 11,825,366,000 9,670,339,000 12,926,739,800 17,598,123,200 16,634,612,400 12,140,358,800 13,088,685,800 13,650,809,600 12,440,110,200 15,422,861,600 14,871,107,200 15,292,409,600 11,011,503,500 15,211,034,800 13,422,618,000 13,785,521,100 11,360,564,300 9,324,433,600 12,434,482,300 16,930,240,300 15,984,064,700 11,689,451,100 12,575,939,500 12,976,792,100 11,988,947,500 14,231,286,600 14,347,948,300 7,222,732,785 5,199,260,088 7,293,085,863 6,206,280,620 6,615,835,412 5,189,578,858 4,514,174,809 5,669,524,875 8,026,633,625 7,139,764,921 5,499,686,556 5,811,799,856 5,992,288,697 5,445,590,468 5,747,178,581 6,619,627, % 89.9% 90.0% 90.1% 90.0% 89.2% 89.2% 90.5% 90.7% 90.9% 89.2% 90.3% 89.9% 90.4% 89.8% 90.7% 18,100 18,187 17,959 18,107 18,118 18,215 18,113 18,354 18,098 18,260 18,071 18,280 17,853 18,041 18,129 18,309 GB11 GB2 GB3 GB7 GB10 GB16 GB18 GB19 GB23 Average Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Tumor Normal Bases in target region 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 37,907,452 Bases sequenced (after quality filtering) 13,131,668,438 15,347,465,250 13,166,976,000 19,206,244,350 15,339,901,050 11,468,843,400 15,170,651,550 15,538,926,450 12,128,320,050 7,011,711,450 5,650,933,500 14,091,186,400 15,738,777,000 14,953,158,400 14,816,946,800 14,022,177,600 12,916,793,800 16,474,197,800 16,953,925,400 Bases mapped to genome 11,963,549,123 13,223,548,275 11,311,371,900 16,550,041,425 13,199,632,350 9,808,973,700 12,915,997,200 13,548,743,925 10,467,140,775 6,243,157,500 4,813,953,675 13,649,358,600 15,240,934,600 14,494,731,100 14,337,060,700 13,586,140,700 12,546,153,300 15,970,331,600 16,413,209,000 Bases mapped to targeted region 5,810,671,762 6,308,931,924 5,064,920,652 7,260,768,459 6,269,434,020 4,390,823,275 5,936,111,837 6,578,671,027 4,857,360,894 3,636,657,497 2,761,983,035 6,832,648,356 7,590,432,296 7,001,829,474 6,885,494,921 6,628,531,932 6,093,028,356 7,797,904,735 8,064,438,870 Average # of reads per targeted base Targeted bases with at least 10 reads (%) 92.4% 92.8% 93.1% 93.6% 92.7% 92.5% 93.0% 91.1% 92.9% 95.3% 94.8% 90.3% 90.5% 90.9% 90.9% 90.4% 90.7% 90.8% 91.3% Known SNPs identified in targeted region 18,704 18,539 18,673 18,535 18,575 20,515 20,579 18,297 19,612 18,756 18,976 18,027 18,154 18,126 18,270 18,188 18,716 17,811 17,968
5 Supplementary Table 3 - Summary of Mutation Spectrum for Intrahepatic Cholangiocarcinoma and Gallbladder Carcinoma point mutations insertions/deletions (ins/del) Tumor Sample C:G to T:A C:G to G:C C:G to A:T T:A to C:G T:A to G:C T:A to A:T 1 bp del other del 1 bp ins other ins TOTAL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL CHOL GB GB GB GB GB GB GB GB GB TOTAL
6 Supplementary Table 5. Clinical Characteristics of Intrahepatic Cholangiocarcinoma Patients Based on IDH Mutation Status IDH Wild Type Mutant p n (%) Total 26 6 Age, median Sex Male 11 (42) 2 (33) Female 15 (58) 4 (67) Race White 23 (88) 5 (83) Black 2 (8) 0 (0) Unknown 1 (4) 1 (17) Stage (42) 2 (33) 2 11 (42) 1 (17) 3 0 (0) 0 (0) 4A 3 (12) 3 (50) 4B 1 (4) 0 (0) Size (cm), median Histologic Grade (0) 0 (0) 2 19 (73) 2 (33) 3 5 (19) 4 (67) 4 1 (4) 0 (0) Unknown 1 (4) 0 (0) Positive Nodes 1 (4) 2 (33) Multifocal Disease 6 (23) 1 (17) 1 Microscopic Vascular Invasion Institution 8 (31) 2 (33) JHH 11 (42) 2 (33) MSKCC 10 (38) 2 (33) Mayo 3 (12) 2 (33) Bucharest 2 (8) 0 (0)
7 Supplementary Table 6A. Statistical Analyses of Somatic Mutations in Intrahepatic Cholangiocarcinoma Gene p value (uncorrected) p value (Bonferroni) p value (Benjamini-Hochberg) BAP1 6.38E E E-12 PBRM1 1.53E E E-06 ARID1A 3.65E IDH1 4.61E FGFR2 4.32E RBBP CSMD SLC39A OLFM MB21D EPHA SAV PTEN APOE JUN REG3G DNAH STK TDG SORCS SORCS SNTG DDX EPHA FTMT OR4C NXPE OR52L THSD7B TP CPA LINC ZNF IDH MAGEC GATA C12ORF ALB POU3F
8 EFCAB FOXB RPL ADAMTSL POTEB HN1L CCT8L SYT ASCL C22ORF SUPV3L HRNR SPIB C15ORF SYCP TNFAIP FBXO CAPZB PCDHB ISL PIK3CA MDFIC ANKRD20A C21ORF ANO KIF5C CEP MAPK RP11-830F GARNL UNC5D FAM69A ARRDC FOXF ADRA2B PIGR ADAMTS SNX FOXC P4HA ARID5B IRF2BP HLA-DRB
9 TGFBR ATP2A MAN2B LRRC4C PIK3C2G PCSK SEL1L COX ALS2CR NCOA KLHL FAT CTNNA FLT TTC MST1L TLE FAT AGO WDR C2ORF UBE2O ENPEP MAP3K RP11-111F CASP8AP MAST MYOM FRMPD MMRN ATP2B IGKV1D TRBV ZNF300P NAP1L KRTAP IGLV TRBV MAGEA MAGEA10-MAGEA MED PTPRT CPS
10 SNTN F KIAA ACN CEP RREB RPL24P FAM208B VPREB TPR BZRAP C7ORF IGLV C10ORF MAP KRTAP DICER LAIR IFNA OR4C50P NHSL DOCK AP3S NRAS KRTAP CISD NBPF ZNF OR5E1P RHEBL NLRC LY6H NIPBL KRAS IQCJ CLEC4C PTPLAD ZNF CREBBP HSPA1B KIF13B KRTAP AC
11 SEC22B ATM USP RP1L EEF1E DCTN OR5P1P LIF NEURL PSMA IL NF TIMP GSTM ZNF HIST1H3F OR10AG C16ORF KRTAP GATS EMC NAT IZUMO ZNF75A LACTB NME FBN OR10A TMEM DNM1P OR51L COL5A OR56B OR7A STAP DRAP OR4A C3ORF C11ORF OR51F OR4D OR10J LYSMD
12 FOXR FGF OR5F OR1E FAM49B OR2AG HNRNPCL LOC RNF144B NUP MGMT NSMCE OR10G OR2AE OR2T MANSC RNF OR11L MLF GSTO CYP2A7P "MARCH2" KRTAP TNFRSF12A BCDIN3D OR2T IQCK NT5C3B TNFRSF13B CD1B NDUFV NEUROD OR56A CLEC10A CD1A SLC25A MED ZDHHC SUN CRYM MRGPRX OR6C OR5B
13 ZNF CCDC GPR SIRPB ZPBP MC5R MAGEB CCDC TYMS H1FNT OSR RAD51C SYNGR SLC25A KCTD PROCA COQ GSTM RERG FGF MOB1B ZDHHC XIRP SCAMP PRR23B GPR PRSS TMOD C7ORF MRPS SERPINB IKZF OR2AJ CASP IDI OR1N TMPRSS11A KRTAP PA2G GSX PABPC SKA TMEM178A
14 NDUFS KRTAP KIR2DS CATSPER RAD51AP TPSD UNG SLC38A MANEA AGK ZDHHC RNF CSMD VSTM OR10G EPSTI DNAH FBXL OAT IDO SMAD IGFBPL MSANTD MBNL GABRA HOXC PCOLCE ZCCHC CD200R IFIT B4GALT ADK SGK C8ORF44-SGK SLC25A BCL2L SFRP ARIH2OS DCAF4L ANGPTL EXOG HNRNPF ZNF
15 ADSS HOXB WNT8B XBP ZNF "MARCH4" NIM CYP2C MOSPD XK HCRTR ENO MDM SERPINE HTR2C WWTR TMEM200A KNOP CHI3L VAT1L CMKLR FETUB OLFM SEPSECS FUT APLF ACAA PPIE RP11-266K SSUH GPR LRRC MPPED REXO UTP NDRG WNT10B TRAIP PTBP CLPP SMAD TEX SYT
16 ADAD LILRA ZNF RBFA POM121L C6ORF SRPX FLG EPCAM TBX TPM DRD CDKN2A UPB GLUL PARK CLEC18A PGK CETP SGPP KCTD IRF CDC DYRK ATXN PARM IKZF AGPAT HS3ST KRTAP OPRD LOX PRKAA TMCC CCBL CCM COLEC RDH SPDEF ALCAM HP1BP RSPRY GBP
17 SLC16A SERPINA CDS DOK YAP ZNF TUBB BTN1A SLC41A ANGPT TRIM SMCR7L BMP POTEKP ZBTB MTL CYP4F SLC35C ZNF NPTX RAD51D NOX RBM NEIL FGGY DNAJC CHST CHRDL SAMD ABHD PSAPL TRIM PHOX2B ZNF ATF7IP S1PR JMJD MEG ACTR3B SNX ATIC RASSF CHM
18 WASF4P TMEM ZNF CHRM HAPLN KAT CYP26A PELI ZNF ALDOA SMAP RACGAP RBM C15ORF TAB ANKRD ECD SPATA SDR42E ELL CYP4F EIF3L TMEM TTYH PIGZ WRAP ZNF PRB TMPPE FAM198A SNX GTF3C PAPSS EXD SIGLEC LRFN KLF TACR FAM126B "MARCH7" ASTL DLAT SLC20A
19 SLFN ZIC PAAF GPR LRRC RELA FBXO UGT3A TUBGCP CENPI LGI LARP DPYSL MTMR BCAS ZNF SLC6A ISLR COLGALT SGK ASB TSTD ZNF KRT DCHS CADM PLEKHO IQCJ-SCHIP NR1I ATG SHC BPIFB DTX3L PJA GAL3ST TPTE CIR COASY TCF KIF2B CBWD CHST ANGEL
20 GPR SIX PAX KLHL C16ORF KLHL DTNB CXORF ARAF ALX RNASEL KBTBD SLC7A CCDC64B RPTN HRC KLHL GPR PAX HEXA SCG ASAH TLR CD2AP DBH PGBD SLC26A GPR SV2C RBFOX PCK FPGS MASP HMCN SP ABCG ALOX PRKCZ FAM5C CCDC CTSF PRKCH F13A
21 PLD HIC TRIM CYP24A UBASH3A GOLGA6B TMCO SLC26A ANKRD20A EIF2B SLC6A SLC25A C1ORF CASC KRT VEGFA NFIB SIGLEC SUGP DCAF12L TUBB4A WDPCP PRLR HP CAMK2B IL12RB APEH SLC30A TOMM70A FZD IL12RB SATB TMEM PTCHD CWF19L RFX CHRM PDPK TRMT TKTL ARMC PDXDC PROM
22 BHLHE ACSBG NDST ACHE ARHGAP FLRT CD SPATA ANXA COLGALT HAS SLC27A PTPRA GALNT STON GABRB DSC ZNF SAGE SMURF PHF DVL TTLL GP1BA UROC MUM ZNF TRMT QSOX KIRREL DCST GALNT ITPRIP E2F LETM ZNF FTSJD GOLGA8DP GRIA HSPA CXORF PIGT KIAA
23 CHGB CBFA2T PIF NPAS AGGF DVL TBL1X CDH FAM47A CDH NCOA PCK MORC ANKRD CCNF LSS GYS CDH SYN ADRA1D FPGT-TNNI3K HNRNPUL MUC3A AGAP LRRTM PLA2G4E TNNI3K PCDHB CAPN KIAA ADD CTCFL ZNF AGBL DLL PRAMEF N4BP KLC ADAM SEC23IP TMC PTH1R ADAM
24 VAV PLEKHG PADI CSK CNTN MPO FJX CTCF ITIH TMEM LILRA SMARCAL HERC ZNF TLL ZNF GOLGA6A KCNH PAK DSG ZXDB RAG CDH TOPORS PCDHGA PANK PAMR C9ORF CNTN ZNF PTPN SARM MYBL DYRK1B SULF ZNF804A EFTUD PSD NYX TRPV CEACAM FAM171A OVCH
25 R3HDM PPP2R2C TTC PDZD DIAPH USH2A SULF HTR7P GSN LEPR ACTN RYR KIF KCNA ATP8B EGFLAM AR TSHZ ZNF TRIM PRKD PODN MED PRAM F VSIG BNC IMPG POLN ZFPM HIRA AMH EGF INCENP NPAP CYP4F SLCO1B SH3RF RBM GPR WWC PCDHB GRM
26 ABCB KIAA FBXO PCDHA GTF2IRD GMIP OTOA EPHB GAREM CDH GRM LAMC ROCK PCDHA STARD EPHB NDST SEC31A TPO ELAC TGFBRAP DNAH CPT1C ANKRD36B KDM3A LDHA RPS6KC WWC SLITRK THBS TAS1R KIT DUSP RGAG LIFR VWA GIGYF DLGAP PDS5B ARHGEF TIGD GPR ADAMTS
27 MICAL TRPV ZNF ZNF CRB NPR DENND5B HIP1R CTBP FAM135A PCDH ANKS1B HPS TMTC ADAMTS SIX ROBO MUC CGNL RFC RASAL LPHN CNTNAP MROH UBE4B EPHA GPR KIAA PRAMEF STON1-GTF2A1L ZMYM GRM IGSF FGFR MMS22L LLGL TXNDC TRO ERCC6L STXBP ADAMTS VWDE MTUS
28 HEPHL TNN HDAC C17ORF KIFC CAND TNK MYO3A RPAP PIK3C2A PCDH UNKL IQGAP KCNU APBA PALM2-AKAP PTPRK MYT1L SMC KIF MICALL SH2D3C FGFR ARHGEF SLC4A ZNF COL6A SMG KIAA PEAR ADCY LY KCNH EEA CHRD ADAMTS COL24A ZMYM PRRT CNTN ADCY PCDHA ITSN
29 COL11A KIAA CCDC THSD RBBP KDM2B ANKRD USP RIMBP ENPP LY75-CD MYOM EPHB C12ORF INPP5D ZSWIM RP11-108K RYR COL4A KCNMA DUOX PTCHD HELZ ZCCHC HIPK HR CHD ADAMTS COL11A DENND ZFC3H POGZ MCF2L PCDH NRXN SCN2A EML HCN MUC5B COL22A AKAP COL16A CAMTA
30 POM121C MPDZ NID BAZ2A USP CACNA1S SLC4A GLI DNAJC ADAMTS MON ZNFX PLEKHG INSRR NBPF ZDBF PHRF ASXL SCN4A POTEF PREX INF POTEG PPL SIGLEC PHLPP HECW CCDC88A POLR2A YLPM CLASP FLG DNM TRIP KNDC ABCA AL ASTN SBF PLCE PLXNA NES PCDH
31 WDR ATG2A NHS ANK PLXNA ANAPC SVIL PTCH NOTCH CR SCN1A MPRIP DOCK SON SPEF C OTOF C6ORF FN CEP XIRP C NBPF ANKRD20A SCN10A UNC13C SALL CDC42BPB GPR PIKFYVE LRBA TTC WDR FMN TANC SPTB ZNF EYS ADAMTSL SBNO KAT6A MYO DIDO
32 RANBP GOLGB NBPF COL12A SOGA ACACB VCAN LAMA CACNA1D CFB ACACA TECTA LAMA WBP UTRN WDFY VARS AKAP DMD HELZ CACNA1C CHD ANK PCNT DYNC2H SDK PRKDC TNRC CELSR ASPM CDH CSMD SRRM DOCK MYO15A SPTBN BIRC WDFY BAHCC HERC VARS NBPF DCHS
33 HYDIN LRP GPR MDC AHNAK SSPO PLXNA PLEC DNAH NEB SYNE MUC TTN OBSCN
34 Supplementary Table 6B. Statistical Analyses of Somatic Mutations in Gallbladder Carcinoma Gene p value (uncorrected) p value (Bonferroni) p value (Benjamini-Hochberg) TP E E E-09 KCNK KLF FRG1B GIPC CSHL MUC TEAD CLK COPRS ZNF AP SPIC DCLK KIF5B ATP1B ELF IRF CRELD SSFA SMAD ICA EPS15L WAC ZIC DNAH TICAM TMPRSS MST1L NPAS FAM171B MLL PBRM XRN SUN POM ZEB PEX ADIRF
35 IQSEC CCL YEATS RGPD NRK RP11-420K KIAA MIR205HG IGLC OOSP CNTN IGLV FMN MPRIP KRTAP GPHB LCE1E C7ORF LINC TRAV PHF5A CFL VPS HOPX NHLH TM4SF FAM201A OPALIN TAF HIVEP TMEM9B GSTA CLEC4D WFDC RP11-413C CHMP2A PLSCR CXORF DRAM CHCHD RP11-627G TEX HIST1H3C
36 FRG2B OR4C OR4C OR10AG ATP1B OR5H RRP TSC22D OR6N OR51B TMED OR2A MYADML DGKZP OR5M NAT OR2A OR4D OR51V ZNF CRYBB OR9Q ST6GALNAC FGF CRYAA NEUROD COQ10A TBC1D HOXC TMEM179B ARL NCR C3ORF PLCXD DGAT2L OR2M SIAH RELL PRR TMEM GRXCR PARP IBSP
37 CD TMEM CD200R FCGR1A OTUB UCP GNAT NUBP PYCARD C22ORF HNRNPA OR10T TAS2R OR52E COPS KIR3DX GPR TSPAN NIF3L PNMA CT47B ZNF ACTBL TXNIP TRIM OR13F NPY5R FAM71D NXF OR10AB1P AGK KIAA F11R IFLTD ZNF DNAJB RNF WDR TRAF RIMS CBR SFXN CYP20A
38 OR1L HYAL SYPL CKM C2ORF UFSP NKAPL GNAZ SAPCD LGMN KLHDC CHRNA TAPBPL TBL1XR B4GALT SERPINB CDK STAM ALG RP11-561N KRT KIAA PRR HSD17B7P HEXIM C19ORF TRMT AHNAK RNF CHRM TSPAN CNR KPNA SMTNL PORCN RIOK VMP HCLS CALCR ZP TDRD PSTPIP TMEM
39 QRSL FAM98A B3GNT PLA2G TMEM NAE DNAH MDH1B MOGAT ATL LMBR "MARCH11" ADRA2B HTR1A IKZF XPNPEP APOB CD TRIM TFCP2L FAM110A RALGPS NPBWR SMARCD HOXA ZNF C9ORF KLHL ALLC CRY LCTL XKRX CD2AP HSPBP BACE DCAF12L SMYD ZNF ACOT MSL NCOA CALHM PRDM
40 GPNMB CCDC PPM1J HCK LILRB CHRM C22ORF ZNF DEK TRIM TLE PRDM FSHR GDF ELTD ZBTB B3GNT ECD FRMD ASTL PHF21B LRPAP CDC RNMTL ZNF HLX ENO KNG LOC KRT HNF4A OC TUBBP KRT MYBPH PAOX FBXO ZSCAN5C TBC1D RP11-683L FAM117A FAM178B CD
41 CRTC CKAP2L LEMD PADI PPM1B C9ORF TOR4A JRK FASTKD ZYG11A STIP GPR TCF7L NCSTN XPNPEP MLNR CPNE CDC25A SLC46A TAS2R PLD AMHR EDAR BBS DGCR AMPH PRODH NARF DGKA CCT VEZT EIF2D TRPV MESP CEACAM EBF PVRL ANKEF CACNB CCDC CDH KIFAP CAMK2B
42 GPR CYP4F VIT FOLH MAZ TCHHL DCAF12L LCP PLXDC ZNF SATB IL12RB SUSD IL4I CRTC ZNF COG FBXW FAM160B SWT BEGAIN KIRREL PRKG KLHL SPHK PRF CPNE NOP LRCH EOMES SPINT ZFP PGAP HLA-DQB DES GYLTL1B EXOC SDAD ZNF FTSJ OSBP ANKRD ZNF
43 NGEF STON NOL ANKRD34A CYLD PI4KAP HGS COPG WSCD FAM47A C2CD4C EBF BEST RNF PCDHB SRBD TRPC LRRC37B CDH ZNF UNC5C CD TBX EXTL BNC TAF SPPL2C CPED FOXG MYO NLRP CHPF ADCK PIK3CA PPP1R3F UBASH3A PPM1N SLC9A DACT HCN LRP GBA AMOTL
44 NLRP CNTN SLC15A ZNF LRIG CDH AP1B L3MBTL EPHA ANKRD EMC ANKRD20A JAKMIP R3HDM RASA RIPK GLI XRRA SULF CNGA PTPRE ATP11B EPHB NCKAP1L CASS SPATA31C KCNC ZNF SMG GPAT OTUD7B DDX MKL CCAR MICALL PCDHGB MTHFR SLC4A SUGP KIAA INTS KANSL MLXIP
45 ZNRF KIAA0226L IMPG RNF CNTN SEMA4D RBM DGKI PPP1R9B ASB ZNF CILP TTBK EPHA TTLL ITGA2B PCDHA ZNF804B PRAMEF INSM PCDHA C6ORF SIN3A VAV ABCB AFF KCNB PLEKHG ATN ADCY AKAP ADAMTS KLHL SETDB DENND5A ULK FAM193B LINGO PCDHB TIE KDM2A TRO FARP
46 PPP1R3A EPB41L TRAPPC CASKIN EPHA MAP1S NLRP HNRNPUL GIGYF ITGA KIAA ASAP GRIA ADCY OTUD7A PPP1R PTGFRN HYOU NCAPD SYCP POTEJ ARHGAP NRG TRIM AGL VWA5B SLC12A SEMA6D STON1-GTF2A1L POTEE ATAT MAP3K CTNND UBE2O COL20A KIAA ADCY AUTS FGFR SLIT QSER MEGF CILP
47 NCAM CDSN PCDH PITPNM PIK3CG ACE EHMT COL1A ITGAV FHAD CDH UNC13B GPR PCDHA COL4A HDAC SI AC ERBB ARID HIP1R DAGLA DUOX NUP MAPK8IP SBF IFT SMARCC ZNF IFT HELZ PRAMEF PXDN CUX NRXN KIAA ITSN CUL ANKRD EGFR ADAMTS NCOA AKAP
48 C4ORF TNR KIF21B NEO MPDZ CDC42BPB GLTSCR PAPLN SETD1A RNF ALPK SEMA5B SCN4A LRP IRS PTPRZ RAI SIPA1L SNAPC NFASC FNDC MYH SPG CASZ LRRK DOCK GPR PLXNB COL14A NOTCH SPTA WDR COL11A IGSF9B DYSF PAPPA ACACA MYH7B DSCAM CEP BRD MYO9B SCN2A
49 USP NIPBL CREBBP IGF2R CACNA1G CHD ASH1L TG ITPR ZAN TENM PDE4DIP C5ORF KNDC ZZEF ZNF ASPM MAP1B TLN MICAL SPTBN ZFHX SDK AKAP CUBN ANKRD20A DMD SPEN CSMD CMYA PKHD1L ALMS DNAH CELSR TENM LRP1B PLXNA BIRC FAT HERC RELN DNAH XIRP
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devseek (Sequence(Analysis(Panel(for(Neurodevelopmental(Disorders
ACSL4 Mental/retardation,/XBlinked/63 XLBR ADSL Adenylosuccinase/Deficiency AR AFF2 Mental/retardation,/XBlinked,/FRAXE/type XLBR ALG6 Congenital/disorder/of/glycosylation/type/Ic AR ANK3 Mental/retardation,/autosomal/recessive/37
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Sample Metrics. Allele Frequency (%) Read Depth Ploidy. Gene CDS Effect Protein Effect. LN Metastasis Tumor Purity Computational Pathology 80% 60%
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