Table S1.

SOLiD data somatic mutations

SubjectChromosomePositionBase changeAmino acid changeMean coverageGeneVariant typeGermline coverageTumor CoverageOrganoid coverageGermline allele frequencyTumor allele frequencyOrganoid allele frequencyShared (S), tumor unique (T), or organoid unique (O)
11209,797,208T/AK705I332LAMB3SNV29845923928599S
2179,407,388C/ANA493,67TTNSNV48963435802019S
2179,486,728C/AW6034L344,33TTNSNV25352026003943S
325,665,813G/AP824S775,67TOP2BSNV694112750612224S
3119,582,332G/AR357W401GSK3BSNV31664024712839S
3195,605,915C/GNA45,33TNK2SNV53711202017S
465,298,248A/GNA11,33RP11-204H9.2SNV15172076100S
5112,175,021C/TQ1244*96,67APCSNV961336112134S
64,059,028G/AV514I57PRPF4BSNV8234551217S
88,999,186C/TNA83,33PPP1R3BSNV11311918068100S
11106,810,698C/GE232Q693,33GUCY1A2SNV508114542702724S
11117,306,398C/AR1673L301DSCAML1SNV34939016403129S
1257,849,972C/TP132S180INHBESNV1223239502132S
1332,972,674G/AE3342K846,67BRCA2SNV490143461601728S
1599,442,705G/ANA351IGF1RSNV24160320902639S
163,777,892C/TG2348R49,67CREBBPSNV45762805368S
202,845,936C/TA402V187,33VPS16SNV1053471100819S
X41,027,389C/TR852*164,67USP9XSNV25111812507993S
1775,775,39G/AR248W205,33TP53SNV23528010106979S
2110,363,653G/CE804Q163,67KIF1BSNV1281841790817S
143,814,930C/GNA103MPLSNV861279601721S
299,172,162G/ANA737,33INPP4ASNV60699661002430S
2179,486,342A/GI6005T899,67TTNSNV1422224105301628S
2179,507,003G/AR4567C307TTNSNV7145515204445S
31,414,000G/AV504I375,67CNTN6SNV5301584390116S
3112,991,517G/AA310T20,67BOCSNV7342104114S
423,825,968T/GK271T465PPARGC1ASNV79315344901626S
4146,467,864C/TA262V152SMAD1SNV2872414503842S
5112,155,013C/-NA150,67APCIndel17915511806090S
5170,818,803G/AA118T240,67NPM1SNV3281792150018O
657,075,028T/AI51F474RAB23SNV62117662505143S
1192,533,992T/AY2605N783FAT3SNV87759687604041S
1677,353,825G/AT818M106,33ADAMTS18SNV1291226805372S
177,576,927C/ANA144TP53SNV17512413306499S
1939,996,053A/CK352T60,33DLL3SNV67704401316S
346,307,365G/AR260Q656CCR3SNV69368658902320S
1225,398,281C/TG13D207,33KRASSNV32610918708591S
31227,300,460C/TR601Q693,67CDC42BPASNV65558783901435S
448,073,695C/GNA237TXKSNV2472821820018O
5112,175,480G/TE1397*349APCSNV4082893500236S
632,184,739C/AC615F133,33NOTCH4SNV1041721241547S
1064,968,097G/CS892C285,33JMJD1CSNV32820432402468S
10114,912,204G/ANA130,67TCF7L2SNV961871091732S
11117,308,068C/TR1287Q87DSCAML1SNV611376321594S
11118,342,652C/GP293A446,33MLLSNV3904624870939S
12120,653,800T/GK4T27PXNSNV194913*0180T
12121,416,813T/CF81S18,33HNF1ASNV822*250016O
1544,843,120T/CV65A161,33EIF3JSNV1921451470025O
1588,690,618G/AR138W494,33NTRK3SNV50049049302699S
177,577,095G/TD281E192,67TP53SNV1602971210895S
1845,371,862T/CNA276SMAD2SNV29723030102099S
197,976,387G/TV377F39,67MAP2K7SNV42512651277S
1225,398,284C/GG12A227,33KRASSNV2962651210426S
41160,388,795G/TD66Y63,33VANGL2SNV562111301946S
1226,566,974T/A−538-154,67PARP1SNV1705324143813S
1227,216,861C/TR500H284,67CDC42BPASNV3575344403239S
1228,402,727C/AQ586K23,33OBSCNSNV268*360022O
2179,643,820C/TR1330H160,33TTNSNV3012515506043S
310,070,375G/AD12N99,67FANCD2SNV235392503620S
56,743,939A/TI161F96,67PAPD7SNV233253204072S
538,960,005C/TE643K211,33RICTORSNV537336402742S
5112,173,917C/TR876*312APCSNV5916927604398S
719,156,452T/AS33C68TWIST1SNV8332890017O
82,887,015C/TE2562K81,67CSMD1SNV14069905035S
838,275,833C/TR357Q84,33FGFR1SNV1081313218557S
8103,307,432G/AP1347L628UBR5SNV71779108806868S
9113,496,548C/TR216W318,67MUSKSNV4319842712822S
1111,373,733G/AR312W205,67CSNK2A3SNV3244624701333S
1740,491,345C/TR152Q228,33STAT3SNV4084723007098S
202,842,501G/AR317H45,67VPS16SNV58116802721S
X1,404,820C/TNA99,67CSF2RASNV1014815005640S
X153,592,746G/ANA32,67FLNASNV229*670019O
1225,398,285C/AG12C140,67KRASSNV2405612614156S
177,578,406C/TR175H31TP53SNV3355508096S
51242,016,664C/TR96*431EXO1SNV53238537601734S
299,180,106C/ANA5,33INPP4ASNV141107555S
4103,446,721G/ANA74,33NFKB1SNV94587101421S
4104,070,038T/AQ1244L243,67CENPESNV38822611702210S
5112,175,621C/TQ1444*280APCSNV43622617803688S
630,856,718G/AR40Q200DDR1SNV18720620723364S
6162,683,713C/TD86N210,33PARK2SNV2202461650819S
7141,424,934C/TR444C235WEE2SNV18627524402340S
1017,142,212-/ANA200,67CUBNIndel2172041810718S
1564,275,855C/TR64H58,33DAPK2SNV5465560320S
1727,208,869C/TE227K33FLOT2SNV39263405094S
184,891,888G/TD351Y419SMAD4SNV583353321052100S
1225,398,281C/TG13D182KRASSNV20216418004995S
1421,854,022G/TP2499H35,67CHD8SNV3138380518S
177,578,406C/TR175H28,67TP53SNV43142905097S
6145,809,000G/AD307N125,67TOE1SNV29087912547S
2170,009,480G/ANA96LRP2SNV93321630384S
314,200,245T/GS343R127,33XPCSNV185989903317S
4114,186,052G/ANA28,67ANK2SNV557*240029O
5112,174,864AA/-NA256,33APCIndel50510016403643S
632,944,234T/AL273H316BRD2SNV47312435108176S
776,111,907G/-NA23,33DTX2Indel31152402712S
841,166,327C/TA118T11,67SFRP1SNV1017803512S
8103,307,229T/GK1390T542UBR5SNV6611358300170T
971,504,018T/GF147C237,33PIP5K1BSNV363512980023O
977,359,089T/GK1690Q274,33TRPM6SNV405963220021O
189,522,319G/AE289K246,67RALBP1SNV422312871233S
191,455,191C/AL153I32,67APC2SNV77101105082S
1950,374,886T/GK182T104,67AKT1S1SNV91871360016O
1956,042,661C/TG102D12,33SBK2SNV6191202125S
208,639,221G/CQ244H355,33PLCB1SNV4401854411167S
X591,711G/AG27R54,33SHOXSNV45645405620S
177,577,114C/TC275Y87,67TP53SNV1511110108268S
7141,404,534A/-NA13,33RP11-348A7.1Indel82*300017O
144,154,629G/AE634K125,67KDM4ASNV134911521182S
1198,225,575G/CE106Q232NEK7SNV33115620911942S
2148,657,319C/AS127*442,33ACVR2ASNV76030326405094S
3178,916,725C/TR38C603,67PIK3CASNV75045960205477S
3184,293,701G/AA314T60,33EPHB3SNV5949732161S
5112,175,423C/TQ1378*330APCSNV40322835906891S
798,565,256T/AY2476N169,67TRRAPSNV2606418507588S
83,432,515T/GE433D148CSMD1SNV2566712102586S
10412,306C/AR726I548,33DIP2CSNV61641461502155S
108,115,818C/GN388K353,67GATA3SNV4463143010654S
1064,967,678G/CP1032A454,67JMJD1CSNV65927543002147S
11116,719,906G/AS983F45SIK3SNV4137570222S
11117,392,003G/AT412M107,33DSCAML1SNV1271177801126S
13110,804,709C/TA1634T141COL4A1SNV1221231781842S
1668,842,430C/AP87Q207,67CDH1SNV2751262220617S
4153,247,288C/AR505L583,33FBXW7SNV78338258502546S
1225,398,284C/AG12V176,33KRASSNV29411112411328S
177,578,406C/TR175H25TP53SNV3927902667S
819,793,472T/CE795G153,67CLSTN1SNV18616111401446S
112,164,486G/AE107K430,67TNFRSF8SNV4534743651938S
1165,876,941C/TQ223*128UCK2SNV15711311401357S
233,482,484A/TK441N344,67LTBP1SNV38934130401834S
2121,708,928G/AV122M48,33GLI2SNV5733550629S
2171,884,902C/TE347K267,67TLK1SNV3453231351622S
2179,547,627A/GV10647A110,67TTNSNV168778701434S
2179,622,344C/AG3489W305TTNSNV34429927241248S
2215,593,455G/AS131L597BARD1SNV63955559711238S
31,444,098A/CI900L305,67CNTN6SNV42923125703894S
325,659,978C/AL1089F140,67TOP2BSNV191136951316S
330,732,969C/TR528C49TGFBR2SNV77343602989S
3171,455,712C/TV44M134,33PLD1SNV2087711801026S
5112,175,675AG/-NA288,33APCIndel38225722601154S
76,038,819C/TG209R590,67PMS2SNV61161254911238S
848,715,930G/AR3286W173PRKDCSNV2241731221639S
8121,282,371C/AS1057R190,67COL14A1SNV3031201491831S
994,486,903C/TD485N156,67ROR2SNV19613913512447S
1081,006,67C/TS214L38,67GATA3SNV5330332739S
1089,692,905G/TR130L234PTENSNV28121220901446S
11108,128,322A/CN789H147ATMSNV14912516712854S
1252,374,912A/GE195G352ACVR1BSNV35229840613569S
1253,686,729G/AV2046M52ESPL1SNV46476301538S
1915,276,227C/TG110E125,67NOTCH3SNV1648113212642S
X44,920,568G/ANA55KDM6ASNV6347553190T
X71,813,093C/AG1052V264,67PHKA1SNV32426520511572S
7140,453,136A/TV28E422BRAFSNV4743953970635S
1089,692,904C/TR130*233PTENSNV27821220901645S
  • Overview of all somatic mutations identified by SOLiD sequencing. Unique mutations are highlighted in boldface. The allele frequency is the percentage of reads in which the mutant allele has been detected. SNV, single-nucleotide variant.

  • * Low coverage for samples with a unique mutation (might have resulted in the inability to identify a mutation).