Secuenciación*Genómica*y*Medicina*Personalizada*del*Cáncer

Transcripción

1 Secuenciación*Genómica*y*Medicina*Personalizada*del*Cáncer Ricardo Armisén Y. Centro de Investigación y Tratamiento del Cáncer U-CANCER: Red de Medicina Traslacional en Cáncer Programa de Fisiopatología!Instituto de Ciencias Biomédicas Facultad de Medicina Universidad de Chile rarmisen@bitmed.med.uchile.cl

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3 ! Rayos X Agente de daño! Radicales oxidantes! Desaminación y Tautomerización! Luz UV! Hidrocarburos Policíclicos aromáticos! Rayos X! Agentes antitumorales! Errores de replicación Check-Points! Inhibición de: Transcripción Replicación Apoptosis Tipo de daño! Alteraciones estructurales de base! Fractura monocaternaria! Dimero de T! Alquilación de bases! Fractura bicatenaria! Mal complementación Segregación cromosómica Mecanismos de reparación BER NER BER NER HR NHEJ MMR! Mutaciones! Aberraciones! Cromosómicas! Cáncer! Envejecimiento! Enfermedad Genética

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5 Mutaciones*en*cáncer*

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11 The Cancer Gene Census is a catalogue of genes for which mutations have been causally implicated in cancer. Currently, more than 1% of all human genes are implicated via mutation in cancer. Approximately 90% have somatic mutations in cancer, 20% bear germline mutations that predispose to cancer and 10% show both somatic and germline mutations. Cancer Somatic Mut Cancer Germline Mut Symbol Name GeneID Chr Chr Band ABL1 v-abl Abelson murine leukemia viral oncogene homolog q34.1 yes CML ABL2 v-abl Abelson murine leukemia viral oncogene homolog q24-q25 yes AML ACSL3 acyl-coa synthetase long-chain family member q36 yes pros AF15Q14 AF15q14 protein q14 yes AML AF1Q ALL1-fused gene from chromosome 1q q21 yes ALL AF3p21 SH3 protein interacting with Nck, 90 kda (ALL1 fused gene from 3p21) p21 yes ALL AF5q31 ALL1 fused gene from 5q q31 yes ALL AKAP9 A kinase (PRKA) anchor protein (yotiao) q21-q22 yes pap AKT1 v-akt murine thymoma viral oncogene homolog q32.32 yes brea AKT2 v-akt murine thymoma viral oncogene homolog q13.1-q13.2 yes ovar ALDH2 aldehyde dehydrogenase 2 family (mitochondrial) q24.2 yes leiom ALK anaplastic lymphoma kinase (Ki-1) p23 yes yes ALC ALO17 KIAA1618 protein q25.3 yes ALC APC adenomatous polyposis of the colon gene q21 yes yes colo ARHGEF12 RHO guanine nucleotide exchange factor (GEF) 12 (LARG) q23.3 yes AML ARHH RAS homolog gene family, member H (TTF) p13 yes NHL ARID1A AT rich interactive domain 1A (SWI-like) p35.3 yes clea ARID2 AT rich interactive domain q12 yes hep ARNT aryl hydrocarbon receptor nuclear translocator q21 yes AML ASPSCR1 alveolar soft part sarcoma chromosome region, candidate q25 yes alve ASXL1 additional sex combs like q11.1 yes MDS ATF1 activating transcription factor q13 yes mal ATIC 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/imp cyclohydrolase q35 yes ALC ATM ataxia telangiectasia mutated q22.3 yes yes T-PL Tum Mut

12 Cambio*de*paradigma:** el*perfil*molecular*es*mas*o*tan*importante*como*el*tejido*de*origen?* * Muta%on(spectrum(in(Adenocarcinoma( Muta%on(spectrum(in(Squamous(Cell(Carcinoma( KRAS*mutaDon* EGFR*MutaDon* ALK*TranslocaDon* PIK3CA*mutaDon* CTNNB1*mutaDon* ROS*1*translocaDon* BRAF*mutaDon* NRAS*mutaDon* HER2*mutaDon* RET*translocaDon* OTHER* FGFR1*amplificaDon* PIK3CA*mutaDon* DDR2*mutaDon* PTEN*MutaDon* PDGFRA*amplificaDon* OTHER* Muta2ons&in&TP53&and&STK11/LKB1&are&common& occurrences,&not&included&in&pie&chart&due&to&high&overlap& with&other&muta2ons& Muta2ons&in&TP53&are&common&occurrences,&not&included& in&pie&chart&due&to&high&overlap&with&other&muta2ons& Heists&et&al&Cancer&Cell&2012&

13 PIK3CA( BRAF( KRAS( large_intesdne* endometrium* urinary_tract* ovary* skin* stomach* lung* thyroid* central_nervous_system* upper_aerodigesdve_tract* others* breast* skin* NS* ovary* lung* haematopoiedc_and_lymphoid_dssue* eye* central_nervous_system* others* thyroid* large_intesdne* lung* biliary_tract* ovary* endometrium* haematopoiedc_and_lymphoid_dssue* stomach* thyroid* prostate* others* large_intesdne* Heists&et&al&Cancer&Cell&2012& pancreas*

14 EGFR* EGF*binding* EGF*binding* Tyrosine*kinase* AutophosphorylaDon* 2* 5* 7* 13* 16*17* 18_21* 22_24* 28* mutadons*associated* with*drug*resistance* D761Y* T790M!(50%) *! D770_N771(ins*NPG)* D770_N771(ins*SVQ)* D770_N771(ins*G).N771T* V769L* S7681* (<1%)! (5%)! 688* 728* 729* 761* 762* 823* 824* 875* Exon!18! (nucleo<de,biding!loop)! Exon!19! Exon!20! Exon!21! (ac<va<on!loop)! G719C! G719S! G719A! V689M* N700D* E709K/Q* S720P* (5%)! mutadons*associated* with*drug*sensidvity* * * *!E746,A750!!E746_T751*!E746_A750*(ins*RP)*!E746_T751(ins*A/I)*!E746_T751(ins*VA)*!E746_S752*(ins*A/V)*!L747_E749(A750P)*!L747_A750(ins*P)*!L747_T751*!L747_T751(ins*P/S)*!L747_S752*!L747_752(E746V)*!L747_752(P753S)*!L747_S752(ins*Q)*!L747_P753*!L747_P753(ins*S)*!S752_1759* * (45%)! V765A* T783A* L858R!(40,45%! N826S* A839T* K846R* L861Q* G863D* (<1%)! (40,45%)! Sharma,*2007* Nature*Reviews*Cancer*

15 Tissue*Overview*for*Pancreas* * KRAS*(58%)* TP53*(40%)* CDKN2A*(29%)* MEN1*(25%)* SMAD4*(22%)* CTNNB1*(20%)* CDKN2a(p14)*(19%)* DAXX*(18%)* GNAS*(17%)* ATRX*(17%)* APC*(13%)* ARID1A*(8%)* MLL3*(7%)* MAP2K4*(5%)* SMARCA4*(5%)* PIK3CA*(3%)* STK11*(3%)* PTEN*(3%)* BRAF*(2%)* Scale!(sample!#)! 0.00* * 1,000.00*1,500.00*2,000.00*2,500.00*3,000.00*3,500.00*4,000.00*4,500.00*5,000.00*

16 Name! Method! Sensi<vity! #!loci/gene! analyzed! BEAMING* ~Emulsion*PCR* 0.01%! 1/1! pardal* LiGAMP* LM_PCR* 0.01%! 1/1! pardal* Pyrosequencing* 454* 5%* 10,000/3* pardal* Technical!Validity! Whole*Genome* Shotgun*sequencing* 20%* 3E9/20,000* in*progress* Whole*Exome* Shotgun*sequencing* 20%* 30E6/20,000* in*progress* OncoMAP* Mass*Spec* 20%! 400/33* CLIA! SNaPShot* Single*Base*Extension* 5,10%! 40/13* CLIA! FoundaDonONE* Capture+NGS* 10%* 600kb/182* CLIA! UDT_Seq* HT*Amplicon* Sequencing* 1%_5%* 157,000/50* demonstrated*

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19 Ultra,Deep! Coverage! Coverage!per! sample! Number!of! samples! Instrument! throughput! Region! size! Number!of! samples! Instrument! throughput! Gene! Panel!

20 Genome!technologies! Diagnosis!and!prognosis!for! individual!pa<ents! Individualized!profile!of! cancer!altera<ons! Target!therapy!trials! Targeted*agents* Cancer* genome* alteradons* Targeted*agents* Cancer* genome* alteradons*

21 Moores Cancer Center UC San Diego U.de Chile e n de coordinar apoyo a la n de centros ación entre n con otros mentando la s y centros a dispone de Ricardo*Armisén*(MD/PhD)* Katherine*Marcelain*(MV/PhD)* FausDno*Alonso*(MD/Ms)* Ricardo*Verdugo*(MV/PhD)* Olga*Barajas*(MD)* Mónica*Ahumada*(MD)* Iván*Gallegos*(MD)* CrisDna*Fernández*(MD)* Renato*Carrascoza*(Ing.)* Janet*Marchant*(C.A.)* Jessica*Toro*(Bq.)* Larry*González*(Ing.*Comp.)* Daniela*Diez*(TM)* Edgardo*Salamanca*(Bt.)* Pablo*Báez*(DCBM)* Eduardo*Sagredo*(DCBM)* Alfredo*Sagredo*(DCBM)* Claudio*Capelli*(DCBM)* Cesar*Echeverría*(PostDoc.)* Fernanda*Morales*(DBQ)* Rodrigo*Andaur*(DBQ)* Kelly*Frazer*(PhD)* Richard*Schwab*(MD)* Olivier*Harismendy*(PhD)* Anil*Sadarangani*(PhD)** Catriona*Jamieson*(MD/PhD)* Programa de Investigación Asociativa (HVDUUROODQGR OD DUWLFXODFL Q \ WUDEDMR colaborativo de nuestros científicos FALP Olga*Barajas*(MD)* Eva*Bustamante*(PhD)* Ana*María*Carrasco*(MD)** Equipo*medico*