Volume 156, Issue 8, Pages 2242-2253.e4 (June 2019) Real-Time Targeted Genome Profile Analysis of Pancreatic Ductal Adenocarcinomas Identifies Genetic Alterations That Might Be Targeted With Existing Drugs or Used as Biomarkers  Aatur D. Singhi, Ben George, Joel R. Greenbowe, Jon Chung, James Suh, Anirban Maitra, Samuel J. Klempner, Andrew Hendifar, Javle M. Milind, Talia Golan, Randall E. Brand, Amer H. Zureikat, Somak Roy, Alexa B. Schrock, Vincent A. Miller, Jeffrey S. Ross, Siraj M. Ali, Nathan Bahary  Gastroenterology  Volume 156, Issue 8, Pages 2242-2253.e4 (June 2019) DOI: 10.1053/j.gastro.2019.02.037 Copyright © 2019 AGA Institute Terms and Conditions

Figure 1 Summary of the most prevalent genomic alterations in 3594 PDACs. The mutational matrix shows missense mutations (green), truncating mutations (black), splice-site mutations (brown), intragenic/in-frame deletions (orange), copy number loss/deletion (red), copy number gain/amplification (blue), gene fusion (violet), and an absence of the aforementioned genomic alterations (gray). Gastroenterology 2019 156, 2242-2253.e4DOI: (10.1053/j.gastro.2019.02.037) Copyright © 2019 AGA Institute Terms and Conditions

Figure 2 Comparison of alternative drivers of the RTK/Ras GTPase/MAPK pathway in (A) KRAS–wild-type and (B) KRAS-mutant PDACs. Recurrent genomic alterations in BRAF, GNAS, EGFR, FGFR2, ERBB2, MET, MAP2K4, ERBB3, FGFR1, RAF1, ALK, RET, NTRK1, NRAS, ERBB4, and FGFR3 were more often identified in KRAS–wild-type PDACs than KRAS-mutant PDACs. Gastroenterology 2019 156, 2242-2253.e4DOI: (10.1053/j.gastro.2019.02.037) Copyright © 2019 AGA Institute Terms and Conditions

Figure 3 Summary of kinase fusion genes identified in KRAS wild-type PDAC. Various fusion genes involving BRAF, FGFR2, RAF1, ALK, RET, NTRK1, ERBB4, FGFR3, EGFR, and MET were identified in 51 of 445 (12%) KRAS–wild-type PDACs. In the majority of fusion genes, a serine/threonine kinase or tyrosine kinase catalytic domain was fused to an oligomerization domain and may represent a common mechanism of activation. Gastroenterology 2019 156, 2242-2253.e4DOI: (10.1053/j.gastro.2019.02.037) Copyright © 2019 AGA Institute Terms and Conditions

Figure 4 Comparison of germline vs somatic genomic alterations, as assessed by mutant allele frequencies. Among genomic alterations identified by targeted genomic profiling, likely germline genomic alterations were defined on the basis of a previously validated computational method that takes into account mutant allele frequency, tumor content, tumor ploidy, and copy number.26 In total, 40 genes were found to be likely germline in origin. The majority of these genes are members of the BRCA-FANC DNA repair pathway. Gastroenterology 2019 156, 2242-2253.e4DOI: (10.1053/j.gastro.2019.02.037) Copyright © 2019 AGA Institute Terms and Conditions

Figure 5 Targetable alterations and predictive biomarkers for treatment identified in PDAC through comprehensive genomic profiling. (A) Actionable targets in PDAC can be categorized into 2 pathways: RTK/Ras/MAPK signaling and DNA damage repair. (B) KRAS wild-type PDACs harbored targetable alterations that included fusion (n = 51), amplification (n = 35), missense mutation (n = 30), and intragenic/in-frame deletion (n = 16) in genes in the RTK/Ras/MAPK pathway. Predictive biomarkers for treatment were found in the DNA damage repair pathway and consisted of alterations in genes of the BRCA-FANC pathway (n = 489) and an MSI and/or TMB-H phenotype (n = 7). Gastroenterology 2019 156, 2242-2253.e4DOI: (10.1053/j.gastro.2019.02.037) Copyright © 2019 AGA Institute Terms and Conditions

Supplementary Figure 1 Key pathways altered in PDAC. The majority of genomic alterations in 3594 PDACs can be categorized into 12 pathways: RTK/Ras/MAPK activation, DNA damage repair, cell cycle control, transforming growth factor-β TGF-β) signaling, histone modification, SWI/SNF complex, PI3K/mTOR signaling, WNT/β-catenin pathway, RNA splicing, Notch pathway, angiogenesis, and Hedgehog signaling. Gastroenterology 2019 156, 2242-2253.e4DOI: (10.1053/j.gastro.2019.02.037) Copyright © 2019 AGA Institute Terms and Conditions

Supplementary Figure 2 Genomic alterations in GNAS-mutant PDACs. Prior sequencing studies have shown that PDACs with GNAS mutations are highly specific for an IPMN origin.24,25 Comprehensive genomic profiling identified co-occurring genomic alterations in GNAS mutant PDACs that were distinct from GNAS wild-type PDACs (Supplementary Table 5). These genes may be involved in the pathogenesis of IPMN-associated PDACs and serve as potential biomarkers for early detection strategies. Gastroenterology 2019 156, 2242-2253.e4DOI: (10.1053/j.gastro.2019.02.037) Copyright © 2019 AGA Institute Terms and Conditions