Clinically Relevant Genomic Alterations Research Articles

Genetic insights into thymic carcinomas and thymic neuroendocrine neoplasms denote prognosis signatures and pathways.

Thymic carcinomas (TCs) and thymic neuroendocrine neoplasms (TNENs) are two aggressive subtypes of thymic malignancy. Traditional therapy for advanced TCs and TNENs has limited outcome. New genomic profiling of TCs and TNENs might provide insights that contribute to the development of new treatment approaches. We used gene panel sequencing technologies to investigate the genetic aberrations of 32 TC patients and 15 TNEN patients who underwent surgery at Shanghai Chest Hospital between 2015 and 2017. Patient samples were sequenced using a 324-gene platform with licensed technologies. In this study, we focused on clinically relevant genomic alterations (CRGAs), which are previously proven to be pathogenic alterations, to identify the pathology-specific mutational patterns, prognostic signatures of TCs and TNENs. The mutational profiles between TCs and TNENs were diverse. The genetic alterations that ranked highest in TCs were in CDKN2A, TP53, ASXL1, CDKN2B, PIK3C2G, PTCH1, and ROS1 , while those in TNENs were in MEN1, MLL2, APC, RB1 , and TSC2 . Prognostic analysis showed that mutations of ROS1, CDKN2A, CDKN2B, BRAF, and BAP1 were significantly associated with worse outcomes in TC patients, and that mutation of ERBB2 indicated shortened disease-free survival (DFS) and overall survival (OS) in TNEN patients. Further investigation found that the prognosis-related genes were focused on signal pathways of cell cycle control, chromatin remodeling/DNA methylation, phosphoinositide 3-kinases (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR), and receptor tyrosine kinase (RTK)/RAS/mitogen-activated protein kinase (MAPK) signaling. We profiled the mutational features of 47 Chinese patients with thymic malignancy of diverse pathologic phenotypes to uncover the integrated genomic landscape of these rare tumors, and identified the pathology-specific mutational patterns, prognostic signatures, and potential therapeutic targets for TCs and TNENs.

The Challenges and Opportunities of the Implementation of Comprehensive Genomic Profiling in Everyday Clinical Practice with Non-Small Cell Lung Cancer: National Results from Croatia

Non–small cell lung cancer (NSCLC) has become the best example of precision oncology’s impact on outcomes in everyday clinical practice, significantly changing the expectations of all stakeholders, including medical professionals, society, and most importantly, patients. Consequently, the implementation of the precision oncology concept in medical systems, in order to achieve optimal and proven curative effects in NSCLC, is imperative. In this study, we investigated the development, challenges, and results associated with the implementation of precision oncology in NSCLC on a national level in Croatia. We conducted a multicenter, retrospective, cross-sectional analysis on the total population of Croatian patients with metastatic lung cancer, on whose tumors specimen comprehensive genomic profiling (CGP) testing was performed during 2020 and 2021. A total of 48 patients were included in the study. CGP revealed clinically relevant genomic alterations (CRGA) in 37 patients (79%), with a median of 2 (IQR 1–3) CRGA per patient. From the panel of recommended tests, KRAS, MET, and EGFR were the most common alterations, detected in 16 (34%), 5 (11%), and 3 (6%) patients, respectively. CGP revealed additional targetable mutations in 29 (60%) patients who would not have been tested (and consequently, whose mutations would not have been detected) according to the existing everyday standard of practice in Croatia. The tumor mutational burden was reported as high (≥10 Muts/Mb) in 19 patients (40%). CGP analysis reported some kind of targeted therapy for 34 patients (72%). CGP revealed other potentially targetable mutations, and it also determined TMB to be high in a significant number of patients. In conclusion, when possible, CGP should be used as an upfront backbone diagnostic and treatment-oriented work-up in patients with NSCLC.

Predicting Prostate Cancer Molecular Subtype With Deep Learning on Histopathologic Images

Microscopic examination of prostate cancer has failed to reveal a reproducible association between molecular and morphologic features. However, deep-learning algorithms trained on hematoxylin and eosin (H&E)-stained whole slide images (WSI) may outperform the human eye and help to screen for clinically-relevant genomic alterations. We created deep-learning algorithms to identify prostate tumors with underlying ETS-related gene (ERG) fusions or PTEN deletions using the following 4 stages: (1) automated tumor identification, (2) feature representation learning, (3) classification, and (4) explainability map generation. A novel transformer-based hierarchical architecture was trained on a single representative WSI of the dominant tumor nodule from a radical prostatectomy (RP) cohort with known ERG/PTEN status (n = 224 and n = 205, respectively). Two distinct vision transformer-based networks were used for feature extraction, and a distinct transformer-based model was used for classification. The ERG algorithm performance was validated across 3 RP cohorts, including 64 WSI from the pretraining cohort (AUC, 0.91) and 248 and 375 WSI from 2 independent RP cohorts (AUC, 0.86 and 0.89, respectively). In addition, we tested the ERG algorithm performance in 2 needle biopsy cohorts comprised of 179 and 148 WSI (AUC, 0.78 and 0.80, respectively). Focusing on cases with homogeneous (clonal) PTEN status, PTEN algorithm performance was assessed using 50 WSI reserved from the pretraining cohort (AUC, 0.81), 201 and 337 WSI from 2 independent RP cohorts (AUC, 0.72 and 0.80, respectively), and 151 WSI from a needle biopsy cohort (AUC, 0.75). For explainability, the PTEN algorithm was also applied to 19 WSI with heterogeneous (subclonal) PTEN loss, where the percentage tumor area with predicted PTEN loss correlated with that based on immunohistochemistry (r = 0.58, P = .0097). These deep-learning algorithms to predict ERG/PTEN status prove that H&E images can be used to screen for underlying genomic alterations in prostate cancer.

Abstract P5-14-10: Targetable alterations and genomic signatures within breast cancer brain metastases: Data from comprehensive genomic profiling of 761 breast cancer brain metastases

Abstract Background: Breast cancer brain metastasis (BCBM) represents an area of unmet clinical need. We previously demonstrated the genomic differences between primary BC and BCBM. In this study we examined the genomic differences between BCBM by BC subtypes and the potential actionable targets that might be taken forward for each subtype in clinical trials. Material and Methods: A total of 761 BCBMs were analyzed by comprehensive genomic profiling (CGP) for alterations in up to 395 genes (Foundation Medicine, USA). The samples were classified by immunohistochemistry (IHC) of the BCBM to ER+ (ER+/HER2-, ER+/HER2+), ER-/HER2+ and ER-/HER2-. Homologous recombination deficiency (HRD-gLOH; cutoff 16%), tumour mutational burden (TMB; cutoff 10 mutations/Mb), microsatellite instability (MSI) and PD-L1 prevalence and expression by IHC using the VENTANA SP142 assay (Immune Cell Score [IC] cutoff 1%) were also investigated. Results: For all BC subtypes the most enriched gene alterations in BCBM (>20% prevalence) were: TP53, MYC and PIK3CA. ESR1 and ERBB2 were more prevalent in ER+ and HER2+ tumours respectively, with ESR1 alterations significantly enriched in ER+/HER2- BCBMs (p< 0.0001). Frequently altered genes by BCBM subtype were: ER+/HER2-: CDH1 (8%) and BRCA2 (7%); ER+/HER2+: PIK3C2B (11%), MDM4 (11%), TBX3 (9%) and AKT2 (8%); ER-/HER2+: LYN (9%). Significantly enriched genes (p< 0.01) by BCBM subtype were: HER2+: CDK12 (15%); ER-/HER2-: BRCA1 (14%), CCND3 (9%), VEGFA, JAK2 (8% each) and the immune checkpoint inhibition (ICPI) biomarkers PDCD1LG2 (PDL2), CD274 (PDL1) (7% each). HRD-gLOH was high in ER+/HER2-: (43%) and ER-/HER2-: (70%). TMB and MSI were present in 10%-21% and 1-3% of BCBM respectively, whereas PDL1 protein expression by subtypes was: ER+/HER2- 23%, ER+/HER2+ 27%, ER-/HER2+ 57% , ER-/HER2- 48%. Table 1 summarizes the proportion of BCBMs with actionable alterations and selected clinical trials in BCBM. Conclusion: Clinically-relevant genomic alterations were identified across all BCBM subtypes. High HRD-gLOH, TMB and MSI were observed across all the BCBMs subtypes whereas PDL1/PDL2 alterations were a distinctive feature of ER-/HER2- BCBM. These data highlight the need to assess the genomic landscape of BCBM to enable rational treatment decisions with targeted agents, as well as to enable enrichment of relevant populations within clinical trials. Table 1. Selected studies with targeted therapy and/or immunotherapy in breast cancer brain metastases. The percentage (%) of actionable alterations by ER and HER2 status is summarized. ND: Not Detectable. Citation Format: Athina Giannoudis, Ethan Sokol, Shakti Ramkissoon, Talvinder Bhogal, Jeff Ross, Kimberly McGregor, Evangelia Razis, Rupert Bartsch, Richard S. Huang, Carlo Palmieri. Targetable alterations and genomic signatures within breast cancer brain metastases: Data from comprehensive genomic profiling of 761 breast cancer brain metastases [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-14-10.

Mutational landscape of low-grade serous carcinoma of the ovary.

5578 Background: Tumor genomic profiling is a critical component of precision oncology allowing the detection of genomic alterations (GA) that are potential therapeutic targets. We present an analysis of comprehensive genomic profiling (CGP) of a large series of low grade serous ovarian carcinoma patients assayed in a nationwide cancer network. Methods: 40 Pts with advanced low grade serous ovarian carcinoma (LGSOC) underwent hybrid-capture based CGP for up to 324 cancer-related genes on archival tumor tissue or 62 genes on circulating tumor DNA ordered during clinical care for treatment decision-making between 01-2013 thru 06-2021. Clinically relevant genomic alterations (CRGA) were defined as associated with targeted therapies or mechanism-driven clinical trials. The treatment histories for these patients were obtained with IRB-approved retrospective review. Results: Median age was 44 years (range, 25-65), 68% were White and 23% were Black. Genomic alterations (GA) were identified in 80% (32/40) of LGSOC, of which 22 (55%) had a clinically relevant genomic alteration (CRGA). There were no apparent racial differences between mutation frequencies. The table below details the frequency of the most common of these clinically relevant mutations. Additionally, 1 patient had an ESR1 activating mutation commonly seen in acquired hormone therapy resistance in breast cancer; and single cases of the following mutations were also noted: TSC1, PTCH1, PTEN, FGFR1, and AKT2. Conclusions: In a large series of Low Grade Serous Ovarian Cancer patients assayed with CGP, 55% of pts had mutations potentially targeted by precision medicine therapy. The most common target is KRAS, seen in 33% of patients, these are potentially treatable with FAK and MEK inhibitors. Another 10% of patients had either a BRCA or ATM mutations making PARP inhibitor therapy an additional targeted treatment option. While mutations in the RAS pathway are most common in LGSOC they are not the only actionable target. Furthermore, this approach might also help identify baseline or acquired resistance to the hormone therapies often used to treat this cancer. The results of this study demonstrate the significant heterogeneity of genomic alterations in this rare cancer and highlight the importance of genomic profiling in this cancer which has a marked propensity for recurrence. [Table: see text]

Mutational landscape of pancreatic adenocarcinoma identified by prospective clinical sequencing in a nationwide cancer network.

4137 Background: Curative treatment of pancreatic adenocarcinoma (PDAC) remains a challenge. Improved understanding of the tumor biology is needed to adequately target therapies for individual patients. Tumor genomic profiling is a critical component of precision medicine for these patients to identify potential genomic alterations that can be targeted for therapy. We present a cohort of PDAC patients who underwent prospective comprehensive genomic profiling (CGP) in a national cancer network. Methods: Between 2013 and 2021, 731 patients with PDAC underwent CGP with hybrid capture of up to 406 cancer-related genes on tumor tissue for treatment decision-making. Clinically relevant genomic alterations (CRGA) were defined as associated with targeted therapies or mechanism-driven clinical trials. Patient demographics and outcomes were retrospectively reviewed with IRB approval. Results: Median patient age at presentation was 58 years (range, 26-87) and a slight majority were male (54%). Most patients presented with stage IV disease (n=457; 63%). Median overall survival (OS) was 26 months for stages I-III and 15 months for stage IV disease. A majority of patients were treated with first line chemotherapy, predominantly gemcitabine or FOLFIRINOX. Surgical resection was performed in 198 patients (27%). Genomic alterations (GA) were identified in 96% of PDAC patients. The most common GA were in KRAS (86%), TP53 (75%), CDKN2A (49%), SMAD4 (21%), ARID1A (7.8%), RNF43 (5%), BRCA2 (4%), and BRCA1 (1%). A mutation in one of the four commonly mutated genes ( KRAS, TP53, CDKN2A, or SMAD4) was identified in 92% (n=675). Common KRAS mutations were G12D(43%), G12V (30%), and G12R(16%). Median OS was significantly worse for patients with mutations in KRAS, TP53 and CDK2NA, while wild type RNF43 demonstrated improved OS (all, P<0.05). 206 patients (28%) had a CRGA based on the Know Your Tumor registry trial, including mutations in BRCA1, BRCA2, BRAF, ATM, CHEK2, and ATK. Tumor Mutational Burden (TMB) was known for 345 patients and included: 292 TMB-low (85%), 49 TMB-intermediate (14%), and 4 TMB-high (1%). PD-L1 status was obtained in 33 patients, with 18 PD-L1 positive (55%). MSI status was noted for 345 patients; only 5 patients (1%) were MSI-high. Of the 39 patients with a BRCA1 or BRCA2 mutation, 30 (77%) were treated with Olaparib. Other commonly utilized therapies included Niraparib (n=56), Regorafenib (n=8), Everolimus (n=35), Erlotinib (n=8), and Cetuximab (n=7). Conclusions: In a large series of PDAC patients assayed with CGP, GA were identified in 96% but only 28% had an actionable mutation. Access to the TAPUR trial allowed for an increase in the patients identified for targeted immunotherapy between 2013 and 2019, although overall use remained low for PDAC. Further research is needed to identify therapies based on the more commonly mutated genes given their association with overall survival.

Racial differences in the mutational landscape of serous endometrial cancer.

5600 Background: Tumor comprehensive genomic profiling (CGP) identifying genomic alterations (GA) that have diagnostic, prognostic and are potentially therapeutically targetable is essential to precision oncology. 2022 NCCN Uterine Neoplasm guidelines recommend tumor genetic evaluation as part of initial evaluation. As racial disparities in endometrial cancer outcomes have been widely reported, we analyzed our CGP results from a large series of serous endometrial cancer patients treated in a nationwide cancer network to identify GA differences that may contribute to worse prognosis and help inform better therapy selection. Methods: 86 Pts with serous endometrial underwent hybrid-capture based CGP for up to 324 cancer-related genes of archival tumor tissue or 62 genes on circulating tumor DNA ordered during clinical care for treatment decision-making between 01-2013 to 07-2021. Clinically relevant genomic alterations (CRGA) were defined as associated with targeted therapies or mechanism-driven clinical trials. Statistical analysis performed with Fisher Exact test comparing Black and White women. Results: Median age was 63 years (range, 38-85), 37% were White, 58% were Black and 5% were Asian. GA were identified in 94% (81/86) of these patients. TP 53 mutations which is characteristic of serous cancer were present in 80 of 86 patients (93%). GA predicted to activate PI3-Kinase pathway signaling ( PIK3CA, PIK3R1, PTEN) were significantly more common in White women occurring in 13 of 32 (41%), compared with 8 of 50 (16%) of Black women (p. < 0.02). An important, but not statistically significant trend of greater percentage of CCNE1 amplification in Black women is also noted, see table below: Mutation frequencies were similar between Black and White women for the following genes: PPP2R1A 23%; MYC 19%; FBXW7 14%; ARID1A 9%. Conclusions: In this 86 patient series of women with Serous Endometrial Cancer we note that PIK3CA mutations, an important resistance factor in anti-HER2 therapy, were significantly more common in White women (41%) compared with Black women (16%) (p. < 0.02) and ERBB2 mutations occurred in 19% of White women and only 10% of Black women. This study cohort also identified a larger percentage of black women with CCNE1 amplification. Increased CCNE1 amplification has been linked to the racial disparities in cancer outcomes and may explain the disparities seen with endometrial cancers. [Table: see text]

Evaluation of stage IV pancreatic adenocarcinomas based on mutational profiling of tumors.

4139 Background: Curative treatment of pancreatic adenocarcinoma (PDAC) remains a challenge, as most patients present with advanced disease that has spread to other organs. The main opportunity for cure for these individuals remains systemic therapy. An improved understanding of the tumor biology is needed to appropriately target therapies for individual patients. We present cohort of Stage IV PDAC patients who underwent prospective comprehensive genomic profiling (CGP) in a national cancer network to evaluate genomic mutations, treatment patterns and survival. Methods: Between 2013 and 2021, 458 patients with Stage IV PDAC underwent CGP with hybrid capture of up to 406 cancer-related genes on tumor tissue for treatment decision-making. Clinically relevant genomic alterations (CRGA) were defined as associated with targeted therapies or mechanism-driven clinical trials. Patient demographics and outcomes were retrospectively reviewed with IRB approval. Results: Median patient age at presentation was 59 years (range, 26-84) and a majority were male (55%). Median overall survival was 15 months. Most patients were treated with first line chemotherapy, predominantly gemcitabine or FOLFIRINOX. GA were identified in 98% (n = 447) of PDAC patients. The most common genomic alterations were in KRAS (85%), TP53 (75%), CDKN2A (52%), SMAD4 (21%), ARID1A (9%), BRCA2 (5%), RNF43 (4%), and BRCA1 (1%). A mutation in one of the four commonly mutated genes ( KRAS, TP53, CDKN2A, or SMAD4) was identified in 94% (n = 426). Median overall survival was significantly worse for patients with mutations in KRAS or TP53 (both, P < 0.05). 185 patients (40%) had an actionable mutation based on the Know Your Tumor registry trial, including mutations in BRCA1, BRCA2, BRAF, CHEK2, ATM, ATK and STK11. MSI status was noted for 226 patients; only one patient was MSI-high. Tumor Mutational Burden (TMB) was known for 228 patients and was split as follows: 199 TMB-low (87%), 27 TMB-intermediate (12%), and 2 TMB-high (1%). TMB status was not associated with OS (P = 0.21). PD-L1 status was obtained in 20 patients, with 9 PD-L1 positive (45%); this was not associated with OS (P = 0.66). Of the 38 patients with a BRCA1 or BRCA2 mutation, 31 (82%) were treated with Olaparib. Other commonly utilized therapies included Niraparib (n = 56), Regorafenib (n = 8), Everolimus (n = 34), Erlotinib (n = 8), and Cetuximab (n = 6). Conclusions: In a large series of Stage IV PDAC patients assayed with CGP, GA were identified in 98% of tumors but only 40% had an actionable mutation. Most patients continue to be treated with conventional chemotherapy despite a sizeable group with targetable mutations. Further work is needed to identify targeted therapies for the more common mutations in PDAC given their impact on overall survival.

Therapeutic implications of mutations in high grade serous ovarian carcinoma when evaluated by race.

e17590 Background: Individualizing oncologic treatment by using precision oncology techniques that allow for detection of genomic alterations (GA) has become critical. We present an analysis of comprehensive genomic profiling (CGP) of a large series of high grade serous ovarian carcinoma (HGSOC) patients assayed in a nationwide cancer network. Racial disparities in genomic alterations may assist in better targeting therapies, predicting drug resistance, and potential germline mutations. Methods: 312 patients with HGSOC underwent CGP with hybrid capture on tumor tissue for treatment decision-making between 01-2013 to 06-2021. Clinically relevant genomic alterations (CRGA) were reported as targetable marker. Statistical analysis performed with Fisher Exact test. Results: Median age was 55 years (range, 23-81), 71.2% were White, 16.4% were Black, 3.9% were Hispanic, and 1.3% were Asian. GA were identified in 98.7% (308/312) of these patients. TP53 mutations were present in 286 of 312 patients (91.7%) and interestingly, while not statistically significant (p = 0.06) was present in 98% of black women and 89.2% of white women. BRCA1 mutation was present in 14.4% of white women and in 17.6% of black women. BRCA2 mutation was present in 9.9% of white women and 9.8% of black women. Several interesting mutations were identified, see table below. Conclusions: In this 312-patient series of women with HGSOC, we note several prominent mutations in the tumors. While not statistically significant, there is a trend of larger number of poorer prognostic mutations in black women including p53, KRAS and CCNE1. Some studies have found the amplification of CCNE1 and mutation of homologous recombination repair genes to be mutually exclusive in HGSOC which may compel us to find other therapeutic interventions than the PARP inhibitors for these patients.[Table: see text]

Abstract PD4-09: Comprehensive assessment of the genomic landscape of breast cancer brain metastases reveals targetable alterations and genomic signatures relevant to immune-checkpoint and PARP inhibitors

Abstract Background: Central nervous system (CNS) disease secondary to breast cancer (BC) is a growing clinical problem and a cause of significant morbidity and mortality. A better understanding of the genomic landscape is key to understanding its cause and to developing novel treatments. In this study, we examined the genomic landscape of a large cohort of breast cancer brain metastases (BMs) and compared them to a cohort of local breast cancers (BCs) and non-CNS metastases (N-CNS). Material and Methods: We analyzed 822 BMs and compared them to 11,988 local, breast-biopsied BCs and 15,516 N-CNS (unpaired samples) with comprehensive genomic profiling (CGP) for all classes of alterations in at least 324 genes (Foundation Medicine, Cambridge, MA, USA). Homologous recombination deficiency detected by genome-wide loss of heterozygosity (HRD-gLOH; cutoff 16%), tumour mutation burden (TMB; cutoff 10 mutations/Mb), microsatellite instability (MSI) and PD-L1 prevalence and expression by VENTANA SP142 immune cell immunohistochemistry (IHC; cutoff 1%) was also investigated within and across the cohorts. Results: As compared to local BCs, 31 genes were significantly enriched for genomic alterations in BMs with BM prevalence >3% and false-discovery rate (FDR) <0.1. The most enriched genes were: TP53 (71.8%), MYC (25.9%), ERBB2 (24.6%), PTEN (16.7%), CDKN2A and RB1 (10.3% each), NF1 (8.6%), GNAS (7.9%), BRCA1, CDKN2B and ZNF217 (7.8% each), ARID1A (7.3%), CCNE1 (6.7%), ESR1 (6.4%), MAP2K4 (5.8%), AURKA (5.5%) and PIK3R1 (5.1%). Of these 31 genes, 26 were also enriched between BM vs N-CNS. The BM-enriched. genes that lost significance in comparison to N-CNS were: ZNF217, ARID1A, MAP2K4, AURKA and ARFRP1. PIK3CA prevalence was BMs: 30.2%, BCs: 31.8% and N-CNS: 38.9% (no significant difference between cohorts). HRD-gLOH was higher in BMs: 52.0% vs BCs: 33.7% and N-CNS: 31.5%. The prevalence of immune checkpoint inhibition (ICPI) biomarkers in BM were as follows: TMB-High 15.5%, MSI-High 2.0%, PD-L1 (CD274) 3.5% and its paralogue PDCD1LG2 (PD-L2, CD273) 3.4%. All were significantly higher in the BM vs primary BC and N-CNS group (p<0.05, FDR<0.1 for all comparisons). PD-L1 copy number (CN) variation was also higher in BMs: 3.4% vs BCs: 1.6% and N-CNS: 1.1%. PD-L1 positive expression was lower in BMs: 38.7% vs BCs: 54.3% but higher than N-CNS: 26.2%. Higher PD-L1 positive expression was observed in ER-/HER2- BMs: 48.3% vs BCs: 50.0% vs N-CNS: 21.4%. Table 1 summarizes the genomic signatures and PD-L1 positivity in the BC, BM and N-CNS cohorts and within different receptor subtypes. Conclusion: A high prevalence of clinically-relevant genomic alterations in BM is identified in comparison to the local BCs and/or N-CNS disease. A high proportion of BMs have high HRD-gLOH, TMB, MSI and PD-L1 alterations rendering them potentially amenable to treatment with ICPIs and PARP inhibitors. These data reinforce the importance of acquiring BM material and/or cerebrospinal fluid for CGP to enable rationale treatment decisions as well for enrolment into genomically driven BM studies of targeted agents. Table 1.Prevalence (%) of the genomic signatures HRD-gLOH, TMB, MSI and PD-L1+ expression.Site% HRD-gLOH% TMB-H% MSI-H% PDL1+ALLlocal BC33.70%. (2573/7636)5.04%. (527/10464)0.37%. (39/10464)54.25%. (1092/2013)BM52.01%. (362/696)15.51%. (116/748)2.01%. (15/748)38.73%. (55/142)N-CNS31.55%. (3237/10260)9.82%. (1395/14210)0.23%. (32/14210)26.21%. (615/2346)ER+/HER2-local BC31.48%. (119/378)3.41%. (19/557)0.36%. (2/557)40.00%. (14/35)BM43.17%. (79/183)11.40%. (22/193)1.04%. (2/193)23.08%. (9/39)N-CNS29.65%. (126/425)8.92%. (51/572)0.17%. (1/572)12.99%. (10/77)ER+/HER2+local BC19.57%. (9/46)2.78%. (2/72)0.00%. (0/72)42.86%. (3/7)BM26.67%. (16/60)9.68%. (6/62)0.00%. (0/62)27.27%. (3/11)N-CNS47.37%. (18/38)19.57%. (9/46)0.00%. (0/46)14.29%. (1/7)ER-/HER2+local BC32.26%. (10/31)8.70%. (4/46)0.00%. (0/46)100.00%. (5/5)BM33.33%. (23/69)21.33%. (16/75)2.67%. (2/75)57.14%. (4/7)N-CNS34.38%. (11/32)4.26%. (2/47)0.00%. (0/47)42.86%. (3/7)ER-/HER2-local BC52.25%. (186/356)2.70%. (14/518)0.19%. (1/518)50.00%. (30/60)BM70.45%. (174/247)17.41%. (47/270)2.59%. (7/270)48.33%. (29/60)N-CNS43.52%. (84/193)10.04%. (27/269)0.74%. (2/269)21.43%. (6/28) Citation Format: Athina Giannoudis, Ethan Sokol, Shakti H Ramkissoon, Talvinder Bhogal, Kimberly McGregor, Allison Clark, Evangelia D Razis, Rupert Bartsch, Richard SP Huang, Carlo Palmieri. Comprehensive assessment of the genomic landscape of breast cancer brain metastases reveals targetable alterations and genomic signatures relevant to immune-checkpoint and PARP inhibitors [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD4-09.

Precision Oncology in Metastatic Uterine Cancer; Croatian First-Year Experience of the Comprehensive Genomic Profiling in Everyday Clinical Practice.

Comprehensive genomic profiling (CGP) is gradually becoming an inevitable part of the everyday oncology clinical practice. The interpretation and optimal implementation of the results is one of the hot topics of modern-day oncology. According to the recent findings, uterine cancer harbors a high level of gene alterations but is still insufficiently explored. The primary goal of this project was to assess the proportion of patients with targetable mutations. Also, the aim was to define and emphasize potential opportunities as well as the problems we have faced in the first year of testing on the national level. We performed a multicentric, retrospective, nested cross-sectional analysis on the total population of Croatian patients with advanced/metastatic uterine cancer where the tumor CGP was performed during 2020. CGP of the tumor tissue of 32 patients revealed clinically relevant genomic alterations (CRGA) in 27 patients (84%) with a median of 3 (IQR 1-4) CRGA per patient. The most common CRGAs were those of phosphatide-inositol-3 kinases (PIK3) in 22 patients (69%), with 13/22 (59%) of those patients harboring PIK3CA mutation. The next most common CGRAs were ARID1A and PTEN mutations in 13 (41%) and 11 (34%) patients, respectively. Microsatellite status was determined as stable in 21 patients (66%) and highly unstable in 10 patients (31%). A high tumor mutational burden (≥10Muts/Mb) was reported in 12 patients (38%). CGP analysis reported some kind of targeted therapy for 28 patients (88%). CGP determined clinically relevant genomic alterations in the significant majority of patients with metastatic uterine cancer, defining it as a rich ground for further positioning and development of precision oncology.

Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients

BackgroundCell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth.MethodsPlasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES).ResultscfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches.ConclusionscfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.

Clinical genomic profiling to identify actionable alterations for very early relapsed triple-negative breast cancer patients in the Chinese population

Background Triple-negative breast cancer (TNBC) represents about 19% of all breast cancer cases in the Chinese population. Lack of targeted therapy contributes to the poorer outcomes compared with other breast cancer subtypes. Comprehensive genomic profiling helps to explore the clinically relevant genomic alterations (CRGAs) and potential therapeutic targets in very-early-relapsed TNBC patients. Methods Formalin-fixed paraffin-embedded (FFPE) tumour tissue specimens from 23 patients with very-early-relapsed TNBC and 13 patients with disease-free survival (DFS) more than 36 months were tested by FoundationOne CDx (F1CDx) in 324 genes and select gene rearrangements, along with genomic signatures including microsatellite instability (MSI) and tumour mutational burden (TMB). Results In total, 137 CRGAs were detected in the 23 very-early-relapsed TNBC patients, averaging six alterations per sample. The mean TMB was 4 Muts/Mb, which was higher than that in non-recurrence patients, and is statistically significant. The top-ranked altered genes were TP53 (83%), PTEN (35%), RB1 (30%), PIK3CA (26%) and BRCA1 (22%). RB1 mutation carriers had shorter DFS. Notably, 100% of these patients had at least one CRGA, and 87% of patients had at least one actionable alteration. In pathway analysis, patients who carried a mutation in the cell cycle pathway were more likely to experience very early recurrence. Strikingly, we detected one patient with ERBB2 amplification and one patient with ERBB2 exon20 insertion, both of which were missed by immunohistochemistry (IHC). We also detected novel alterations of ROS1–EPHA7 fusion for the first time, which has not been reported in breast cancer before. Conclusions The comprehensive genomic profiling can identify novel treatment targets and address the limited options in TNBC patients. Therefore, incorporating F1CDx into TNBC may shed light on novel therapeutic opportunities for these very-early-relapsed TNBC patients.

1856P - Comprehensive genomic profiling of thymic carcinoma in a sample Chinese population

BackgroundThymic carcinomas (TC) is a kind of a malignant intrathoracic tumor. Herein, we examined the clinicopathological characteristics and analyzed comprehensive genomic profiling (CGP) in 47TC patients to elucidate the potentially clinically relevant genomic alterations (CRGAs) in this population. Methods47 stage I-IV TC patients who underwent surgery at Shanghai Chest Hospital between 2015 and 2017 were analyzed. These patients were sequenced by FoundationOne CDx (F1CDx) which is a FDA approved platform conducted by DIAN (Hangzhou Lab) with the licensed technologies. In this study, we focus on CRGAs which are known or likely pathogenic alterations. ResultsThe 47TC patients included 27 thymic squamous cell carcinoma (TSCC), 14 neuroendocrine tumors of the thymus (NETT) and 7 mixed subtype of TSCC and NETT. The median age of TSCC, NETT and mixed subtype was 59.5, 65 and 74, respectively. The median number of CRGAs in TSCC, NETT and mixed subtype were 1 (range 0-10), 2 (range 0-3) and 2 (range 0-4), respectively. Only one TSCC patient was microsatellite instability-high (MSI-H), which also has the highest TMB (21 Muts/Mb). Among all the four patients with TMB larger than 10 Muts/Mbs, three were TSCC and one was mixed subtype. The top ranked altered genes in TSCC were TP53 (30%), CDKN2A (26), CDKN2B (19%) and ASXL1 (15%). In NETT, the top mutated genes were MEN1 (36%), STAG2 (14%), CDKN2A (14%) and HRAS (14%). Furthermore, the top ranked mutated genes in mixed subtype were TP53 (29%) and CDKN2A (29%). Notably, TP53, ASXL1, TET2, MLL2, EP30, BAP1 were only mutated in TSCC or mixed subtypes. However, mutated of MEN1, STAG2 and HRAS were also founded in NETT subtype. ConclusionsThis was the largest cohort of CGP for TC till now in a sample Chinese population. TSCC and NETT have very different mutated landscapes, while the mixed subtype was more similar with TSCC. The number of CRGA range from 0 to 10 also demonstrated a high tumor heterogeneity for TSCC. In addition, the top mutated genes in TSCC and NETT founded in this study were different from the published results which focused on metastatic thymic carcinoma (mTC). Given the limited treatment options and poor prognosis of patients with TC, CGP has the potential to identify new treatment paradigms and meet an unmet clinical need for this disease. Legal entity responsible for the studyThe authors. FundingShanghai science and technology commission. DisclosureAll authors have declared no conflicts of interest.

Comprehensive genomic profiling of recurrent endometrial cancer: Implications for selection of systemic therapy

ObjectivesTo assess whether comprehensive genomic profiling (CGP) in the setting of routine clinical care allows molecular classification of recurrent endometrial cancer (EC) into the four Cancer Genome Atlas (TCGA) categories: POLE ultramutated, microsatellite instable, copy-number low, and copy-number high and whether this approach can identify genomic alterations (GAs) which inform treatment decisions. MethodsArchival tissues from 74 patients diagnosed with recurrent EC were prospectively analyzed using hybrid-capture-based genomic profiling. Tumor mutational burden and microsatellite instability were measured. Clinically relevant GAs (CRGAs) were defined as GAs associated with targeted therapies available on-label or in mechanism-driven clinical trials. ResultsUsing POLE mutational analysis, mismatch repair status, and p53 mutational analysis as surrogate for ‘copy-number’ status CGP segregated all cases into four TCGA molecular subgroups. While recurrent serous ECs were predominantly copy-number high, we found no clear prevalence of a specific molecular subtype in endometrioid, clear cell or undifferentiated tumors. Every tumor sample had at least one GA and 91% (67/74) had at least one CRGA. In this series 32% (24/74) of patients received a matched therapy based on the results of CGP. Objective responses to the matched therapy were seen in 25% (6/24) of patients with an additional 37.5% (9/24) achieving stable disease leading to a clinical benefit rate of 62.5% with a median treatment duration of 14.6 months (range 4.3–69 months). ConclusionsCGP allows molecular classification of EC into four TCGA categories and allows identification of potential biomarkers for matched therapy in the setting of routine clinical care.

Mutational landscape of cervical cancer identified by prospective clinical sequencing in a nationwide cancer network.

e17022 Background: Tumor genomic profiling is a critical component of precision oncology allowing the detection of genomic alterations (GA) that have the potential to be targeted therapeutically. We present an analysis of comprehensive genomic profiling (CGP) of a large series of cervical cancer (CC) patients assayed in a nationwide cancer network. Methods: 118 Pts with advanced CC underwent CGP with hybrid capture of up to 406 cancer-related genes on tumor tissue or for 62 genes on circulating tumor DNA ordered during clinical care for treatment decision-making between 01-2013 to 05-2018. Clinically relevant genomic alterations (CRGA) were defined as associated with targeted therapies or mechanism-driven clinical trials. The treatment histories for these patients were obtained with IRB-approved retrospective review. Results: Median age was 47 years (range, 27-71), 69% were Caucasian. GA were identified in 88% (104/118) of CC, of which 87 (74%) had a clinically relevant genomic alteration (CRGA). PI3K/AKT/mTOR pathway ( PIK3CA, AKT1/2/3, PIK3R1, PTEN, MTOR, STK11, FBXW7) CRGA were most commonpresent in 73.5% (64/87) of CC. CRGA in other targetable pathways were identified: 24.1% (21/87) in MEK ( KRAS, NRAS, HRAS, BRAF, RAF1, GNAS, NF1, NF2), 9.1% (8/87) in HRD (BRCA1/2, ATM, PALB2, BRIP1) and 24.1% (21/87) in ERBB ( ERBB2, ERBB3, ERBB4, EGFR). One patient was MSI-high and one patient was TMB-high. 29.8% (26/87) of CC patients were ordered a genomically-matched treatment, and 24 pts received treatment; 61.5% (16/26) were agents that were FDA approved in a different tumor type, and 34.6% (9/26) through referral to a matched mechanism driven clinical trial. With access to the clinical trial TAPUR, the frequency of matched treatment through clinical trials increased over time from 2013 to 2018. The PFS for non study related patients was 7 weeks and OS was 19 weeks. Conclusions: In a large series of Cervical Cancer patients assayed with CGP, 27.5% (24/87) of pts received matched treatment, which was predominantly targeted therapy. The comprehensive sensitive and unbiased nature of CGP, coupled with a multidisciplinary molecular tumor board and staff dedicated to genomic interpretation, assisted in achieving a high frequency of patients’ participation in clinical trials and gene-directed treatment.

Mutational landscape of endometrial cancer identified by prospective clinical sequencing in a nationwide cancer network.

e17123 Background: Tumor genomic profiling is a critical component of precision oncology allowing the detection of genomic alterations (GA) that have the potential to be targeted therapeutically. We present an analysis of comprehensive genomic profiling (CGP) of a large series of endometrial cancer (EC) patients assayed in a nationwide cancer network. Methods: 278 Pts with advanced EC underwent CGP with hybrid capture of up to 406 cancer-related genes on tumor tissue or for 62 genes on circulating tumor DNA ordered during clinical care for treatment decision-making between 01-2013 to 05-2018. Clinically relevant genomic alterations (CRGA) were defined as associated with targeted therapies or mechanism-driven clinical trials. The treatment histories for these patients were obtained with IRB-approved retrospective review. Results: Median age was 59 years (range, 37-85), 58% were Caucasian. GA were identified in 97% (271/278) of EC, of which 218 (80%) had a clinically relevant genomic alteration (CRGA). PI3K/AKT/mTOR pathway ( PIK3CA, AKT1/2/3, PIK3R1, PTEN, MTOR, STK11, FBXW7) CRGA were most common, present in 63.8% of EC. CRGA in other targetable pathways were identified: 28.4% in MEK ( KRAS, NRAS, HRAS, BRAF, RAF1, GNAS, NF1, NF2) , 12.5% in HRD (BRCA1/2, ATM, PALB2, BRIP1 ) and 9.9% in ERBB ( ERBB2, ERBB3, ERBB4, EGFR). 26 patients are MSI-high 9.5% (26/271) and 21 patients are TMB-high 7.7% (21/271). 29.8% (65/218) of EC patients were ordered a genomically-matched treatment, and 61 of these patients received the treatment. 69.2% (45/65) were agents that were FDA approved in a different tumor type, and 24.6% (16/65) through referral to a matched mechanism driven clinical trial. With access to the clinical trial TAPUR, the frequency of matched treatment through clinical trials increased over time from 2013 to 2018. The median PFS for non-clinical trial study patients was 9 weeks, and the median OS was 27 weeks. Conclusions: In a large series of Endometrial and Uterine cancer patients assayed with CGP, 27.9% (61/218) of pts received matched treatment, which was predominantly targeted therapy. The comprehensive sensitive and unbiased nature of CGP, coupled with a multidisciplinary molecular tumor board and staff dedicated to genomic interpretation, assisted in achieving a high frequency of patients’ participation in clinical trials and gene-directed treatment.

Oncology precision medicine for hepatobiliary and pancreatic cancer: An institutional review.

e14626 Background: Hepatobiliary cancers - hepatocellular carcinoma (HCC), intra or extrahepatic cholangiocarcinoma (I/EC), and gallbladder carcinoma (GB) - and pancreatic adenocarcinoma (PC) remain a leading cause of death with little improvement in long-term outcome. Recent studies have suggested that these cancers harbor actionable mutations to varying degrees. The aim of our study was to examine the number of patients (Pts) with these primary tumors who underwent molecular testing in a large vertically integrated health system. Subsequently, we analyzed the percentage of that population who may be candidates for oncology precision medicine (OPM) directed therapy. Methods: We identified Pts with HCC, IC, EC, GB in an IRB reviewed OPM database of our system over a one year period. Pts who underwent molecular panel testing were selected out, and their molecular alterations were identified and stratified by cancer type. Results: 304 total Pts were identified. 61 (20%) underwent molecular testing broken down as follows: 17/132 (13%) I/EC and HCC, 3/11 (27%) GB, and 41/161 (25%) PC. Quantity not sufficient for testing was in 10/61 (16%), of which 5/10 (50%) were resubmitted and tested successfully. 6/61 (10%) were cancelled or deemed not appropriate. Test recommended potential actionability was 8/17 (47%) of I/EC and HCC, 2/3 (67%) of GB, and 25/41 (61%) of PC. Conclusions: OPM is a dynamic area of increasing testing and learning. We found 13-27% of hepatobiliary and pancreatic Pts had molecular testing, which suggests the potential to increase molecular screening for this difficult group of tumors. Total genetic alterations (TGA) and clinically relevant genomic alterations (CRGA) per patient are similar to Ross et al. ( http://ow.ly/k52a30nBMnU ) for GB. Final interpretation regarding pragmatic actionability (patient on drug) and clinical outcomes are still under investigation.[Table: see text]

Abstract P3-06-18: Comprehensive genomic profiling of carcinosarcomas of the breast

Abstract Background: Carcinosarcomas of the breast (BCSC) are exceptionally rare and the underlying genomic drivers are still being elucidated. Comprehensive genomic profiling (CGP) determines the tumor mutation burden (TMB) and identifies all four classes of genomic alterations (GA) that have potential to direct personalized treatment strategies. Methods: CGP by hybridization capture of exons from up to 315 cancer-related genes and select introns of 28 genes commonly rearranged in cancer was applied to ≥ 50ng of DNA extracted from 9 consecutive BCSC and sequenced to high, uniform median coverage (&amp;gt;500X). Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined by principal components analysis of optimized loci. Results: The 9 BCSC patients had a median age of 57 yrs (range 49-78 yrs). CGP was performed on the primary BCSC in 4 cases and on metastasis biopsies in 5 cases (4 lung and 1 lymph node). The mean GA/tumor was 6.6 and clinically relevant GA (CRGA)/tumor was 1.3. The most frequent non-CRGA were in TP53 (89%), MYC (56%) and LYN (40%). The most frequent CRGA were in PIK3CA (33%), and NF1, BRCA1, PTEN, RICTOR, FGFR1, AKT2 and STK11 (all at 11%). The median TMB for all BCSC was 2.4 mut/Mb with 1 (11%) tumor with a TMB &amp;gt; 20 mut/Mb and 8 BCSC (88%) with TMB &amp;lt; 5 mut/Mb. Five of 5 BCSC (100%) that were available for MSI status testing were microsatellite stable. Conclusions: On CGP, BCSC feature a high frequency of GA, but only a modest frequency of CRGA and high TMB. However, when the CRGA and TMB positive cases are combined (77.8% overall in this series), the opportunity for personalized targeted and immunotherapies are significant. Thus, further investigation of precision therapies for BCSC in the clinical trial setting appear warranted. Citation Format: Gay LM, Elvin JA, Vergilio J-A, Killian JK, Ramkissoon S, Severson E, Daniel S, Hammerich A, Sokol E, Frampton G, Chung J, Trabucco S, Ali S, Reddy P, Schrock AB, Miller VA, Ross JS. Comprehensive genomic profiling of carcinosarcomas of the breast [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-18.

Comprehensive Genomic Profiling and Precision Pathology for Clinically Advanced Salivary Gland Myoepithelial Carcinoma

Myoepithelial carcinomas of salivary glands (MyC) are generally low-grade malignancies that can arise de novo or in the background of a pre-existing pleomorphic adenoma (CPA). However, on occasion, MyC can present or progress into inoperable locally advanced and/or metastatic disease. DNA was extracted from 40 microns of FFPE sections from 24 cases of relapsed, refractory and metastatic MyC. Comprehensive genomic profiling (CGP) was performed using a hybrid-capture, adaptor ligation-based next-generation sequencing assay. Tumor mutational burden (TMB) was calculated from a minimum of 1.11 Mb of sequenced DNA and reported as mutations/Mb. The results were analyzed for all classes of genomic alterations (GA), including base substitutions (sub), insertions and deletions (short variants), fusions, and copy number changes including amplifications (amp) and homozygous deletions. At the time of CGP, 10 (42%) MyC were stage III and 14 (58%) were stage IV. Of 22 cases where the primary site was known, 16 (73%) arose in the parotid, 1 (5%) in the submandibular SG, and 5 (22%) from accessory SG.Tabled 1Abstract 247MyC cases24Genomic alterations (GA)/case2.3Clinically Relevant GA (CRGA)RICTOR amp & PIK3CA sub (21% each) PTCH1 & PDGFRB sub (8 % each) NF1 & BRCA2 sub (4% each)Non-actionable GACDKN2A loss (25%) CDKN2B & HRAS sub (21% each) TERT, MYC, TP53 & NOTCH1 subs (13% each)TMB > 20 Mut/Mb2 (8%)TMB < 10 Mut/Mb22 *(92%)* No cases of ERBB2 GA and no cases of MSI-high status. Open table in a new tab * No cases of ERBB2 GA and no cases of MSI-high status. Clinically advanced MyC are similar to the usually less aggressive SG tumors, adenoid cystic, and acinic cell carcinomas in having a low frequency of GA, a low TP53 mutation frequency, low TMB, and general paucity of CRGA when compared to the usually more aggressive adenocarcinomas which may feature targetable driver alterations in ERBB2 and other pathways. However, the findings of potentially targetable alterations in RICTOR, PTCH1, NF1, and BRCA2 and the presence of high TMB, albeit in a relatively small percentage of MyC cases, encourage the continued use of CGP.