ERBB2 Alterations Research Articles

Real world data analysis of next generation sequencing and protein expression in metastatic breast cancer patients

Next generation sequencing (NGS) together with protein expression analysis is back bone of molecularly targeted therapy in precision medicine. Our retrospective study shows our experience with NGS of 324 genes in combination with protein expression in patients with advanced breast cancer (aBC). The primary purpose was to analyze the prevalence of individual genetic alterations combined with protein expression to define potential targets for an individualized therapy. Between April 2018 and September 2019, 41 patients with aBC were offered a NGS test. The test was used to detect clinically relevant genomic alterations and to support further targeted therapy decisions. Hormone receptors, ERBB2 of tumors and PD-L1 was stained by immunohistochemistry. The data was recorded up to September 2019. After prior consent 41 results were available for further analysis. The most common BC subtypes were triple-negative (n = 16), HR+/ERBB2− (n = 15), and ERBB2+ (n = 9), with one missing data of the primary tumor. 27 patients had more than one genetic alteration. The most common alterations were PIK3CA (n = 14) and ERBB2 alterations (n = 11). Followed by ESR1 (n = 10), FGFR1 (n = 7) and PTEN (n = 7). 68% of the alterations were clinically relevant (tier I and II of ESCAT classification). The most common treatment recommendation was ERBB2-directed therapy (single or double blockade, trastuzumab emtansine and lapatinib) followed by alpelisib in combination with fulvestrant. Comprehensive genomic profiling combined with protein expression analysis in aBC allowed a guided personalized therapy for half of our patients. So far there are no well-defined tools allowing interpretations of genomic alterations detected by NGS in combination with protein expression and other factors.

Characterization of ERBB2 alterations in non-small cell lung cancer.

e21553 Background: ERBB2 alteration (mutation and/or amplification) is associated with poor survival in non-small cell lung cancer (NSCLC) and is commonly reported as a resistance mechanism to EGFR tyrosine kinase inhibitors. Several clinical trials are ongoing for the management of ERBB2-altered NSCLC. Here we report the prevalence of different ERBB2 alterations in NSCLC. Methods: We retrospectively analyzed ERBB2 alterations in NSCLC tumors that underwent next-generation sequencing (NGS) with Caris Life Sciences. De-identified pathological and molecular information was collected. ERBB2 copy number of greater than 6 was defined as amplification; mutations were classified among 7 groups based on their mechanism of action. Results: A total of 12946 NSCLC tumors with ERBB2 NGS results were available. Among them, 12492 had ERBB2 copy number alteration (CNA) data available. 321 tumors (2.5%) had ERBB2 alteration (mutation or amplification). Among them, ERBB2 was mutated in 197 tumors (1.5%) and amplified in 134 (1.1%) tumors. Type of ERBB2 mutation, respective median age and distribution among sex is in the table. 10 tumors with ERBB2 mutation (7.46%) also showed ERBB2 amplification. Six percent of tumors (8/135) with ERBB2 exon 20 insertion mutations had co-occurring ERBB2 amplification. One tumor for each extracellular domain (ECD) and transmembrane group had co-occurring ERBB2 amplification. Eight tumors with ERBB2 mutation had an overlapping EGFR L858R or exon19del mutation. Seven of these 8 tumors were from the ECD group (7/21) and all had mutations in the S310 locus. One tumor was from the transmembrane group. Conclusions: Exon 20 insertion mutation is the most commonly found ERBB2 mutation among NSCLC, a few of them had co-occurring ERBB2 amplification. One third of tumors with extracellular domain ERBB2 mutation had EGFR mutation. Tarloxitinib (NCT03805841), trastuzumab deruxtucan (NCT03505719), pyrotinib (NCT02500199), poziotinib (NCT03318939) are just a few of the novel ERBB2 inhibitors available in clinical trials. It will be critical to utilize next generation sequencing to effectively capture uncommon mutations and amplifications in ERBB2 so that patients may be offered therapy directly targeted to their genomic alterations. [Table: see text]

Genomic profiling of breast cancer brain metastases reveals targetable alterations.

2525 Background: Genomic characterization of breast cancer brain metastases (BCBMs) has thus far been limited. The objective of this study was to describe the landscape of genomic alterations in patients (pts) with BCBMs. Methods: Targeted next-generation DNA sequencing of > 300 cancer-related genes (OncoPanel) was prospectively performed on primary and metastatic (met) tumors in 321 pts with a diagnosis of BCBM between August 2016 and April 2019 at Dana-Farber Cancer Institute (table). Enrichment analysis of genomic alterations was performed using a two-sided Fisher exact test and differences in tumor mutation burden (TMB) between groups were assessed using two-sided Mann-Whitney U test. Multiple comparison correction was performed using the Benjamini-Hochberg procedure. Results: All subtypes were represented in BCBM (25 HR+/HER2-; 24 HR+/HER2+; 27 HR-/HER2+; 18 TNBC; 5 unknown; n = 99) and extracranial (EC) samples: (96 HR+/HER2-; 32 HR+/HER2+; 22 HR-/HER2+; 41 TNBC; 31 unknown; n = 222). BCBMs were found most commonly to have mutations or copy number alterations in TP53, ERBB2, PIK3CA, GATA3, PTEN, ESR1, CDH1, BRCA2, ARID1A, BRCA1 (>5% frequency, table). Two pts acquired ERBB2 amplification (amp) between the matched primary breast sample and brain met. In pair-wise comparisons of BCBMs to unmatched primaries or EC mets, only ERBB2 amp was significantly enriched (table, † = adjusted p < 0.05). There was no significant difference in TMB between BCBM and EC mets (median 9.12 vs 7.26, p = 0.15). In contrast, TMB was significantly higher in BCBMs compared to unmatched primaries (median 9.12 vs 7.26, p=0.005). Conclusions: BCBMs display similar mutations and copy number alterations compared to primary tumors and EC mets in pts with BCBM. These data suggest that BCBMs contain actionable genomic alterations that are most often also reflected in EC disease. Alterations in ERBB2, PIK3CA/PTEN, and BRCA1/2 represent potentially targetable alterations in pts with BCBM. [Table: see text]

Comprehensive molecular profiling of intrahepatic cholangiocarcinoms in Chinese population and therapeutic experience.

e16663 Background: The genomic alterations of intrahepatic cholangiocarcinoma in Chinese population have not been fully revealed. Molecular profiling may provide reference to clinical management especially targeted therapy. Methods: A prospective study was conducted in 122 intrahepatic cholangiocarcinoma patients accepted chemotherapy with or without targeted therapy. All patients had results of next generation sequencing assay that analyzes 489 cancer-associated genes. Results: The most commonly mutated genes were TP53 (34%), KRAS (25%), ARID1A (17%), CDKN2A (12%), FAT1 (12%), and NOTCH3 (12%). ERBB2 alterations were found in 13 (11%) patients, 10 of 13 were gene amplification. Application of Trastuzumab achieved a disease control rate of 7/8 and response rate of 6/8. Twenty-two patients with wild type KRAS/NRAS/BRAF accepted Cetuximab combined chemotherapy. Disease control rate and response rate were 78% and 47% respectively. Fifty-four patients accepted anti-VEGF treatment combined chemotherapy. Disease control rate and response rate were 85% and 60% respectively. Better therapeutic efficiency (P = 0.001) and longer progress free survival (P = 0.04) were observed in Bevacizumab treated group than chemotherapy alone. Two patients (1.6%) had signatures of microsatellite instability (MSI-H), and both benefited from immunotherapy. Conclusions: This study provides an over view on genetic alterations in Chinese intrahepatic cholangiocarcinoma patients, and indicates the potential clinical implications for targeted therapies.

ERBB2 amplifications and mutations in 109 advanced breast cancer patients by next-generation sequencing.

3565 Background: In advanced breast cancer (ABC) HER2 status is based on ASCO/CAP immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) criteria. Next generation sequencing (NGS) of tissue and blood can detect aberrations in ERBB2 such as copy number gain/amplifications (cng/amp) and mutations. Methods: We retrospectively identified patients (pts) seen at Northwestern University between 2015 and 2019 with ABC and an alteration in ERBB2 identified by tissue and/or circulating tumor DNA (ctDNA) NGS. We included pts with testing by Guardant360, TempusX, and/or FoundationOne platforms. NGS reports were evaluated for non-synonymous mutations and cng/amp. HR and HER2 status were determined based on the most recent pathologic assessment. Mutations were categorized as pathologic if they were consider oncogenic (level 1-2 evidence with direct functional data), likely oncogenic, or predicted oncogenic, based on OncoKB (Chakravarty et al., JCO PO 2017). Results: 109 cases of ABC (6 locally advanced, 103 metastatic) with ERBB2 alterations were identified. Tissue NGS was available from 43%, ctDNA from 72%, and both from 19%. The positive predictive value (PPV) of ERBB2 amp/cng by tissue NGS to predict HER2+ using the gold standard as IHC/FISH was 94% (33/35). The PPV of ERBB2 amp by ctDNA was 93% (40/43). ERBB2 mutations were detected in 52 pts. Of these, 23 pts were considered to harbor pathologic ERBB2 mutations, (19 oncogenic, 2 likely oncogenic, 1 predicted oncogenic) detected by ctDNA and tissue in 4, ctDNA in 16, and tissue in 3 pts. The most frequently detected mutations were V777L and S310. Four pts had co-mutations of ERBB2 V777L and S310F. Disease subtype among those with ERBB2 pathologic mutations was HR+ HER2- in 57%, HER2+ in 26%, and triple negative in 17%. In all patients with serial ctDNA analysis and pathologic ERBB2 mutations, the mutation was detected on the first analysis. Pathologic ERBB2 mutation represented the mutant with the highest mutant allele frequency (MAF) in 30% and top 3 highest MAF in an additional 35%. PIK3CA was co-mutated in 48%. Conclusions: The PPV of ERBB2 amp/cng by tissue and ctDNA NGS was high, and has potential utility for cancers where HER2 IHC/FISH is not standardly assessed or cases where biopsy is challenging. ERBB2 pathologic mutations were found in all breast cancer subtypes. When present, they were identified on the initial ctDNA analysis and often represented a significant clone, supporting its role as a ‘driver mutation’.

Gastric-type adenocarcinoma of the cervix: Genomic drivers and clinical outcomes.

6030 Background: Cervical Gastric-type adenocarcinoma (CGA) is a non-HPV-associated adenocarcinoma, comprising 10% of all cervical adenocarcinomas (Park et al, 2019). The optimal management approach is unclear, given that most data in advanced cervical cancer is driven by HPV-positive disease. We summarize our experience with this rare tumor type at a large cancer center. Methods: A retrospective review was performed for all women diagnosed with CGA 6/1/2002- 7/1/2019. Patients who did not follow up after a single visit were excluded. Kaplan-Meier survival analysis was performed to determine progression-free survival (PFS) and overall survival (OS) from date of diagnosis. Tumors from a subset of patients were subjected to MSK-IMPACT targeted sequencing and analysis (Zehir et al, 2017). Results: A total of 68 women were identified; 47 met inclusion criteria. The median age at diagnosis was 52 years (range 27-83). The majority of patients were white (70%), an additional 19% were Asian. The majority of patients (60%, n=28) presented with advanced disease (FIGO 2018, stage II-IV), while 40% (n=19) were Stage I. Of note, 26% (n=12) had positive pelvic lymph nodes and 13% (n=6) had ovarian metastases at time of surgical resection. For upfront treatment: 13% (n=6) had surgery alone of whom 83% had stage 1 disease, 36% (n=17) had surgery followed by adjuvant therapy, 30% (n =14) received definitive chemo-radiation (CRT). All patients with stage IV disease 15% (n=7) received chemotherapy alone. At completion of primary treatment, 19% (n=9) of patients had persistent disease. In patients who received CCRT, 65% (n=22) recurred, the majority (64%) within 12 months of completion of upfront therapy. Pelvic recurrence was the most common site (n=14, 64%). With a median follow up time of 30 months (range 1-159), the median PFS for Stage I was 34.4 months, compared to 17.5 months in patients with Stage II-IV disease (p= 0.29). Of the 24 patients that had MSK-IMPACT, the most common mutation was TP53 (n=16, 64%) followed by mutations in the RAS pathway (n=8, 33%), PIK3CA (n=3, 12.5%), STK11 (n=3, 12.5%), and ERBB2 alterations (n=2, 8.3 %). 2 (8.3%) women enrolled on a clinical trial based on their NGS results, one targeting ERBB2 and one targeting PIK3CA. Conclusions: Consistent with prior published literature, CGA is an aggressive form of cervical cancer with poor median OS in the advanced setting. With universal HPV vaccination, HPV negative cervical cancer will represent a larger percentage of newly diagnosed cancers and further research is needed to identify the optimal management approach.

Exon-16-skipping ERBB2 (ERBB2ΔEx16) as a novel resistance mechanism against EGFR tyrosine kinase inhibitors in non-small cell lung cancer (NSCLC).

9528 Background: In addition to ERBB2 amplification/protein overexpression, activating ERBB2 alterations have been increasingly discovered in diverse human cancers with varying incidence. ERBB2ΔEx16 is an alternatively spliced isoform of ERBB2, lacking the entire exon 16 which encodes a small extracellular domain. ERBB2ΔEx16 was recently reported to lead to oncogenic activation of ERBB2 and osimertinib resistance in EGFR T790M+ non-small cell lung cancer (NSCLC). Methods: A total of 38,680 Chinese cancer patients whose tumor specimen or circulating cell-free DNA underwent genomic profiling by targeted next-generation sequencing of cancer-related genes were retrospectively reviewed. Clinicopathological features and treatment history of ERBB2ΔEx16+ patients were evaluated. RNA sequencing was performed to validate the presence of exon-16-skipping ERBB2 at the transcriptional level. Results: A total of eighteen ERBB2ΔEx16+ patients (11 NSCLC, 2 colorectal cancer, 2 gastric cancer, and 3 others) were identified (0.047%, 18/38,680). ERBB2 exon 16 skipping may result from large fragment deletion spanning the whole or partial region of exon 16 (72.2%, 13/18), base substitution at the splice acceptor site (16.7%, 3/18) and deletion of the splice donor site (11.1%, 2/18). ERBB2 exon 16 skipping, including large fragment deletion and splice site deletion, was validated at the RNA level by RNA sequencing in 3 patients with available samples. Co-occurrence of ERBB2 amplification and ERBB2 mutations were found in 83.3% (15/18) and 50% (9/18) of cases, respectively. Concurrent copy number variations were prevalent in CDK12 (55.6%, 10/18), CDKN2B (44.4%, 8/18), NKX2.1 (38.9%, 7/18) and PTPRD (33.3%, 6/18). Among the 11 cases of ERBB2ΔEx16+ NSCLC, 9 had coexisting activating EGFR mutations (exon 19 deletions, exon 21 L858R) and received prior treatment with EGFR tyrosine kinase inhibitors (TKIs), with 2 harboring acquired EGFR T790M mutation and 1 EGFR copy number gain. Further analysis of the matched pretreatment samples in 3 EGFR-mutated NSCLC patients confirmed that ERBB2ΔEx16 was acquired during EGFR TKI therapy. In the 7 cases of other cancers, 4 to 31 non- ERBB2 mutations were identified in each sample, with TP53 being the most frequently mutated gene. Conclusions: Our data suggest that ERBB2ΔEx16 may be a general mechanism of EGFR TKI resistance in a subset of EGFR-mutated NSCLC patients, in addition to being an oncogenic driver as reported in some solid malignancies including colorectal, gastric and ovarian cancers.

Urothelial cancer harbours EGFR and HER2 amplifications and exon 20 insertions.

To review the genomic landscape of advanced urothelial carcinoma (UC) to assess the frequencies of EGFR and ERBB2 (HER2) alterations. Tumour specimens from 3753 patients with advanced UC were assayed with hybrid capture-based comprehensive genomic profiling of 180-395 genes. Tumour mutational burden (TMB) was assessed on 0.8 or 1.1Mb of DNA, and is reported as mutations per megabase. In 3753 cases of UC, EGFR alterations were detected in 4.1% (154) and were most commonly amplifications (64%; 99/154), while exon 20 insertions (EGFRexon20ins ) were the second most common alteration (18%; 27/154). Alterations in ERBB2 were observed in 15% (552/3753) of cases and, similarly, ERBB2 amplification was the most commonly observed alteration (278/552; 50%); ERBB2exon20ins occurred in 3.6% (20/552) of cases. EGFRexon20ins and ERBB2exon20ins occurred in younger patients (median age 62 vs 69years, P = 2.6E-2 and 60 vs 68years, P = 7.8E-4), and these cases had significantly lower TMB (median 3.6 vs 7.2, P = 2.7E-4 and 2.5 vs 10, P = 1.2E-7) and less frequent TP53 alterations (3.7% vs 83%, P = 4.3E-14 and 20% vs 68%, P = 9.8E-4) compared to cases with other EGFR or ERBB2 alterations. EGFR and ERBB2 alterations occur in 4% and 15% of UC, respectively. EGFRexon20ins and ERBB2exon20ins were present in 0.7% and 0.5% of UC overall and collectively define a small, but distinct, subset of UC with infrequent co-occurrence of other drivers and low TMB. Given recent promising clinical studies of inhibitors with activity against exon 20 insertions in non-small cell lung cancer, consideration should be given to developing a trial inclusive of patients with UC harbouring these alterations.

Abstract P4-05-10: Comparative analysis of genomic landscape reveals heterogeneity in HER2-positive primary breast cancers and residual disease following neoadjuvant therapy

Abstract Background: Neoadjuvant therapy is currently standard of care for patients with HER2-positive (HER2+) breast cancer. Patients with residual disease after neoadjuvant therapy have a higher risk of metastatic recurrence compared to patients achieving pathologic complete response (pCR). While both primary breast cancer and residual disease may harbor cancer cell subpopulations with high metastatic potential, residual disease after neoadjuvant targeted therapy may include larger subpopulations of therapy-resistant cells. A better understanding of the differences in genomic aberrations in residual disease following neoadjuvant therapy in comparison to primary breast cancer is essential to choice of novel post-neoadjuvant treatment strategy for HER2+ patients with residual disease. Methods: We are currently building a large ethnically diverse, breast cancer cohort with integrated genomic data. We analyzed clinical data of stage 1-3, HER2+ breast cancer. pCR after neoadjuvant therapy was defined as ypT0N0 or ypTisNo. Using the xT 595-gene panel (Tempus Labs, Inc.) with matched tumor-normal samples in a subset of the cohort, we evaluated genomic heterogeneity between HER2+ primary breast cancers and residual disease following neoadjuvant therapy. Results: There were 469 HER2+ early stage invasive breast cancer patients in the study cohort with a median follow-up of 6.0 years. The mean age at diagnosis was 53.6 (SD=13.4) years. 52.7% are European Americans and 39.2% are African Americans. 61.8% were hormone receptor-positive (HR+)/HER2+ and 37.7% were HR-/HER2+. Although patients undergoing neoadjuvant chemotherapy (n=191) had lager tumor and more nodal positive disease compared to patients undergoing adjuvant therapy (n=213), the two groups have similar recurrence-free survival rate (adjusted hazard ratio 0.88, 95% CI 0.50-1.55). In patients undergoing neoadjuvant therapy, 72 (37.7%) achieved pCR. Women with HR-/HER2+ tumors had higher pCR rate (58.9%), compared with 24.6% in women with HR+/HER2+ tumors (p<0.001). pCR was a very strong predictor for recurrence: the 5-year recurrence-free survival was 0.97 for patients with pCR in contrast to 0.75 for patients without pCR. Of the 38 patients whose tumor DNAs were sequenced to date, there were 23 primary tumors and 15 residual tumors. Compared to primary HER2+ tumors, residual tumors had lower frequency of somatic alterations in ERBB2 (33% vs. 74%, p=0.02), CDK12 (13% vs. 48%, p=0.039), and ATM (0% vs. 26%, p=0.063) compared to the primary tumors. The overall tumor mutational burden was 2.1 m/MB (range: 0.4-42.5) in primary tumors and 2.9 m/MB (0-12.5) in residual tumors (p=0.94). Median ERBB2 copy number is 10 (range: 2-20) in primary tumors and 3 (2-20) in residual tumors. Alterations in the CDK4 pathway (CDK4, CCND1, CDKN2A, and RB1) were more frequently detected among tumors with loss of ERBB2 amplification (50%) than tumors with ERBB2 amplification (10%, p=0.011), suggesting they may be mutually exclusive. In particular, 4 of the residual tumors had mutations in the CDK4 pathway and none co-occurred with ERBB2 amplification. Conclusions: These preliminary data support the importance of integrating genomic sequencing of residual tumors to identify potentially non-HER2 druggable targets as a post-neoadjuvant treatment strategy. Alternative approaches including addition of novel therapies such as CDK4 inhibitors may have the potential to reduce costs associated with extended use of HER2-targeted therapies when unlikely to improve overall survival for non-HER2 amplified tumors. Citation Format: Masaya Hattori, Dezheng Huo, Nike Beaubier, Padma Sheila Rajagopal, Toshio Yoshimatsu, Yonglan Zheng, Elisabeth Sveen, Galina Khramtsova, Fang Liu, Taylor Abboushi, Kevin White, Olufunmilayo Olopade. Comparative analysis of genomic landscape reveals heterogeneity in HER2-positive primary breast cancers and residual disease following neoadjuvant therapy [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-05-10.

Abstract P6-10-08: AKT1 alterations following exposure to endocrine-based therapy in patients with hormone-receptor positive (HR+) metastatic breast cancer (MBC): Clinical and functional implications

Abstract Background: The AKT1 oncogene represents a central node in the well-characterized PI3K/AKT/mTOR signal transduction pathway involved in the regulation of cellular proliferation as well as therapeutic resistance. With the emergence of multiple targeted therapies for HR+ MBC, we sought to explore the prevalence of AKT1 alterations, the spectrum of co-occurring mutations, and any potential impact on response to endocrine-based therapy, including CDK 4/6 and PIK3CA inhibitors. Methods: Presence or absence of AKT1 mutation was interrogated via cell-free DNA (cfDNA) analysis (Guardant assay) among patients with HR+/HER2- MBC receiving treatment at the Massachusetts General Hospital who underwent routine clinical cfDNA testing. Genomic sequencing results were then compared to detailed clinical annotation based upon retrospective chart review. In the laboratory, HR+/HER2- T47D breast cancer cells were transfected with AKT1, under the control of a doxycycline-inducible promoter, to induce AKT1 overexpression. Sensitivity to escalating doses of fulvestrant and palbociclib were interrogated via cell-titer-glo viability assay in vitro. Results: Among 272 patients with HR+/HER2- MBC, we identified 13 patients with AKT1 mutation (4.7%). 12/13 (92%) patients had a canonical AKT1E17K alteration, one patient (8%) had an AKT1 E49K alteration. AKT1 mutations occurred concurrently with alterations in ESR1 (31%), PIK3CA (23%), TP53 (23%), ERBB2 (15%), and RB1 (8%). All patients had been exposed to some form of anti-estrogen prior to sequencing, either via (neo)adjuvant therapy and/or in the metastatic setting; 5/13 (38%) had exposure to a CDK4/6 inhibitor prior to cfDNA sequencing. Following the identification of an AKT1 alteration, examples of rapid clinical progression on fulvestrant, CDK4/6i, and/or everolimus were identified, however the presence of an AKT1 alteration was not sufficient to predict pan-resistance to these agents, as counter-examples of clinical benefit were also identified. In an index patient with an AKT1 mutation and prior progression on letrozole and palbociclib, subsequent treatment with fulvestrant and abemaciclib did not yield clinical benefit, highlighting the potential role of AKT1 in mediating clinical resistance to endocrine therapy and CDK4/6i. In the pre-clinical model, HR+/HER2- breast cancer cells demonstrated resistance to both fulvestrant and palbociclib following upregulation of exogenous AKT1 expression. Updated clinical data with additional patients and response to regimens incorporating an anti-estrogen, a CDK4/6 inhibitor, an mTOR inhibitor, and/or a PIK3CA inhibitor will be presented at the meeting. Conclusions: Activating AKT1 mutations can be identified via targeted sequencing of cfDNA in patients with HR+/HER2- MBC, and may play an important role in mediating resistance to anti-estrogens, CDK4/6 inhibitors, and other emerging targeted therapies. Heterogeneity in response to endocrine-based therapy following the identification of an AKT1 alteration may be related to tumor-extrinsic factors, the AKT1 allelic fraction, or cooperativity between multiple resistance drivers. Further research is needed to confirm these findings and guide optimal therapeutic sequencing strategies for patients with HR+/HER2- AKT1 mutant MBC. Citation Format: Seth Wander, Pingping Mao, Maxwell Lloyd, Kailey Kowalski, Gabriela N. Johnson, Giuliana Malvarosa, Beverly Moy, Leif W. Ellisen, John Iafrate, Nikhil Wagle, Aditya Bardia. AKT1 alterations following exposure to endocrine-based therapy in patients with hormone-receptor positive (HR+) metastatic breast cancer (MBC): Clinical and functional implications [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-10-08.

Genomic profiling of pleomorphic and florid lobular carcinoma in situ reveals highly recurrent ERBB2 and ERRB3 alterations.

Pleomorphic LCIS (P-LCIS) and florid LCIS (F-LCIS) are morphologic variants distinguished from classic LCIS by marked nuclear pleomorphism and/or an expansile growth pattern with or without necrosis. Given the rarity of these LCIS variants, little data exist regarding their molecular pathogenesis, natural history, and optimal management. The purpose of this study was to genomically profile LCIS variants to gain further insight into their biology. Nineteen cases of pure LCIS variants (17 P-LCIS, 2 F-LCIS) diagnosed on core needle biopsy at our institution from 2006 to 2017 were included, five of which were upgraded to invasive cancer at excision. Macrodissected lesions were analyzed by a hybrid-capture next generation sequencing assay that surveyed exonic sequences of 447 genes for mutations and copy number variations (CNVs) and 191 regions across 60 genes for structural rearrangements. LCIS variants were all confirmed as E-cadherin negative by immunohistochemistry. Receptor profiles among the 17 P-LCIS cases included HR+/HER2- (nine cases), HR+/HER2+ (three cases), HR-/HER2+ (two cases), and HR-/HER2- (three cases). The two F-LCIS cases were HR+/HER2- and HR+/HER2+. All LCIS variants had genetic alterations consistent with a lobular phenotype including 1q gain (16 cases), 16q loss (18 cases), and CDH1 mutations (18 cases). Highly recurrent ERBB2 alterations were noted including mutations (13 cases) and amplifications (six cases). Other significant alterations included mutations in PIK3CA (six cases), RUNX1 (four cases), ERBB3 (four cases), and CBFB (three cases), as well as amplification of CCND1 (five cases). A TP53 mutation was identified in one case of HR-/HER2+ P-LCIS with signet ring cell features that lacked 1q gain and 16q loss. P-LCIS and F-LCIS contain genetic alterations characteristic of lobular neoplasia; however, these LCIS variants are distinguished from classical LCIS reported in the literature by their highly recurrent ERBB2 alterations.

Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis

Background: We have reported that BRAF V600E mutations and microsatellite instability-high (MSI-H) are more prevalent in a population-based cohort of metastatic colorectal cancer (mCRC) patients than has been reported from clinical trials or hospital-based patient groups. The aim was to explore if other mutations in mCRC differ in prevalence between these cohorts in relation to mismatch repair status and primary tumor location and if presence of bone or brain metastases is associated with any mutations.Material and methods: A population-based cohort of 798 mCRC patients from three regions in Scandinavia was used. Forty-four cancer related genes were investigated in a custom designed Ampliseq hotspot panel. Differences in survival were analyzed using the Kaplan–Meier estimator and the Cox regression analysis.Results: Determination of mutations was possible in 449/501 patients for 40/44 genes. Besides BRAF V600E, seen in 19% of the tumors, none of the other mutations appeared more prevalent than in trial cohorts. BRAF V600E and MSI-H, seen in 8%, were associated with poor prognosis as was right-sided primary tumor location (39%) when compared to left-sided and rectum together; however, in a multivariable regression, only the BRAF mutation retained its statistical significance. No other mutations were associated with poor prognosis. ERBB2 alterations were more common if bone metastases were present at diagnosis (17% vs. 4%, p = .011). No association was found for brain metastases. Fifty-two percent had an alteration that is treatable with an FDA-approved targeted therapy, chiefly by EGFR-inhibitor for RAS wild-type and a check-point inhibitor for MSI-H tumors.Conclusions: Right-sided tumor location, BRAF V600E mutations, but no other investigated mutation, and MSI-H are more commonly seen in an unselected cohort than is reported from clinical patient cohorts, likely because they indicate poor prognosis. Half of the patients have a tumor that is treatable with an already FDA-approved targeted drug for mCRC.

Genomic Characterization of ERBB2-Driven Biliary Cancer and a Case of Response to Ado-Trastuzumab Emtansine.

Biliary tract cancers (BTCs), which include intrahepatic cholangiocarcinoma (ICC), extrahepatic cholangiocarcinoma (EHC), and gallbladder cancer (GBC), have limited treatment options. We sought to comprehensively examine the clinical and molecular characteristics of BTCs with amplification or mutation of ERBB2. Demographic, outcome, and treatment response data were collected for patients with ERBB2-altered BTC identified by next-generation sequencing with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets from 2014 to 2018. A total of 517 patients with BTC underwent next-generation sequencing (ICC, n = 313; EHC, n = 93; GBC, n = 111). Twenty-eight patients (5.4%) had ERBB2 alterations, including 2.7% with ERBB2 gene amplification, 2.3% with ERBB2 mutation, and 0.4% with concurrent amplification and mutation. The prevalence of ERBB2 gene alterations was significantly higher in GBC (12.6%) than in ICC (2.2%) and EHC (7.5%; P < .001). In ERBB2-amplified tumors, the median fold change was 6.4 (range, 2.1 to 19.7), while in ERBB2-mutant tumors, the most frequent mutated domain was the extracellular domain (32%), with all mutations in this region involving the S310 codon. Frequent co-altered genes in this cohort were TP53 (54%), PIK3CA (21%), and CDKN2A (18%); KRAS amplification/mutation was found in 7% of patients. One patient with ERBB2-amplified EHC who enrolled in a basket trial (ClinicalTrials.gov identifier: NCT02675829) had a partial response to the human epidermal growth factor receptor 2-targeted antibody-drug conjugate ado-trastuzumab emtansine. ERBB2 alterations are present in 5.4% of BTCs. When present, the degree of ERBB2 gene amplification is often high, and S310 codon mutations are the most common hotspot. These features, along with the presented case, support further development of human epidermal growth factor receptor 2-targeted therapy in ERBB2-mutant and/or -amplified BTC.

Molecular Profiling of Hepatocellular Carcinoma Using Circulating Cell-Free DNA.

Molecular profiling has been used to select patients for targeted therapy and determine prognosis. Noninvasive strategies are critical to hepatocellular carcinoma (HCC) given the challenge of obtaining liver tissue biopsies. We analyzed blood samples from 206 patients with HCC using comprehensive genomic testing (Guardant Health) of circulating tumor DNA (ctDNA). A total of 153/206 (74.3%) were men; median age, 62 years (range, 18-91 years). A total of 181/206 patients had ≥1 alteration. The total number of alterations was 680 (nonunique); median number of alterations/patient was three (range, 1-13); median mutant allele frequency (% cfDNA), 0.49% (range, 0.06%-55.03%). TP53 was the common altered gene [>120 alterations (non-unique)] followed by EGFR, MET, ARID1A, MYC, NF1, BRAF, and ERBB2 [20-38 alterations (nonunique)/gene]. Of the patients with alterations, 56.9% (103/181) had ≥1 actionable alterations, most commonly in MYC, EGFR, ERBB2, BRAF, CCNE1, MET, PIK3CA, ARID1A, CDK6, and KRAS. In these genes, amplifications occurred more frequently than mutations. Hepatitis B (HBV)-positive patients were more likely to have ERBB2 alterations, 35.7% (5/14) versus 8.8% HBV-negative (P = 0.04). This study represents the first large-scale analysis of blood-derived ctDNA in HCC in United States. The genomic distinction based on HCC risk factors and the high percentage of potentially actionable genomic alterations suggests potential clinical utility for this technology.

718P - Comprehensive genomic profiling (CGP) of gall bladder adenocarcinoma (GBAC) in patients from distinct ancestral populations

BackgroundGBAC is an aggressive neoplasm with an abysmal 5-year survival rate and no approved targeted therapies. Incidence of GBAC varies greatly across global geographical regions, with highest reported rates in South and East Asia. We evaluated whether GBAC patients have differential genomic profiles as correlated to ancestry. MethodsCGP was performed by an adaptor-ligation/hybrid capture-based assay of coding DNA of 315 cancer-related genes and select introns of 28 genes that are frequently involved in genomic rearrangements to detect base substitutions, insertions and deletions, copy number alterations, and rearrangements. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was assessed across 114 homopolymeric loci. Patient ancestry was determined by single nucleotide polymorphism microarray data, ancestry informative markers, and principal component analysis. ResultsThe genomic profiles of tumour samples from 881 patients with GBAC were reviewed. Of these samples, 22 (2.50%) were derived from individuals of South Asian ancestry (SAS), 61 (6.92%) from East Asian (EAS) ancestry and the remainder were distributed among African, American, and European ancestry (Others). Age and gender were similar across all three groups, except for an enrichment in SAS male patients (SAS male 68.2%, EAS male 32.7%, Others male 31.2%; p=0.001). MSI was uncommon in all three groups (0.007% overall) and TMB was low (median 2.6 mut/mb). The most commonly altered genes across all three groups were TP53, CDKN2A/B and SMAD4 (all: 64%, 53%, 17%) while alterations in ERBB2 (23% v 30% v 14%, p=0.03) and CTNNB1 (14% v 11% v 3%, p=0.001) were enriched in SAS and EAS populations. Amongst ERBB2 altered cases, amplifications were seen at similar frequencies across all three groups (80% v 72% v 72%), while less than half of all ERBB2 point mutations occurred at the S310 codon (18/67, 27%). ConclusionsGBAC patients of SAS and EAS ancestry were enriched for ERBB2 and CTNBB1 relative to other ancestries. Follow-up studies are needed to understand the genomic context of this finding, as well as the influence of cancer predisposition genes in the context of ancestry specific oncogenesis. Legal entity responsible for the studyFoundation Medicine Inc. FundingFoundation Medicine Inc. DisclosureM. Javle: Research grant / Funding (self): QED Therapeutics; Honoraria (self): Merck & Co; Advisory / Consultancy: EDO Pharma; Advisory / Consultancy: More Health; Honoraria (self): Taiho Pharmaceutical; Honoraria (self): Seattle Genetics; Research grant / Funding (self): Meclun; Research grant / Funding (institution): Arqule; Research grant / Funding (institution): Lilly; Advisory / Consultancy: Origimed; Research grant / Funding (self): Novartis. S. Akumalla: Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. R. Madison: Full / Part-time employment: Foundation Medicine; Shareholder / Stockholder / Stock options: Roche. J. Newburg: Shareholder / Stockholder / Stock options: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche. B.M. Alexander: Leadership role, Full / Part-time employment, Officer / Board of Directors: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche; Advisory / Consultancy, Personal Fees: AbbVie; Advisory / Consultancy, Personal Fees: Schlesinger Associates; Advisory / Consultancy, Personal Fees: Bristol-Myers Squibb; Advisory / Consultancy, Personal Fees: Precision Health Economics; Research grant / Funding (self), grants outside submitted work: Puma Biotechnology; Research grant / Funding (self), grants outside submitted work: Celgene; Research grant / Funding (self), grants outside submitted work: Eli Lily. J. Chung: Full / Part-time employment: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche. V.A. Miller: Full / Part-time employment: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche; Advisory / Consultancy, Scientific Advisory Board: Revolution Medicines. J. Lee: Full / Part-time employment: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche. J.S. Ross: Leadership role, Full / Part-time employment: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche; Officer / Board of Directors: Celcius Therapeutics. A.B. Schrock: Full / Part-time employment: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche. G.M. Frampton: Full / Part-time employment: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche. S.M. Ali: Full / Part-time employment: Foundation Medicine Inc; Shareholder / Stockholder / Stock options: Roche; Advisory / Consultancy, Scientific Advisory Board: Incysus Therapeutics, Inc.; Advisory / Consultancy: Revolution Medicines. All other authors have declared no conflicts of interest.

1888P - Next-generation sequencing for better treatment strategy of cancer of unknown primary (CUP)

BackgroundCancer of unknown primary (CUP) consists of diverse histology types of cancer and have shown poor prognosis. In the era of precision medicine, next-generation sequencing (NGS) may contribute new therapeutic target which could improve treatment outcomes of CUP. MethodsPatients who were diagnosed with CUP and underwent NGS exam between August 2017 and August 2018 at Samsung medical center were included for the study. NGS data were analyzed, and medical records were reviewed retrospectively to evaluate clinical characteristics and response to various treatments. ResultsA total of 21 patients with CUP who had NGS data were analyzed. The median age was 58 (range, 35-78 years). Male was dominant (57.1%) and most of the patients were ECOG 1 (90.5%). Among the patients, 14 (66.7%) were poorly differentiated carcinoma, 6 (28.6%) patients were adenocarcinoma, and one patient was squamous cell carcinoma. Most common metastatic site was lymph node (57.1%), followed by bone (38.1%), lung (19.0%), pleura (19.0%). Paclitaxel combined with carboplatin was most frequently used regimen for the first-line treatment (57.1%). Cisplatin-based chemotherapy was used second most (28.6%). One patient showed complete remission during the first-line treatment whereas 7 patients and 5 patients achieved the best response of partial response and stable disease, respectively. Median progression-free survival was 4 months (95% CI: 0.316-7.684), and median overall survival was not reached. Except four patients, 17 (81.0%) patients showed 25 gene alterations on the NGS results. TP53 mutation was observed most commonly (n=6, 25.6%), followed by ERBB2 alterations (n=3, mutations [n=2], amplification [n=1]), KRAS mutation (n=2), MET amplification (n=2), CDKN2A deletion (n=2), and MYC amplification (n=2). One patient harbored ERBB2 amplification was treated with trastuzumab combined with paclitaxel, and the patient demonstrated sustained partial response at 9 months, until the data cut-off date. ConclusionsMost of CUP patients had variety actionable gene alterations. Precision medicine based on molecular analysis with NGS will improve the prognosis of the patients with CUP. Legal entity responsible for the studyThe authors. FundingHas not received any funding. DisclosureAll authors have declared no conflicts of interest.

BSCI-12. COMPREHENSIVE GENOMIC ANALYSIS OF BRAIN METASTASES FROM MULTIPLE CANCER TYPES

PURPOSE: Brain metastases occur in approximately 8–10% of patients with cancer, and the incidence has increased over the past decades. The most common primary tumors responsible for brain metastases are lung cancer, melanoma, renal cell carcinoma (RCC), breast cancer and colorectal cancer. The precise mechanisms by which genomic and transcriptional abnormalities drive the formation of brain metastases remain unclear. Here, we conducted comprehensive genomic and transcriptional analysis with paired primary tumor tissue (or extracranial metastasis tissue) and brain metastasis tissue using whole-exome sequencing (WES), mRNA-Seq and global methylation profiling. METHODS: Frozen, paired brain metastasis tissue and primary tumor tissue (or extracranial metastasis tissue) and white blood cells were acquired from RCC (n=12), breast cancer (n=17), lung cancer (n=15) and melanoma (n=14) patients, followed by extraction of DNA and RNA. WES and mRNA-Seq were performed on the Illumina HiSeq4000 platform. For methylation profiling, DNA was analyzed using Illumina Infinium MethylationEPIC Beadchip arrays. RESULTS: Somatic mutations or methylation of VHL gene were identified in 81.8% of RCC patients. Gene Set Enrichment Analysis revealed significant enrichment for hypoxia pathway transcripts in RCC brain metastases relative to primary tumors. The most common alterations in breast and lung cancer patients were TP53 mutations with frequencies of 50.0% and 73.3%, followed by ERBB2 alterations (43.8%) in breast cancer patients and mutually exclusive alterations of EGFR (33.3%) and KRAS (26.7%) in lung cancer patients. Mutually exclusive alterations of NRAS (42.9%) and BRAF (42.9%) were also observed in melanoma patients. Gene expression and epigenetic analysis revealed characteristics of brain metastases depending on primary cancer types. CONCLUSIONS: Comprehensive genomic analysis of brain metastases from four different cancer types revealed that brain metastasis tissues have unique genomic, transcriptional and epigenetic profiles according to histopathology groups. Therefore, the therapeutic strategies should be designed based at least in part on tumor histiogenesis.

Abstract 1026: Oncogenic alterations in FGFR3 and ERBB2 lead to ligand-independent activation of PPARG in bladder cancer

Abstract PPARG is genomically activated in muscle-invasive bladder cancer through focal PPARG gene amplification and hotspot mutations in its heterodimer partner, RXRA. However, more than half of the PPARG-activated bladder tumors and cell lines do not have identifiable somatic alterations in either PPARG or RXRA. Using a PPARG-driven reporter assay in RT112 bladder cancer cell line, we screened probe compounds to identify candidate drivers of ligand-independent PPARG activation. We found that pan-FGFR inhibitors and MEK1/2 inhibitors antagonized the PPARG-driven reporter assay with potency similar to reported values for their cognate targets (1-20 nM) and interestingly, RT112 cells carry an FGFR3-TACC3 oncogenic fusion. In addition to the expected effects of these inhibitors on phospho-MEK1/2 and phospho-ERK1/2, they also inhibited production of canonical PPARG targets, including FABP4. In a second subset of cell lines, a parallel story was also observed for the effects of ERBB2 inhibitors in ERBB2 hotspot mutant bladder cancer. Taken together, these data uncover additional mechanisms for functional activation of PPARG in bladder cancer, suggest potential resistance mechanisms for FGFR and ERBB2 inhibitors, and provide a rationale for therapeutic combinations of PPARG modulators. Citation Format: Jonathan T. Goldstein, Ashton C. Berger, Craig A. Strathdee, Matthew Meyerson. Oncogenic alterations in FGFR3 and ERBB2 lead to ligand-independent activation of PPARG in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1026.

Abstract 929: Paired tumor and cfDNA in patients with HER2-mutant solid tumors treated with neratinib reveals convergence of multiple on-target resistance mechanisms: Results from the SUMMIT "Basket" Trial

Abstract Background: Somatic mutations in ERBB2 occur across various tumor types at relatively low frequencies and can lead to constitutive kinase signaling and oncogenic transformation. SUMMIT is an ongoing basket trial of neratinib, an irreversible pan-HER tyrosine kinase inhibitor, in pts with ERBB2 mutant cancers (NCT01953926). Methods: Pts with advanced solid tumors and locally documented ERBB2 mutations received neratinib 240 mg daily (N=8) +/- fulvestrant at the labeled dose for pts with ER+ breast cancer (N=6) as part of the global Phase II SUMMIT basket study. Pre- and post-treatment tumor and cfDNA were subjected to NGS using MSK-IMPACT for tissue (410 genes) and MSK-ACCESS for plasma (129 genes) to identify SNVs, indels, and copy number alterations. Results: In total, 14 pts had successful sequencing of both paired tissue and cfDNA sample (10 breast, 2 gallbaldder, 1 bladder, and 1 unknown primary). All pts achieved clinical benefit on neratinib including 2 CRs, 7 PRs, and 5 SDs. In 1 gallbladder pt, paired tissue sequencing identified loss of the pretreatment clonal ERBB2 mutation but retention of a truncal TP53 mutation, suggesting emergence of a distantly related ERBB2 wildtype clone. In the remaining 13 patients, the pretreatment ERBB2 mutation was retained in tissue at progression. 64% (9/14) pts had at ≥1 acquired alteration in tissue including 3 pts who acquired secondary alterations in ERBB2, both clonal and subclonal ERBB2 mutations as well new focal amplifications. Consistent with this finding, plasma cfDNA sequencing revealed 57% (8/14) of pts acquired ≥1 secondary ERBB2 mutation with the majority occurring at known activating hotspots. Analysis of mutant allele frequencies of these emergent ERBB2 alterations, in comparison to other variants, suggested the majority were subclonal with evidence of multiple independent subclones arising in the same patient. Two pts developed known ERBB2 gatekeeper mutations (T798I and L785F). Conclusion: In pts with ERBB2-mutant solid tumors with clinical benefit on neratinib, a potential on-target resistance mechanism was identified in 71% (10/14, including 7 with acquired gain-of-function ERBB2 mutations, 2 with ERBB2 both gain-of-function and gatekeeper mutations, and 1 with outgrowth of an ERBB2 wildtype clone). Collectively, these data provide additional evidence that ERBB2 mutations lead to oncogene addiction in solid tumors. We also demonstrate that tumor and cfDNA sequencing provides complementary information that can be integrated to more fully elucidate potential resistance mechanisms. Citation Format: Helen H. Won, S. Duygu Selcuklu, Sarina A. Piha-Paul, Cristina Saura, Jordi Rodon, Ingrid A. Mayer, Sherene Loi, Geoffrey I. Shapiro, Janice Lu, Adam Brufsky, Catherine Zimel, Myra Melcer, Maurizio Scaltriti, Lisa D. Eli, Richard E. Cutler Jr., Alshad S. Lalani, Richard P. Bryce, Carlos Arteaga, Funda Meric-Bernstam, Michael F. Berger, David B. Solit, Alison Schram, David M. Hyman. Paired tumor and cfDNA in patients with HER2-mutant solid tumors treated with neratinib reveals convergence of multiple on-target resistance mechanisms: Results from the SUMMIT "Basket" Trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 929.

Abstract 3406: Comprehensive genomic analysis of brain metastases from multiple cancer types

Abstract Purpose: Brain metastases occur in approximately 8-10% of patients with cancer, and the incidence has increased over the past decades. The most common primary tumors responsible for brain metastases are lung cancer, melanoma, renal cell carcinoma (RCC), breast cancer and colorectal cancer, and the prognosis is still very poor with an overall 2-year survival rate of 8%. The precise mechanisms by which genomic and transcriptional abnormalities drive the formation of brain metastases remains unclear. Here, we conducted comprehensive genomic and transcriptional analysis with paired primary tumor tissue (or extracranial metastasis tissue) and brain metastasis tissue using whole-exome sequencing (WES), mRNA-Seq and global methylation profiling. Methods: All patient samples were collected at the University of Texas MD Anderson Cancer Center. Frozen, paired brain metastasis tissue and primary tumor tissue (or extracranial metastasis tissue) and white blood cells were acquired from RCC (n=12), breast cancer (n=17), lung cancer (n=15) and cutaneous melanoma (n=14) patients. DNA and RNA were extracted from regions of frozen tissue with at least 70% viable tumor cells and peripheral blood leukocytes. Libraries for WES and mRNA-Seq were prepared and sequenced on the Illumina HiSeq4000 platform. For methylation profiling, DNA was subjected to bisulfite conversion and analyzed using Illumina Infinium MethylationEPIC Beadchip arrays. Results: Genome-wide hypermutation due to POLE or POLD1 mutations was observed in one breast cancer patient and two lung cancer patients. Two of these cases acquired the hypermutation during development to brain metastasis. Somatic mutations or methylation of VHL gene were identified in 81.8% of RCC patients, and two patients had somatic VHL mutations in brain metastases only. Interestingly, Gene Set Enrichment Analysis revealed significant enrichment for hypoxia pathway transcripts in the RCC brain metastases relative to primary tumors. The most common alterations in breast and lung cancer patients were TP53 mutations with frequencies of 50.0% and 73.3%, followed by ERBB2 alterations (43.8%) in breast cancer patients and mutually exclusive alterations of EGFR (33.3%) and KRAS (26.7%) in lung cancer patients. Mutually exclusive alterations of NRAS (42.9%) and BRAF (42.9%) were also observed in melanoma patients. Gene expression and epigenetic analysis revealed characteristics of brain metastases depending on primary cancer types. Conclusions: Comprehensive genomic analysis of brain metastases from four different cancer types revealed that brain metastasis tissue has unique genomic, transcriptional and epigenetic profiles according to histopathology groups. Therefore, the therapeutic strategies should be designed based at least in part on tumor histiogenesis. Citation Format: Kazutaka Fukumura, Xizeng Mao, Xingzhi Song, Grant M. Fischer, Jie Yang, Erik P. Sulman, Michael A. Davies, Jianhua Zhang, Jason T. Huse. Comprehensive genomic analysis of brain metastases from multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3406.