Genomic Loss Of Heterozygosity Research Articles

Clinical and Technical Validation of OncoIndx® Assay-A Comprehensive Genome Profiling Assay for Pan-Cancer Investigations.

Comprehensive next-generation sequencing (NGS) assays enable the identification of clinically relevant mutations, enhancing the capability for targeted therapeutic interventions. In addition, genomic alterations driving the oncogenic roadmap and leading to resistance mechanisms are reshaping precision oncology. We report the workflow and clinical and technical validation of the OncoIndx® NGS platform-a comprehensive genomic profiling (CGP)-based assay for pan-cancer investigation. We evaluated the concordance between the OncoIndx® test findings and clinically established hotspot detection using SeraSeq reference standards. OncoIndx is a hybridization capture-based NGS assay for the targeted deep sequencing of all exons and selected introns of 1080 cancer-related genes. We show the outcome in the form of tier I and tier II single nucleotide variants (SNVs), copy number alterations (CNAs), and specific gene fusions. OncoIndx® also informs genome-wide tumor mutational burden (TMB), microsatellite instability (MSI), homologous recombination deficiency (HRD), and genomic loss of heterozygosity (gLOH). A total of 63 samples were utilized for validation with reference standards, clinical samples, and orthogonal assessment for genomic alterations. In addition, 49 cross-laboratory samples were validated for microsatellite instability (MSI), and for the tumor mutation burden (TMB), 18 samples as reference standards, 6 cross-laboratory samples, and 29 TCGA samples were utilized. We show a maximum clinical sensitivity of 98% and a positive predictive value (PPV) of 100% for the clinically actionable genomic variants detected by the assay. In addition, we demonstrate analytical validation with the performance of the assay, limit of detection (LoD), precision, and orthogonal concordance for various types of SVs, CNAs, genomic rearrangements, and complex biomarkers like TMB, MSI, and HRD. The assay offers reliable genomic predictions with the high-precision detection of actionable variants, validated by established reference standards.

Neoadjuvant talazoparib in patients with germline BRCA1/2 mutation-positive, early-stage triple-negative breast cancer: exploration of tumor BRCA mutational status

BackgroundTalazoparib monotherapy in patients with germline BRCA-mutated, early-stage triple-negative breast cancer (TNBC) showed activity in the neoadjuvant setting in the phase II NEOTALA study (NCT03499353). These biomarker analyses further assessed the mutational landscape of the patients enrolled in the NEOTALA study.MethodsBaseline tumor tissue from the NEOTALA study was tested retrospectively using FoundationOne®CDx. To further hypothesis-driven correlative analyses, agnostic heat-map visualizations of the FoundationOne®CDx tumor dataset were used to assess overall mutational landscape and identify additional candidate predictive biomarkers of response.ResultsAll patients enrolled (N = 61) had TNBC. In the biomarker analysis population, 75.0% (39/52) and 25.0% (13/52) of patients exhibited BRCA1 and BRCA2 mutations, respectively. Strong concordance (97.8%) was observed between tumor BRCA and germline BRCA mutations, and 90.5% (38/42) of patients with tumor BRCA mutations evaluable for somatic-germline-zygosity were predicted to exhibit BRCA loss of heterozygosity (LOH). No patients had non-BRCA germline DNA damage response (DDR) gene variants with known/likely pathogenicity, based on a panel of 14 non-BRCA DDR genes. Ninety-eight percent of patients had TP53 mutations. Genomic LOH, assessed continuously or categorically, was not associated with response.ConclusionThe results from this exploratory biomarker analysis support the central role of BRCA and TP53 mutations in tumor pathobiology. Furthermore, these data support assessing germline BRCA mutational status for molecular eligibility for talazoparib in patients with TNBC.

AFT-50 EndoMAP: A phase IB/II multicohort study of targeted agents and/or immunotherapy for patients with recurrent or persistent endometrial cancer (EC).

TPS5642 Background: The landscape in the management of recurrent or persistent endometrial cancer (EC) continues to evolve. Anti-PD-1/PD-L1 immune checkpoint inhibitors (ICI) as monotherapy or when combined with the VEGF-targeted tyrosine kinase inhibitor, lenvatinib, have demonstrated promising response rates in patients (pts) with microsatellite instability-high (MSI-H)/mismatch repair-deficient (dMMR) and MS-stable (MSS)/MMR-proficient (MMRp) EC, respectively. Recent studies have also shown a benefit with adding ICI to standard of care chemotherapy in the frontline setting. Pts with MSI-H/dMMR tumors seem to derive the greatest benefit. Approximately, 30% of recurrent EC pts fall into this category. Pairing ICI with targeted therapies carries the potential to elicit prolonged anti-tumor effects. Atezolizumab (Atezo) is a humanized monoclonal PD-L1 inhibitor that has demonstrated monotherapy antitumor activity in relapsed recurrent EC, and other solid tumors (e.g. NSCLC, HCC) as monotherapy and as part of combinatorial therapy. The AFT-50/EndoMAP study is a phase IB/II non-randomized, multicenter, 2-arm, multi-cohort platform trial designed to evaluate the efficacy and safety of biomarker-driven combination regimens, both with Atezo (AFT-50A) and without Atezo (AFT-50B) with biomarker-defined targeted agents in pts with recurrent or persistent EC. Methods: Eligible pts have recurrent or persistent EC with no more than 2 prior lines of therapy. FoundationOne CDx (F1CDx) NGS assay will be used for genomic tumor profiling. In AFT-50A, pts may be eligible for one of the following doublets: Atezo+talazoparib (tumors with genomic loss of heterozygosity (gLOH ≥16%), Atezo+Trastuzumab emtansine (ERBB2/HER2 mutated or amplified tumors), and Atezo+Tiragolumab (MSI-H and/or TMB-H). The Atezo+bevacizumab (biomarker unmatched) and Atezo+ipatasertib (PIK3CA/PTEN/AKT1-altered tumors) cohorts have completed accrual. Each cohort will enroll ~20 pts with potential adjustment to account for statistical and clinical considerations. AFT-50A pts will receive Atezo in addition to a targeted agent (per study-approved dosing schedule) until progression, unacceptable toxicity, pt withdrawal, death, or study termination. AFT-50B pts will be eligible for inavolisib (PIK3CAm/PTEN and AKT1wt-altered tumors) + letrozole or giredestrant + abemaciclib (RB1wt, estrogen receptor positive tumors). The primary endpoint for AFT-50A is confirmed overall response rate (ORR) for each arm, and for AFT-50B is 6-month progression free survival. Secondary endpoints include disease control rate, duration of response, OS, safety and tolerability. As a platform study, additional arms may be added, as supported by evolving understanding of EC and molecular targets. EndoMAP is actively enrolling at 20 sites in the US with a target of 25 sites nationwide. Clinical trial information: NCT04486352 .

Precision needle-punch tumor enrichment from paraffin blocks improves the detection of clinically actionable genomic alterations and biomarkers.

While many molecular assays can detect mutations at low tumor purity and variant allele frequencies, complex biomarkers such as tumor mutational burden (TMB), microsatellite instability (MSI), and genomic loss of heterozygosity (gLOH) require higher tumor purity for accurate measurement. Scalable, quality-controlled, tissue-conserving methods to increase tumor nuclei percentage (TN%) from tumor specimens are needed for complex biomarkers and hence necessary to maximize patient matching to approved therapies or clinical trial enrollment. We evaluated the clinical utility and performance of precision needle-punch enrichment (NPE) compared with traditional razor blade macroenrichment of tumor specimens on molecular testing success. Pathologist-directed NPE was performed manually on formalin-fixed, paraffin embedded (FFPE) blocks. Quality control of target capture region and quantity of residual tumor in each tissue block was determined via a post-enrichment histologic slide recut. Resultant tumor purity and biomarker status were determined by the computational analysis pipeline component of the FDA-approved next-generation sequencing (NGS) assay, FoundationOne®CDx. Following NPE implementation for real-world clinical samples, assay performance and biomarker (MSI, TMB, gLOH) detection were analyzed. In real-world clinical samples, enrichment rate via NPE was increased to ~50% over a 2.5-year period, exceeding the prior use of razor blade macro-enrichment (<30% of cases) prior to NPE implementation due to proven efficacy in generating high quality molecular results from marginal samples and the ease of use for both pathologist and histotechnologists. NPE was associated with lower test failures, higher computational tumor purity, and higher rates of successful TMB, MSI and gLOH determination when stratified by pre-enriched (incipient) tumor nuclei percentage. In addition, challenging cases in which tumor content was initially insufficient for testing were salvaged for analysis of biomarker status, gene amplification/deletion, and confident mutant or wild-type gene status determination. Pathologist-directed precision enrichment from tissue blocks (aka NPE) increases tumor purity, and consequently, yields a greater number of successful tests and complex biomarker determinations. Moreover, this process is rapid, safe, inexpensive, scalable, and conserves patient surgical pathology material. NPE may constitute best practice with respect to enriching tumor cells from low-purity specimens for biomarker detection in molecular laboratories.

Pan-Cancer Interrogation of MUTYH Variants Reveals Biallelic Inactivation and Defective Base Excision Repair Across a Spectrum of Solid Tumors.

Biallelic germline pathogenic variants of the base excision repair (BER) pathway gene MUTYH predispose to colorectal cancer (CRC) and other cancers. The possible association of heterozygous variants with broader cancer susceptibility remains uncertain. This study investigated the prevalence and consequences of pathogenic MUTYH variants and MUTYH loss of heterozygosity (LOH) in a large pan-cancer analysis. Data from 354,366 solid tumor biopsies that were sequenced as part of routine clinical care were analyzed using a validated algorithm to distinguish germline from somatic MUTYH variants. Biallelic germline pathogenic MUTYH variants were identified in 119 tissue biopsies. Most were CRCs and showed increased tumor mutational burden (TMB) and a mutational signature consistent with defective BER (COSMIC Signature SBS18). Germline heterozygous pathogenic variants were identified in 5,991 biopsies and their prevalence was modestly elevated in some cancer types. About 12% of these cancers (738 samples: including adrenal gland cancers, pancreatic islet cell tumors, nonglioma CNS tumors, GI stromal tumors, and thyroid cancers) showed somatic LOH for MUTYH, higher rates of chromosome 1p loss (where MUTYH is located), elevated genomic LOH, and higher COSMIC SBS18 signature scores, consistent with BER deficiency. This analysis of MUTYH alterations in a large set of solid cancers suggests that in addition to the established role of biallelic pathogenic MUTYH variants in cancer predisposition, a broader range of cancers may possibly arise in MUTYH heterozygotes via a mechanism involving somatic LOH at the MUTYH locus and defective BER. However, the effect is modest and requires confirmation in additional studies before being clinically actionable.

The Utility of NGS Analysis in Homologous Recombination Deficiency Tracking.

Several tumor types have been efficiently treated with PARP inhibitors (PARPis), which are now approved for the treatment of ovarian, breast, prostate, and pancreatic cancers. The BRCA1/2 genes and mutations in many additional genes involved in the HR pathway may be responsible for the HRD phenomenon. The aim of the present study was to investigate the association between genomic loss of heterozygosity (gLOH) and alterations in 513 genes with targeted and immuno-oncology therapies in 406 samples using an NGS assay. In addition, the %gLOHs of 24 samples were calculated using the Affymetrix technology in order to compare the results obtained via the two methodologies. HR variations occurred in 20.93% of the malignancies, while BRCA1/2 gene alterations occurred in 5.17% of the malignancies. The %LOH was highly correlated with alterations in the BRCA1/2 genes, since 76.19% (16/21) of the BRCA1/2 positive tumors had a high %LOH value (p = 0.007). Moreover, the LOH status was highly correlated with the TP53 and KRAS statuses, but there was no association with the TMB value. Lin's concordance correlation coefficient for the 24 samples simultaneously examined via both assays was 0.87, indicating a nearly perfect agreement. In conclusion, the addition of gLOH analysis could assist in the detection of additional patients eligible for treatment with PARPis.

Neoplastic and blood-based biomarkers of response in patients with advanced endometrial cancer: Results from NRG GY012.

5525 Background: NRG GY012 is a randomized, 3-arm phase II study, comparing olaparib (O) and the combination of cediranib and olaparib (CO) to the reference arm cediranib (C) for metastatic pre-treated, endometrial cancer (EC). The trial found a trend towards benefit for CO and no benefit for O compared to C. Archival tumor and prospective blood samples were collected for biomarker analysis. Methods: Targeted next-generation sequencing (BROCA-GO) was used to detect pathogenic variants (PV) and loss of heterozygosity (LOH) in DNA from paired blood and archival cancers. The LOH cut-off was identified at 11% for HRD based on testing ovarian cancers with known HRD. Plasma samples collected at baseline, cycle 2 day 1, and end-of-treatment were analyzed via multiplex ELISA for 25 angiogenic and inflammatory circulating protein biomarkers (Angiome); IL6 was of specific interest. Prognostic associations with PFS and OS were analyzed using proportional hazards models (PhM) stratified by histology and adjusted for treatment assignment. Predictive associations (PFS and OS) were analyzed using PhM stratified by histology and including main effects for both treatment assignment and biomarker group plus an interaction term. Results: In 97 patients (pts) with evaluable tumor, BROCA-GO identified 370 somatic PV; TP53 (61%) was the most commonly mutated gene. PV in homologous recombination repair (HRR) genes were identified in 5 cases (5%). Somatic PVs were identified in BRCA2, RAD51B and PALB2. 1 pt had a germline BRCA1 PV. 2 cases had somatic PV that might restore HRR: 1 case with a somatic BRCA2 PV had somatic PVs in CHD4 and TP53BP1; the TP53BP1 frameshift PV was present only in the recurrent and not primary cancer. LOH was available for 45 cases. LOH high occurred in 16 (35.6%) cases and was exclusive to EC with TP53 mutations (p=0.0003). LOH was not associated with outcome in any of the arms. For the circulating biomarker analysis (N=96), median IL-6 was 4pg/ml. IL-6 levels &gt;4pg/ml were associated with increased risk of progression (HR: 1.59; 95% CI: (1.04-2.42); p-value=0.032). In predictive analyses, pts with IL-6 &gt; 4 pg/ml receiving C or C+O had increased PFS (3.8 mo vs 1.9 mo) and OS (11.9 mo vs 5.7 mo) compared to pts receiving O, the interaction p value did not reach statistical significance. Conclusions: LOH high status was not associated with outcome to O. There were too few cases with HRR PVs to determine their relationship to PARPi response. The restriction of LOH high to cancers with TP53 mutation may suggest that genomic LOH in ECs correlates better with aneuploidy than with HRR function indicating that at least some biomarkers of PARPi response vary between tumor types. IL-6 levels were prognostic of PFS but were not predictive of either OS or PFS for pts receiving C compared to pts receiving O in this small study. Further analysis of the complete Angiome and integration with the BROCA-GO dataset are ongoing. Clinical trial information: NCT03660826 .

Exploring the prognostic and predictive impact of genomic loss of heterozygosity (LOH) in patients with metastatic colorectal cancer (mCRC).

3576 Background: Genomic LOH consists in the loss of chromosomal regions and is associated with the homologous recombination repair (HRR) system deficiency (dHRR). In ovarian cancer, LOH-high predicts benefit from platinum-based chemotherapy and PARP inhibitors. In mCRC, the role of LOH has been poorly investigated. Methods: An NGS-based assay (FoundationOne CDx; Foundation Medicine, Inc. Cambrige, MA) was used to determine the percentage of genomic LOH and the presence of pathogenetic mutations in HRR-related genes in archival chemo-naïve tumor tissues of mCRC patients included in a real-world registry and in the AtezoTRIBE (NCT03721653) and AVETRIC (NCT04513951) studies. Both these trials assessed the combination of an anti-PDL1 (atezolizumab or avelumab) with the triplet FOLFOXIRI plus bevacizumab or cetuximab. The prespecified cut-off of ≥14.08 for LOH-high described for mCRC (Sokol et al., JCO Precis Oncol 2020) was adopted. Tumors with at least one biallelic alteration in any of the 27 genes involved in the HRR pathway (Riaz et al., Nat Commun 2017) included in the FoundationOne CDx panel (BARD1, BRCA1, BRCA2, BRIP1, MRE11A, NBN, PALB2, RAD51, RAD51B, RAD51C, RAD51D, RAD52, RAD54L, RBBP8, XRCC2, ABL1, ATM, ATR, BAP1, CDK12, DNMT3A, ERCC4, FANCA, FANCC, FANCG, FANCL, PARP1) were defined dHRR. Results: Overall, 196 samples were analysed. None of 7 MSI-H tumors were classified as LOH-high. Fourteen (7%) and 6 (3%) of 189 MSS tumors were classified as LOH-high and dHRR, respectively. In particular, in LOH-high subgroup, 3 (21%) tumors were defined dHRR, while 3 (50%) tumors were classified LOH-high among dHRR tumors. LOH-high tumors were more frequently BRAF mutated (p = 0.019) and dHRR (p = 0.006) compared to LOH-low. Among patients receiving triplet chemotherapy +/- biologic agent alone (N = 55) or with an anti-PDL1 (N = 58), an interaction effect was shown between the effect of the addition of the checkpoint inhibitor and LOH with higher benefit in the LOH-high subgroup (N = 10) in terms of both PFS (pinteraction= 0.002) and OS (pinteraction&lt; 0.001). In the cohort of patients not receiving the anti-PDL1, longer PFS was observed in patients with LOH-low (N = 125) respect to LOH-high (N = 6) tumors (12.1 vs 5.1 months, HR: 0.11, 95%CI: 0.04-0.26, p &lt; 0.001). No differences in PFS or OS were reported between patients treated with first-line oxaliplatin- (N = 40) vs irinotecan-based doublets (N = 25) or with the triplet FOLFOXIRI (N = 55) vs doublets (N = 65) according to LOH status. No prognostic or predictive impact of HRR deficiency was shown. Conclusions: In MSS mCRC, LOH-high was associated with biallelic alterations in the HRR system, worse prognosis and higher benefit from the addition of anti-PDL1 agents to chemotherapy. Considering the low number of LOH-high tumors in our study, these results deserve confirmation in larger cohorts.

Molecular characterization of nectin-4 in non-small cell lung cancer subtypes.

e21119 Background: Nectin-4 (Nectin cell adhesion molecule-4) is a tumor associated antigen overexpressed in multiple solid tumor types. Studies show that over 60% of NSCLC are nectin-4 overexpressed. As enfortumab vedotin, an antibody-drug conjugate directed against nectin-4, has been FDA approved for advanced urothelial carcinoma, this holds treatment implications. Here, we investigated nectin-4 expression in NSCLC subtypes. Methods: 27,607 NSCLC tumors were tested for whole transcriptome sequencing (WTS, NovaSeq) and NextGen DNA sequencing (592 gene panel or whole exome sequencing, WES) at Caris Life Sciences (Phoenix, AZ). Tumors were analyzed overall in quartiles by nectin-4 expression (Q4-greatest, Q1-least) and further analyzed in the adenocarcinoma (AD) and squamous carcinoma (SQ) cohorts. PD-L1 expression was tested by IHC (Dako 22C3). Immune cell populations were estimated by QuanTISeq. Statistical significance was determined using Chi-square/Fisher-Exact/Mann-Whitney U tests and adjusted for multiple comparisons (q &lt; 0.05). Results: We saw significantly greater expression of nectin-4 in SQ (median TPM- 15.68) versus AD tumors (median TPM - 9.88) (p &lt; 0.05). We saw a greater prevalence of NFE2L2, STK11, ERBB2 mutations and genomic loss of heterozygosity (LOH) but a lower percentage of PD-L1+ tumors in Q4 vs Q1 tumors (all q-value &lt; 0.05, Table 1). mRNA expression of immune checkpoints PDL1, CTLA4, CD80, CD86, HAVCR2, and IDO1 was increased in Q4 tumors (1.1-1.3-fold, all q &lt; 0.05). Q4 tumors had reduced estimates of M1 macrophages, regulatory T cells (Tregs), and CD8+ T cells and increased estimates of neutrophils and NK cells. The association of nectin-4 expression with the immune landscapes of AD and SQ was similar. Q4 tumors in AD and SQ displayed increased expression of the above-mentioned immune checkpoints (q &lt; 0.05). In AD and SQ, estimates of M1 macrophages, Tregs, and CD8+ T cells were reduced, but neutrophils and NK cells were increased in Q4 tumors (q &lt; 0.05). The pattern of molecular alterations was different in AD and SQ. While KEAP1, STK11 and ERBB2 mutations were significantly enriched in AD Q4 tumors, NFE2L2 mutations were significantly enriched in SQ Q4 tumors (Table 1). Prevalence of LOH was higher and PD-L1+ tumors was lower in Q4 tumors in both AD and SQ (Table 1). Conclusions: NFE2L2 alterations in SQ and STK11, KEAP1 mutations in AD, which are associated with poor immunotherapy (IO) response, were enriched in Q4 tumors. This suggests that the immune landscape associated with high nectin-4 expression in NSCLC may be driven by the dysregulated KEAP1-NFE2L2 pathway. Targeted therapy towards nectin-4 may benefit these NSCLC subtypes that do not respond well to IO. [Table: see text]

CDH1-mutated clinically advanced urothelial bladder cancer (UBC): A genomic landscape and real-world clinical outcome study (RWCOS).

4587 Background: CDH1 mutated bladder cancers are characterized by plasmacytoid histology and are associated with an aggressive clinical course. Methods: Cohort 1: 6,676 clinically advanced UBC patients underwent hybrid capture based comprehensive genomic profiling (CGP) to evaluate all classes of genomic alterations (GA) as well as microsatellite instability (MSI), tumor mutational burden (TMB), and genomic loss of heterozygosity (gLOH, high ≥16%). Tumor cell PD-L1 expression was determined by immunohistochemistry (Dako 22C3). GAs were compared between CDH1 mutated and wild-type (WT) patients using Chi-square. Cohort 2: 586 UBC patients underwent a RWCOS using the de-identified Flatiron Health-Foundation Medicine urothelial clinicogenomic database. The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care) between January 2011 and April 2022. Differences in real-world progression-free survival (rwPFS) and overall survival (rwOS) were evaluated by Cox proportional hazard models. Results: Cohort 1: 217 UBC patients featured a CDH1 short variant mutation with 65.2% featuring plasmacytoid histology (PLC). The PLC cohort was slightly younger, with a higher proportion of male patients, and MSI-High status. Cell-Cycle regulatory GAs were significantly higher in the non-PLC cohort, specifically CDKN2A (25.5% vs 9.7%, p=0.01) and CDKN2B (23.6% vs 5.8%, p&lt;0.01). CDH1-mutated UBCs featured a higher MSI high frequency (2.7% vs 0.8%; p=.002), mean TMB (14.8 vs 9.9mut/Mb p&lt;.0001), RB1 GA (52.5% vs 20.3%; p&lt;.0001), PTEN GA (9.2% vs 4.3%; p=.006) and PIK3CA GA (29.5% vs 21.8%; p=.02), but lower gLOH (6.8% vs 15.9%; p=.009), CDKN2A loss (12.4% vs 38.3%; p&lt;.0001), MTAP loss (10.1% vs 25.1%; p&lt;.0001), and FGFR3 GA (9.7% vs 18.1%; p=.002). TP53 GAs and PD-L1 expression levels were similar between groups. From cohort 2: 22 (3.7%) patients featured CDH1 mutations. When compared with the CDH1 WT patients, the age, gender, ethnicity and ECOG status were similar. CDH1 mutation was associated with less favorable outcomes for 270 UBC patients treated with immune checkpoint inhibitors (ICPI) including rwPFS (2.8 vs 3.5 months; p=.096) and rwOS (3.3 vs 9.5 months; p=.03). Similar comparisons for 316 UBC patients treated with chemotherapy showed no significant adverse impact of CDH1 mutation status on either rwPFS (7.9 vs 6.2 months; p=.11) and rwOS (13.4 vs 13.4 months; p=0.83). Conclusions: In addition to its classic association with PLC histology, CDH1-mutated UBC features an unique genomic landscape including higher MSI and TMB, activating GAs in the MTOR pathway, but lower frequency of FGFR3 GAs. RWCOS further supports that CDH1 mutation predicts resistance to ICPI-based treatment, but does not systemic chemotherapy. These findings support CGP to guide therapeutic approaches based on the personalized genomic signature of UBC.

Comprehensive genomic profiling (CGP) of clinically advanced and metastatic cutaneous adnexal carcinomas (CAs; MCADCA): A genomic landscape study.

9587 Background: Cutaneous adnexal tumors are a large group of malignant neoplasms that exhibit morphologic differentiation towards one of the four primary adnexal structures present in normal skin: hair follicles, sebaceous glands, sweat-apocrine glands, and sweat-eccrine glands. Methods: 276 cases of MCADCA underwent hybrid capture-based CGP to evaluate all classes of genomic alterations (GA). Microsatellite instability (MSI) status, tumor mutational burden (TMB), genomic loss of heterozygosity (gLOH), genomic ancestry prediction and COSMIC genomic signature were determined from sequencing results. PD-L1 was measured by IHC (TPS; Dako 22C3). Fisher exact method was used for statistical analysis with the false discovery rate corrected using Benjamini-Hochberg adjustment. Results: Sequencing was performed on the primary cutaneous tumor in 131 (47.4%) and on a local recurrence or metastatic site biopsy in 145 (52.5%) MCADCA. Male preponderance (64-81%) and age distributions mean (59-63 yrs) were similar in all groups with apocrine (APO) older than eccrine (ECC) (72 vs 62 yrs; p = .001). There were 173 (62.7%) sweat gland (SWT) derived, 55 (19.9%) were sebaceous gland (SEB) derived, 14 (5.1%) were hair follicle (HRF) derived and 34 (12.3%) were unclassified (UNK). 150/173 (86.7%) of SWT were ECC and 23 (13.3%) were APO. The SWT cases included 12 (6.9%) digital papillary ca’s (DPA), 11 (6.3%) mucinous ca’s (MAC), 19 (11.0%) poroca’s (POR), 14 (8.1%) spiradenoca’s (SPR), 10 (5.8%) syringoadenoca’s (SRNG) and 77 (44.5%) unclassified ca’s (UNC). GA/tumor were highest in SEB vs SWT (7.9 vs 4.9; p = .004) and lowest in DPA (2.1 vs 5.0 non-DPA; p = .03). There we no ancestry distribution differences. When compared with the SWT group, the SEB group had higher frequencies of RB1 GA (38.2% vs 8.1%; p &lt; .0001) and TP53 GA (76.4% vs 43.4%; p = .0002) indicating likely neuroendocrine differentiation. The MAC group had significantly higher PTCH1 GA than the non-MAC group (36.4% vs 1.8%; p = .044). MSI-High status was highest in the SEB group vs all other groups (SEB 15.7% vs SWT 1.2%; p = .005). gLOH &gt; 16% was most frequent in SEB when compared with SWT (19.6% vs 7.2%; p = .081). The MMR signature was more frequent in SEB than SWT (32.0% vs 2.1%; p = .005). The mean TMB was high in all MCADCA ranging from 10.4 mut/Mb in HRF to 38.8 mut/Mb in MAC with the exceptions of APO (2.7 mut/Mb; p = .001 and DPA 1.4 mut/Mb; p = .003). PD-L1 expression was not significantly different in all the MCADCA with low positive scores SWT vs SEB (37.0% vs 33.3%; NS). Conclusions: As there is limited evidence on the treatment of MCADCA, we provide a repertoire of common GA found. An increased frequency of GA is observed in SEB MCADCA. Clinical trials are needed to evaluate MCADCA-based biomarkers prognostic of ICI response. Only then can we successfully incorporate novel therapeutic strategies in the evolving landscape of treatment.

Characterizing KRAS allele variants within biliary tract cancers.

4088 Background: Biliary tract cancers (BTC) are aggressive malignancies with a poor 5-year survival rate and growing incidence globally. KRAS mutations (mut) in BTC are associated with a poor prognosis; however, PD-L1 inhibition with Durvalumab may lead to an improved survival with KRAS mut (TOPAZ-1 trial). It is important to understand the genomic landscape and immunophenotype of KRAS mut in BTC given the advent of immunotherapeutics and small molecular inhibitors targeting KRAS mut. Methods: A retrospective pooled analysis was performed from the following patient databases: Princess Margaret Cancer Centre, MD Anderson Cancer Center, Foundation Medicine, along with the publicly accessible cBioPortal for Cancer Genomics that includes the American Association for Cancer Research Project Genie cancer registry of real-world data assembled between 19 leading international cancer centers. Any overlapping cases were excluded. Patients included had a diagnosis of a BTC and completed molecular testing from January 2017 to December 2022. Cohort demographics, KRAS allelic variants, concurrent genetic aberrations, and immune biomarkers (PD-L1, TMB, MSI and gLOH) were summarized. Log-rank, Wilcoxon, and Kaplan-Meier tests were conducted for survival analysis. Results: 5,813 BTC patients were included, and 1000 patients (17.2%) had a KRAS mutation. The prevalence of KRAS mut was higher in extra-hepatic cholangiocarcinoma (EH-CCA) (36.1%) and perihilar (PH)-CCA (28.6%) than in intra-hepatic (IH)-CCA (11.82%) and gallbladder cancer (GBC) (7.6 %). The most common KRAS allelic variant was G12D, and the most common co-mutation was TP53, except in PH-CCA, which was G12V and SMAD4, respectively. In this cohort, race was primarily White (73%). The most prevalent variant in North America was G12D, while G12V and Q61H were more prevalent with genomic African American and genomic East Asian descent, respectively. For patients with KRAS mut, GBC had the most PD-L1 high positivity (17%) compared to IH-CCA (7%) and EH-CCA (3%), along with the most MSI-H phenotypes and the highest mean and median TMB compared to other sites, especially in G12V and Q61H variant patients. Genomic loss of heterozygosity was low among all groups. In the survival analysis, patients with the G12V allele subtype had the lowest OS at 17.8 months, followed by Q61H (22.8 months) and G12D (25.1 months) (p = 0.022). Survival analysis with KRAS co-mut ( TP53, SMAD4, CDK2NA, or additional KRAS mut) was not significant (p = 0.7). In a co-variance analysis of KRAS variants and tumour site, there was no difference in IH-CCA and GBC but lower OS in Q61H variants in PH-CCA and G12V variants in EH-CCA (p = 0.0081). Conclusions: This large series adds to the growing body of comprehensive genomic and immune landscape data of KRAS mut in BTC and will be of value in planning specific therapies in this heterogeneous group. Immune profiling studies are ongoing to further describe the immunophenotype of this subset.

AFT-50 EndoMAP: A phase IB/II multi-cohort study of targeted agents for patients with recurrent or persistent endometrial cancer.

TPS5634 Background: The prognosis for women with recurrent or persistent EC after progressing on first-line chemotherapy is poor, with a median overall survival (OS) of 12 months, highlighting the need for more efficacious therapies for this population. Immune checkpoint inhibitors either as monotherapy or when combined with kinase inhibitors have recently demonstrated encouraging response rates in pts with microsatellite instability-high (MSI-H)/mismatch repair-deficient (dMMR) and MS-stable (MSS)/MMR-proficient (MMRp) EC, respectively. Atezo is a humanized monoclonal anti-programmed cell death ligand 1 (PD-L1) inhibitor that has demonstrated monotherapy antitumor activity with an acceptable safety profile in relapsed recurrent EC. Atezo has shown compelling clinical efficacy for pts with certain solid tumors (e.g., urothelial, NSCLC, triple negative breast cancer) as monotherapy and as part of combinatorial therapy. The AFT-50 EndoMAP trial is a platform trial designed to evaluate the efficacy and safety of Atezo in combination with biomarker-defined targeted agents in pts with recurrent or persistent EC. Recognizing pts may have either progressed through or received a checkpoint inhibitor in a prior line of therapy, a non atezo cohort will also be open to enrollment. Methods: This is a phase IB/II non-randomized, multicenter, multicohort, biomarker-driven platform study consisting of two cohorts: A (atezo containing) and B (non atezo). Eligible pts have recurrent or persistent EC and have received no more than 2 prior lines of therapy. FoundationOne CDx (F1CDx) NGS assay will be used for genomic tumor profiling. In cohort A, pts may be eligible for one of the following doublets: Atezo+ipatasertib (PIK3CA/PTEN/AKT1-altered cancers), Atezo+talazoparib (tumors with genomic loss of heterozygosity (LOH) ≥16%), Atezo+Trastuzumab emtansine (ERBB2/HER2 mutated and/or amplified tumors), Atezo+Tiragolumab (MSI-H and/or TMB&gt;10 mut/MB), and Atezo+bevacizumab (biomarker unmatched). Pts will receive Atezo in addition to the targeted agent (at the study approved dosing schedule) until progression, unacceptable toxicity, pt or physician decision to withdraw from the study, death, or study termination. Pts in cohort B, will be eligible for inavolisib (PIK3CA/PTEN/AKT1-altered cancers) + letrozole. Each cohort will enroll ~20 pts; however, the exact size of the cohort may be adjusted. The primary endpoint for Cohort A is confirmed overall response rate (ORR) for each cohort, and for Cohort B is progression free survival at 6 months. Secondary endpoints include disease control rate, duration of response, OS, safety and tolerability, 6-month PFS (cohort A). As a platform study, additional arms may be added, as supported by evolving understanding of EC and molecular targets. EndoMAP is actively enrolling at 17 sites in the US with a target of 25 sites nationwide. Clinical trial information: NCT04486352 .

MP56-03 A COMPLIMENTARY ANALYSIS OF PLASMACYTOID UROTHELIAL CARCINOMA OF THE BLADDER: GENOMIC LANDSCAPE INDEPENDENT OF SOMATIC CDH1 MUTATIONS AND REAL-WORLD CLINICAL OUTCOME STUDY

You have accessJournal of UrologyCME1 Apr 2023MP56-03 A COMPLIMENTARY ANALYSIS OF PLASMACYTOID UROTHELIAL CARCINOMA OF THE BLADDER: GENOMIC LANDSCAPE INDEPENDENT OF SOMATIC CDH1 MUTATIONS AND REAL-WORLD CLINICAL OUTCOME STUDY Kyle Rose, Andrea Necchi, Facundo Davaro, Elizabeth Davaro, Heather Huelster, Joseph Jacob, Grennady Bratslavsky, Dean Pavlick, Douglas Lin, Natalie Danzinger, Petros Grivas, Hikmat Al-Ahmadie, Vamsi Parimi, Philippe Spiess, Bishoy Faltas, Jeffrey Ross, and Roger Li Kyle RoseKyle Rose More articles by this author , Andrea NecchiAndrea Necchi More articles by this author , Facundo DavaroFacundo Davaro More articles by this author , Elizabeth DavaroElizabeth Davaro More articles by this author , Heather HuelsterHeather Huelster More articles by this author , Joseph JacobJoseph Jacob More articles by this author , Grennady BratslavskyGrennady Bratslavsky More articles by this author , Dean PavlickDean Pavlick More articles by this author , Douglas LinDouglas Lin More articles by this author , Natalie DanzingerNatalie Danzinger More articles by this author , Petros GrivasPetros Grivas More articles by this author , Hikmat Al-AhmadieHikmat Al-Ahmadie More articles by this author , Vamsi ParimiVamsi Parimi More articles by this author , Philippe SpiessPhilippe Spiess More articles by this author , Bishoy FaltasBishoy Faltas More articles by this author , Jeffrey RossJeffrey Ross More articles by this author , and Roger LiRoger Li More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003309.03AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Plasmacytoid urothelial carcinomas of the bladder (PUC) represent an aggressive malignancy with somatic CDH1 mutations, poor survival, and few systemic therapy options. We aimed to analyze the genomic landscape of urothelial carcinomas stratified by CDH1 status and PUC histology, while utilizing real-world clinical outcome data. METHODS: 7,903 clinically advanced patients with UCB underwent hybrid capture based comprehensive genomic profiling (CGP) to evaluate all classes of genomic alterations (GAs) as well as microsatellite instability (MSI), tumor mutational burden (TMB), and genomic loss of heterozygosity (gLOH, high≥16%). Plasmacytoid histology was confirmed by pathologic evaluation. GAs were compared by plasmacytoid histology and CDH1-mutated (CDH1-M) vs. wild-type (WT). The Flatiron Heath-Foundation Medicine Urothelial Clinico-Genomic Database (FH-FMI CGDB) was used to characterize overall survival (OS) and progression-free survival (PFS) in CDH1-M vs. WT, stratified by systemic therapy administered. RESULTS: CDH1 mutations were identified in 158 patients, who demonstrated a higher frequency MSI-high status (2.7% vs. 0.8%, p<0.01), mean TMB (14.8 vs. 9.9%, p<0.01), but lower gLOH (6.8% vs. 20.3%, p<0.01). PUC was identified on pathologic analysis in 103 (65%) patients with CDH1 mutations. Table 1 demonstrates the frequency of GAs between these three groups. There were no differences in genes associated with DNA damage response. In the non-PUC cohort, GAs on chromosome 9p21 were increasingly mutated. From the FH-FMI CGDB, 22 patients (3.7%) featured CDH1 mutations, and shared similar demographics to CDH1-WT. These patients demonstrated worse OS (OS 3.3 vs. 9.5 months, p=0.03) and PFS (2.8 vs 3.5 months; p=0.09) when treated with immune checkpoint inhibitors, but no difference following chemotherapy. CONCLUSIONS: CDH1 mutations are not exclusive to PUC, which possesses a distinct genomic profile and natural history. Real-world clinical outcomes support that CDH1 mutations predict resistance to immune checkpoint inhibition, but not chemotherapy. Taken together, these results further support genomic profiling of advanced bladder tumors and treatment individualization based on genomic signatures. Source of Funding: NA © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e774 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Kyle Rose More articles by this author Andrea Necchi More articles by this author Facundo Davaro More articles by this author Elizabeth Davaro More articles by this author Heather Huelster More articles by this author Joseph Jacob More articles by this author Grennady Bratslavsky More articles by this author Dean Pavlick More articles by this author Douglas Lin More articles by this author Natalie Danzinger More articles by this author Petros Grivas More articles by this author Hikmat Al-Ahmadie More articles by this author Vamsi Parimi More articles by this author Philippe Spiess More articles by this author Bishoy Faltas More articles by this author Jeffrey Ross More articles by this author Roger Li More articles by this author Expand All Advertisement PDF downloadLoading ...

Variable Landscape of PD-L1 Expression in Breast Carcinoma as Detected by the DAKO 22C3 Immunohistochemistry Assay.

In 2020, pembrolizumab was approved as a therapy for triple-negative breast cancer (TNBC) with the companion diagnostic DAKO 22C3 programmed death ligand-1 (PD-L1) immunohistochemistry assay. The study aimed to determine the landscape of PD-L1 expression as detected by the DAKO 22C3 PD-L1 assay in breast cancer subtypes and compare the clinicopathologic and genomic characteristics of PD-L1 positive and negative TNBC. PD-L1 expression using the DAKO 22C3 antibody was scored using a combined positive score (CPS) and positive status was defined as CPS ≥10. Comprehensive genomic profiling was performed using the FoundationOne CDx assay. Of the 396 BC patients stained with DAKO 22C3, the majority were HR+/HER2- and TNBC (42% and 36%, respectively). Median PD-L1 expression and frequency of CPS ≥10 was highest in TNBC cases (median: 7.5, 50% CPS ≥10) and lowest in the HR+/HER2- group (median: 1.0, 15.5% CPS ≥10) (P < .0001). A comparison of PD-L1 positive and PD-L1 negative TNBC demonstrated no significant differences in clinicopathologic or genomic characteristics. TNBC tissue samples from the breast did have an observed enrichment for PD-L1 positivity compared to TNBC tissue samples from a metastatic site (57% vs. 44%), but this was not statistically significant (P = .1766). In the HR+/HER2- group, genomic alterations in TP53, CREBBP, and CCNE1 were more prevalent and genomic loss of heterozygosity was higher in the PD-L1(+) group compared to the PD-L1(-) group. The subtypes of breast cancer have distinct patterns of PD-L1 expression, supporting that further research of immunotherapies may include specific evaluation of optimum cutoffs for non-TNBC patients. In TNBC, PD-L1 positivity is not associated with other clinicopathologic or genomic features and should be integrated into future studies of immunotherapy efficacy.

Extracellular domain ERBB2 (ERBB2 ECD+) mutations in urothelial bladder cancer (UBC).

566 Background: Given the recent approval in lung cancer for the first anti-HER2 targeted therapy directed against activating kinase domain exon 20 ERBB2 insertion mutations, considerable interest has arisen in targeting additional locations in the ERBB2 gene in other tumor types. Methods: 5,485 UBC samples were sequenced using a hybrid capture-based comprehensive genomic profiling (CGP) assay to assess all classes of genomic alterations (GA), tumor mutational burden (TMB), microsatellite instability (MSI), genomic loss of heterozygosity (gLOH), trinucleotide signatures and predominant genetic ancestry. Statistical comparisons utilized the Bonferroni correction. Results: 548 (10.0%) of UBC featured ERBB2 gene amplification (amp) and 219 (4.0%) featured an ERBB2 ECD+ sequence mutation (74% S310F and 26% S310Y). ERBB2 ECD+ mutations and ERBB2 amplification were mutually exclusive. 16.4% of ERBB2 ECD+ UBC had more than one E RBB2 sequence mutation. Central pathology review of the 219 ERBB2 ECD+ UBC revealed that 63 (28.8%) featured a micropapillary histologic appearance (MPUC). ERBB2 ECD+ UBC featured more patients with European ancestry than both ERBB2 WT (90.9% vs 84.2%; p=.03) and ERBB2 amp (90.9% vs 83.2%; p=.04). ECD mut+ UBC also featured lower association with African ancestry than ERBB2 amp (2.7% vs 7.8%; p=.04) and lower frequency of gLOH &gt; 16% (9.3% vs 19.1%; p=.04). MSI-High status was similar and rare in all 3 groups (range 0 to 0.9%). ERBB2 ECD+ UBC had a higher frequency of APOBEC signature than ERBB2 amp (82.9% vs 72.4%; p=.03). TMB &gt; 10 mut/mb was higher in ERBB2 amp (49.2% vs 31.4%; p&lt;.0001) and ERBB2 ECD+ (59.8% vs 31.4%; p&lt;.0001) compared to ERBB2 WT as was the mean TMB (11.8 and 17.4 mut/Mb respectively vs 8.9 mut/Mb, p&lt;0.001 for both). Among important UBC individual genes, FGFR3 GA were significantly higher in ERBB2 WT than both ERBB2 amp (19.9% vs 6.2%; p&lt;.0001) and ERBB2 ECD+ (19.9% vs 10.5%; p=.0002). CDKN2A GA were significantly higher in ERBB2 amp (39.1% vs 27.9% ERBB2 WT; p&lt;.0001) only. The higher frequency of KMT2D GA in MPUC+ ECD+ and MPUC- ECD+ UBC (63.4% vs 27.6%; p=.02) was the only genomic difference between these cohorts. Conclusions: ERBB2 ECD mutation driven UBC is a unique form of UBC featuring enrichment of MPUC histology and a unique clinical and genomic landscape including genomic signatures and ancestry.

CDH1-mutated clinically advanced urothelial bladder cancer (UBC): A genomic landscape and real-world clinical outcome study (RWCOS).

564 Background: CDH1 mutated UBCs are characterized by plasmacytoid histology and are associated with an aggressive clinical course at the time of diagnosis. Methods: Cohort 1: 6,676 clinically advanced UBC patients (pts) underwent comprehensive genomic profiling (CGP) to evaluate all classes of genomic alterations (GA), microsatellite instability (MSI), tumor mutational burden (TMB), and genomic loss of heterozygosity (gLOH, high ≥16%). Predominant genetic ancestry was determined using a SNP-based approach and classified as one of the 5 categories: African (AFR), European (EUR), Central and South American (AMR), South Asian (SAS), or East Asian (EAS). Cohort 2: 586 UBC pts underwent a RWCOS using the nationwide (US-based) de-identified Flatiron Health-Foundation Medicine urothelial clinico-genomic database (FH-FMI CGDB). The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care) Jan 2011-Apr 2022. Differences in real-world progression-free survival (rwPFS) and overall survival (rwOS) were evaluated by Cox proportional hazard models. Results: Cohort 1: 217 (3.3%) of UBC had a CDH1 short variant (SV) mutation with 65.2% featuring plasmacytoid histology. When compared with CDH1 wild-type (WT) UBC, the CDH1-mutated UBC had similar age, gender, and genetic ancestry. The CDH1-mutated UBC featured a higher frequency of MSI (2.7% vs 0.8%; p=.002), mean TMB (14.8 vs 9.9 mut/Mb p&lt;.0001), RB1 GA (52.5% vs 20.3%; p&lt;.0001), PTEN GA (9.2% vs 4.3%; p=.006) and PIK3CA GA (29.5% vs 21.8%; p=.02), but less gLOH high (6.8% vs 15.9%; p=.009), CDKN2A loss (12.4% vs 38.3%; p&lt;.0001), MTAP loss (10.1% vs 25.1%; p&lt;.0001) and FGFR3 GA (9.7% vs 18.1%; p=.002). TP53 GA were similar (62.3% vs 60.3%). Cohort 2: 22 (3.7%) featured CDH1 mutations. Compared with the CDH1 WT pts, the age, gender, ethnicity and ECOG status were similar. Evaluation of the RWCOS showed that CDH1 mutation was associated with less favorable outcomes for 270 UBC pts treated with immune checkpoint inhibitors (ICPI) including rwPFS (2.8 vs 3.5 months; p=.096) and rwOS (3.3 vs 9.5 months; p=.03). Similar comparisons for 316 UBC pts treated with chemotherapy showed no significant adverse impact of CDH1 mutation status on either rwPFS (7.9 vs 6.2 months) and rwOS (13.4 vs 13.4 months). Conclusions: In addition to its classic association with plasmacytoid histology, CDH1-mutated UBC features a unique CGP pattern including higher MSI and TMB status and activating GA in the MTOR pathway while harboring a lower FGFR3 GA frequency. RWCOS further supports that CDH1 mutation predicts resistance to ICPI-based treatments but does not impact responsiveness to chemotherapy. These results further support that CGP has the potential to customize the treatment and improve outcomes for UBC patients based on the determination of their genomic signatures.

A Novel Multi-Analytic Clinical Diagnostic Assay to Detect HLA Loss of Heterozygosity in Post-Hematopoietic Cell Transplant Relapse Patients

Genomic loss of heterozygosity in the HLA region (HLA LOH) can be an underlying driver of disease relapse in haploidentical and HLA mismatched hematopoietic cell transplantation (HCT) in which relapsing cells evade donor T-cell allorecognition by deleting non-shared HLA alleles through an acquired somatic uniparental disomy event. The presence of HLA LOH may indicate a loss of graft vs. leukemia effect, render treatments such as donor leukocyte infusion ineffective, and impact donor selection for subsequent allogeneic HCT. A major challenge in developing a clinical diagnostic assay to detect HLA LOH post-HCT is sensitive detection of a loss of genomic material against a background of multiple genomes. Cell enrichment may address this issue by isolating relapsed cells for downstream molecular analysis. However, detection of HLA LOH is most clinically useful early in relapse when the relapsed cells are likely in low abundance, the relapsed cells may not be a single clonal population, and the immunophenotypic aberrancies may be variable and/or unknown. To address these issues, we have developed a comprehensive multi-analytic approach to detect HLA LOH that includes sensitive flow cytometric enrichment of leukemic cells followed by genomic analysis. First, a "difference from normal” flow cytometry approach (ΔN:™), the approach used for determination of residual disease in Children's Oncology Group AML clinical trials, is utilized to characterize the aberrant cells for each patient and relapse episode to ensure specific enrichment of relapsed cells to high purity. Next, two complementary molecular assays are used, including detection of short tandem repeat (STR) loci throughout the HLA region and next-generation sequencing (NGS) of HLA loci to identify deleted HLA alleles. In combination, the two assays provide a sensitive and spatially resolved assessment of LOH across the entire HLA genomic region, enabling molecular characterization of LOH events ranging from an entire HLA haplotype, partial HLA haplotype, or a single HLA locus. The ability to detect a locus-specific HLA LOH event could be useful in mismatched unrelated HCT donor/recipient pairs which may differ at only one or two HLA loci. Validation of the flow cytometric methods and genomic assays were performed separately. DNA isolated from the flow sorting process was shown to be suitable for both genomic assays. The sensitivity of the molecular assays to detect HLA LOH was defined using artificial mixes of DNA from two individuals with allelic mismatching at various HLA loci. Cell lines with known HLA LOH were also used to confirm the performance of the molecular assays. As of this writing, 16 samples from post-HCT relapse patients were tested with this assay and HLA LOH was detected in 3 cases (19%), consistent with published reports on the frequency of HLA LOH detected in allogeneic HCT patients. Samples with a range of relapsed leukemic cells from <1% to 85% and cell sorting output from 800 to 250,000 cells all yielded valid results. Results were reported within an average of 7 days, allowing adequate time for integration into therapeutic decision making. Challenging and unusual patient samples such as those with extremely low blast counts will be presented. Initial results indicate this clinical diagnostic assay provides reliable and accurate detection of HLA LOH during relapse in post-HCT patients. Detection of HLA LOH using our multi-analytic diagnostic approach may also aid in optimizing therapeutic decisions to improve outcomes in allogeneic HCT patients.

P095 - Patient (pt) reported pain and health-related quality of life (HRQoL) by genomic loss of heterozygosity (gLOH) status in men with metastatic castration-resistant prostate cancer (mCRPC) receiving talazoparib (TALA): TALAPRO-1

P095 - Patient (pt) reported pain and health-related quality of life (HRQoL) by genomic loss of heterozygosity (gLOH) status in men with metastatic castration-resistant prostate cancer (mCRPC) receiving talazoparib (TALA): TALAPRO-1

S2429 A Rare Case of Esophageal Adenocarcinoma Presenting as an Isolated Brain Lesion 6 Years After Treatment

Introduction: Esophageal adenocarcinomas account for ∼1% of all cancers in the U.S. The prevalence of central nervous system (CNS) metastases associated with these cancers is around 1.8%. Response rates to standard of care are poor and prognosis is dismal. Often CNS involvement is associated with widely metastatic disease, herein, we present a case of a solitary brain lesion from esophageal adenocarcinoma at first recurrence. Case Description/Methods: A 72-year-old-male with a 40 pack-year smoking presented with progressive dysphagia in March 2015. Contrast enhanced CT of the chest, abdomen and pelvis revealed a constricting mass at the esophagogastric junction that led to endoscopy guided biopsy revealing esophageal adenocarcinoma. He underwent neoadjuvant chemotherapy (cisplatin/5-fluorouracil) and radiation therapy followed by esophagogastrectomy in July of 2015 where diagnosis of stage IIIBT3N2cM0 esophageal adenocarcinoma was confirmed. Clinical and imaging surveillance for 6 years had not shown any progression of cancer. However, in June of 2021, he presented with altered mental status that led to contrast enhanced brain MRI showing a T2 hyperintense left parietal lobe mass with an 8 mm midline shift and surrounding vasogenic edema (Figure). FDG PET-CT head to toes did not show extracranial recurrence. He underwent left posterior temporal craniotomy for resection of tumor confirming the diagnosis of metastatic esophageal adenocarcinoma. IHC showed positivity of cytokeratin7, CDX2 and SATB2. Whole exome sequencing revealed mutations in ARID1A, FH, and TP53 with variants of unknown significance of ATM and CDH. Tumor displayed proficient mismatch repair protein, a combined positive score of 15 for PD-L1, and negative Her2/Neu. Further sequencing showed tumor mutational burden of 4, no genomic loss of heterozygosity, and stable microsatellite repeats. He received gamma-knife radiation to the solitary left temporal lobe lesion. Patient continues to maintain his quality of life with no evidence of clinical and radiographic recurrence. Discussion: Isolated brain metastasis from esophageal adenocarcinoma is a very rare phenomenon. Limited data suggests that the survival of patients with isolated CNS lesions is < 1 year, however, achieving pathologic complete response after neoadjuvant chemo-radiation therapy has shown to improve survival. These esophageal cancers with isolated CNS metastases may share a unique genomic profile and more research is required to understand their alterations.Figure 1.: MRI of the brain. 1A- Pre-op axial OLEA of L. temporal lobe tumor (06/2021), 1B- Pre-op axial coronal T1 (06/2021), 1C- Follow-up T2 MRI.