Comprehensive Genomic Profiling Testing Research Articles

CDK12 alterations and ARID1A mutations are predictors of poor prognosis and therapeutic targets in high-grade salivary gland carcinoma: analysis of the National Genomic Profiling Database.

Due to the diversity of histopathologic types in salivary gland carcinoma, genomic analysis of large cohorts with next-generation sequencing by histologic type has not been adequately performed. We analysed data from 93 patients with salivary duct carcinoma and 243 patients with adenoid cystic carcinoma who underwent comprehensive genomic profiling testing in the Center for Cancer Genomics and Advanced Therapeutics database, a Japanese national genome profiling database. We visualised gene mutation profiles using the OncoPrinter platform. Fisher's exact test, Kaplan-Meier analysis, log-rank test and Cox regression models were used for statistical analysis. In salivary duct carcinoma, a population with CDK12 and ERBB2 co-amplification was detected in 20 of 37 (54.1%) patients with ERBB2 amplification. We identified five loss-of-function variants in genes related to homologous recombination deficiency, such as BRCA2 and CDK12. Cox survival analysis showed that CDK12 and ERBB2 co-amplification is associated with overall survival (hazard ratio, 3.597; P=0.045). In salivary duct carcinoma, NOTCH1 mutations were the most common, followed by mutations in chromatin modification genes such as KMT2D, BCOR, KDM6A, ARID1A, EP300 and CREBBP. In the multivariate Cox analysis, activating NOTCH1 mutations (hazard ratio, 3.569; P=0.009) and ARID1A mutations (hazard ratio, 4.029; P=0.034) were significantly associated with overall survival. CDK12 and ERBB2 co-amplification is associated with a poor prognosis in salivary duct carcinoma. Chromatin remodelling genes are deeply involved in tumour progression in adenoid cystic carcinoma. One such gene, ARID1A, was an independent prognostic factor. In salivary duct carcinoma and adenoid cystic carcinoma, there might be minor populations with mutations that could be targeted for treatment with the synthetic lethality approach.

BRAF mutations and concurrent alterations in patients with soft tissue sarcoma.

BRAF alterations, including V600E and non-V600E mutations and fusions, in soft tissue sarcoma (STS) have been identified in a limited case series. Here, we aimed to evaluate the frequency of BRAF mutations and concurrent alterations in STS to understand their therapeutic action. In this retrospective analysis, we included data from 1964 patients with advanced STS who underwent comprehensive genomic profiling tests at hospitals in Japan between June 2019 and March 2023. The prevalence of BRAF and recurrent concurrent gene alterations were also investigated. BRAF mutations were detected in 24 (1.2%) of 1964 STS patients, with a median age of 47 (range 1-69) years. BRAF V600E was detected in 11 (0.6%) of the 1964 patients with STS, BRAF non-V600E mutations in 9 (4.6%), and BRAF fusions were detected in 4 (0.2%). BRAF V600E was identified in 4 (0.2%) cases of malignant peripheral nerve sheath tumors. The most common concurrent alteration was CDKN2A (11 cases, 45.8%), and the frequency was equivalent to that of the BRAF V600E (5/11 cases, 45.5%) and non-V600E (5/9 cases, 55.6%) groups. Recurrent concurrent alterations, such as TERT promoter mutations (7 cases, 29.2%), were detected at the same frequency in the V600E and non-V600E groups. In contrast, TP53 alterations (4/9 cases, 44.4%) and mitogen-activated protein kinase (MAPK)-activating genes, including NF1, GNAQ, and GNA11 (3/9 cases, 33.3%), were identified as relatively higher in the non-V600E group than in the V600E group (each 1/11 case, 9.1%). We identified BRAF alterations at a rate of 1.2% in all patients with advanced STS. Among them, BRAF V600E and BRAF fusions account for 45.8% and 16.7%, respectively. Collectively, our findings support the clinical characteristics and therapeutic strategies for patients with BRAF-altered advanced STS.

Impact of patient travel time on disparities in precision oncology clinical trials.

3113 Background: Precision oncology revolutionizes cancer care, allowing personalized treatments to improve outcomes. Precision oncology often entails participation in genotype-matched clinical trials, resulting in referrals from institutions providing comprehensive genomic profiling (CGP) testing to those conducting these trials. It is still being determined whether there are regional disparities in precision oncology. Methods: We conducted a retrospective review of 1127 patients (pts) referred to National Cancer Center Hospital (NCCH) for participation in genotype-matched clinical trials following CGP testing performed between June 2020 and June 2022. Travel distance and time were calculated utilizing Google Maps from the patient's residence to the NCCH. A total of 23 covariates were preselected and dichotomized per previous research or expert consensus as follows: age, sex, performance status, body mass index, tumor type, number of lines of prior therapies, number of metastatic sites, liver metastases, brain metastases, pleural or peritoneal effusions, biopsiability, neutrophil, hemoglobin, platelet, albumin, creatinine, total bilirubin, LDH, AST, CRP, place of residence (urban vs. rural), referring hospitals, and household income. All independent variables associated with participation in genotype-matched trials (P < 0.20) were included in a multivariable model, and variable importance was calculated using a machine learning (ML) model (gradient-boosted decision tree). Results: A total of 127 (11%) of 1127 pts were enrolled in the genotype-matched trials. Of 127 pts, 82 (65%) and 45 (35%) participated in phase 1 trials and phase 2/3 trials, respectively. The overall median travel distance and time were 38 km (interquartile range [IQR] 21–107) and 55 minutes (IQR 35–110), respectively. In multivariable regression, travel distance (≥100km vs. <100km) was not associated with the proportion of genotype-matched trial participation (9% vs. 12%; odds ratio [OR], 0.68; 95% confidence interval [CI], 0.42–1.07; P = 0.11); however, in pts with travel time ≥120 minutes, the proportion of genotype-matched trial participation was significantly lower than those with travel time < 120 minutes (7% vs. 13%; OR, 0.54; 95% CI, 0.32–0.89; P = 0.019). The proportion of genotype-matched trial participation decreased as travel time increased from <40 minutes to 40–120 minutes to ≥120 minutes (13% vs. 12% vs. 7%, respectively; OR, 0.67; 95% CI, 0.50–0.88; P = 0.006). Travel time was also identified as an important factor in the ML model, whereas low-income and residence in rural areas were of minor importance. Conclusions: Patients with travel time ≥120 minutes were less likely to participate in genotype-matched clinical trials than those with travel time <120 minutes. Regional disparities may be creating inequities in precision oncology, which warrant immediate action, including decentralization of clinical trials.

Actionability of comprehensive genomic profiling compared to the tissue-based and plasma-based assay in patients with metastatic breast cancer: A real-world study.

1101 Background: Comprehensive genomic profiling (CGP) was officially approved in August 2021 in Japan under the national health insurance system with three CGP tests in June 2019: FoundationOne CDx (F1CDx), OncoGuide NCC Oncopanel (NCC), which are tissue-based assay (TBA), and FoundationOne Liquid CDx (F1LCDx, starting in August 2021) which is plasma-based panel (PBA). The Center for Cancer Genomics and Advanced Therapeutics (C-CAT) has collected genomic and clinical data of 2,617 Japanese breast cancer patients as of October 2022. Here we assess these PBA and TBA to detect pathogenic or driver alterations informative for matched therapy in patients with metastatic breast cancer (mBC). Methods: We queried consecutive mBC patient clinical-genomic data through the C-CAT Research-Use Portal from June 2019 to October 2022 were categorized based on PBA or TBA. We used ClinVar to identify if the called somatic alterations were pathogenic or likely pathogenic, and BoostDM (https://www.intogen.org/boostdm/search) to identify potential driver mutations of breast cancer. The proposed rate of matched therapy was determined. The incidence rates were compared using the Pearson χ2 test. Results: Of 2,617 pts who underwent the CGP test, 2,259 (86%) received TBA (74% F1CDx and 12% NCC). The proportion of pts with ≥1 pathogenic variant with PBA and TBA was not significant (71.5%vs.72.7%; p=0.88), but the proportion of pts with ≥1 driver mutation was significantly higher with PBA than TBA (75.4% vs. 69.8%; p = 0.03). Regarding the proportion of pts who matched therapy or clinical trials presented among the pts for whom data were available, PBA was significantly lower than TBA (27.7% vs.38.5%, p < 0.001). Although data on post-treatment is still being collected, the proportion of tested patients that received matched therapies recommended by molecular tumor boards of each institute was significantly lower for PBA (4.2%vs. 8.3%; p = 0.007). Conclusions: This study is the first analysis of CGP for mBC in Japan using the C-CAT utilization program. Although significant alterations were well-detected in PBA, the proportion of pts who received matched-therapy post-testing was low for PBA. Possible causes include that PBA has fewer companion diagnoses than TBA in Japan and that PBA is more often used in later lines.

The impact of single gene testing (SGT) on subsequent comprehensive genomic profiling (CGP) success in community oncology practice for advanced non-small cell lung cancer (NSCLC): Results from a prospective observational reference laboratory testing program.

6506 Background: CGP concurrently tests tumor tissue for guideline-recommended predictive biomarkers for optimal therapy selection and identification of clinical trials in NSCLC patients. A common practice in the community oncology setting is to first order SGT, then consider CGP when SGT results are negative or after treatment failure. Given the limited tissue available and the scope of alterations not tested by SGT, we sought to characterize the effects of prior SGT on subsequent CGP testing success, and therapeutic opportunities identified by CGP beyond SGT for NSCLC patients in the community setting. Methods: Reference laboratory information systems were used to prospectively contact clinicians across 80 community practices who ordered at least 1 SGT for guideline-recommended genomic variants in NSCLC. CGP was offered for their patients prior to SGT or upon receipt of negative SGT results. SGT included individual assays for BRAF, EGFR, KRAS, MET exon 14 skipping mutations; ALK, RET, and ROS1 rearrangements; and PD-L1 IHC . CGP included DNA-seq for mutations, copy number variants in 523 genes including guideline-recommended genomic variants, MSI, and tumor mutational burden; RNA-seq for rearrangements/fusions/splice variants; and PD-L1 IHC. Results: Among a total of 580 NSCLC patients with CGP ordered (May 2021-December 2022), 168 (29%) had ≥1 SGT ordered prior to CGP (median=5). No patients had all SGT performed, with untested cases ranging from 10% for ALK to 90% for MET exon 14. The same FFPE tissue block was used for CGP in 150/168 (89%) of cases with prior negative SGT. Compared to CGP-only cases, CGP for cases with prior negative SGT was canceled twice as often at tissue review (16% vs 7%; p=.001), had higher DNA extraction failures (13% vs 8%; p=.09), and lower DNA sequencing success (70% vs 83%, p<.001). CGP detected guideline-recommended variants in 51% of all cases. Among prior negative SGT cases, frequencies were higher in genes where SGT was performed less often and is less sensitive than CGP RNA-seq ( RET fusions , MET exon 14 skipping). CGP also identified guideline-recommended variants in genes with no SGT offered during the study period ( ERBB2 mutations , NTRK2/3 fusions), as well as variants with emerging evidence for FDA expedited program-designated clinical trial therapies in 28% of patients, including NRG1 fusions and BRAF non-V600E , KEAP1, KRAS non-G12C, NFE2L2, STK11, and TP53 Y220C mutations. Conclusions: Prior negative SGT doubled subsequent CGP test cancellations for NSCLC due to tissue insufficiency and increased CGP DNA extraction failures. SGT practice in the community oncology setting does not meet practice guideline recommendations and negatively impacts the potential benefit of subsequent CGP for NSCLC patients.

Improved outcomes from reflex comprehensive genomic profiling-guided precision therapeutic selection across a major US healthcare system.

6622 Background: An ever-increasing number of biomarker-guided therapies, some with pan-cancer indications have expanded the oncologist’s toolbox for fighting advanced cancer. Despite this, not all advanced cancer patients receive tumor genomic testing, or are tested for a limited number of targets. Still others are tested too late in their care journey to benefit from precision therapy. To assess the impact of removing testing barriers, we developed a reflex testing protocol where comprehensive genomic profiling (CGP) was routinely ordered by pathologists at time of diagnosis for advanced cancer patients. Methods: Reflex CGP testing was primarily initiated by the pathologist at the time of advanced cancer diagnosis. Testing was performed between 2019 and 2021 via CGP using the ProvSeq 523 lab-developed test, and testing was performed at no cost to the patient. Post-CGP, stage 4 patients were followed for ≥ 12 months. We assessed time to therapy, therapy selection, and overall survival (OS). Therapies were stratified by presence of biomarkers associated with approved targeted therapies (TT), presence of biomarkers for immunotherapies (IO), and/or therapies that were guideline based (GB) and not associated with a specific biomarker. As much key patient information is only consistently available in free-text medical charts, we implemented a novel natural-language processing (NLP) approach based on deep learning and large language models to accelerate abstraction. Results: A cohort of 1,423 advanced cancer patients met the study criteria. The median age was 66 years, 53% were female, and 82% white. The 3 most tested tumor types were 22% non-small cell lung cancer, 16% colorectal cancer, and 12% breast. Overall, 49% (N=704) of patients had a biomarker result considered actionable for an approved TT or IO. Median (IQR) time-to-treatment initiation post-CGP was 19 (2-70) days. In patients with no actionable TT or IO biomarkers (N=719), 63% were treated with chemotherapy-based regimens, 11% with GB, 17% with unmatched TT, and 8% with unmatched IO. Of patients who had only an actionable TT biomarker (N=287), 18% received matched TT and 13% received GB. 36% of patients with only an actionable IO biomarker (N=317) received matched IO monotherapy. 48% of patients with both actionable TT and IO biomarkers (N=100) received matched TT or IO monotherapy, and 5% received GB. Across all tumor types, patients receiving a TT had better OS compared to patients receiving chemotherapy with 12 months OS (%) of 70.1 (95% CI=64.4 - 76.3) for TT-treated patients, compared to 62.9 (95% CI=58.8 - 67.3) for chemotherapy only. Conclusions: CGP-guided precision therapy use is associated with significantly higher survival in a reflex testing population. A reflex protocol can overcome key barriers to the use and timing of genomic testing to improve access to these life-extending treatment modalities.

Prevalence of psychological distress, quality of life, and satisfaction among patients and family members following comprehensive genomic profiling testing: Protocol of the Quality of life for Cancer genomics and Advanced Therapeutics (Q-CAT) study.

Precision medicine is rapidly changing the diagnostic and treatment spectrum of oncology. In May 2019, comprehensive genomic profiling (CGP) (somatic and/or germline) was approved for reimbursement in Japan. While the promise of novel and targeted therapies has elevated hopes for the benefits of CGP, the lack of relevant genomic findings and/or limited access to relevant therapies remain important themes in this field. These challenges may also negatively influence the psychology of both cancer patients and their family members. However, few studies have reported longitudinal data on quality of life (QOL) with CGP. Here, we report the protocol of a prospective study, Q-CAT (QOL for Cancer genomics and Advanced Therapeutics among patients and their family members), which aims to explore the mental burden on patients and families arising from the implementation of CGP testing by collecting real-world longitudinal data using outcomes obtained with an electronic patient report, known as ePRO. This study has been registered with the Japan Registry of Clinical Trials (jRCT1030200039).

Human resources for administrative work to carry out a comprehensive genomic profiling test in Japan.

Comprehensive genomic profiling (CGP) tests have been nationally reimbursed in Japan since June 2019 under strict restrictions, and over 46,000 patients have taken the test. Core Hospitals and Designated Hospitals host molecular tumor boards, which is more time-consuming than simply participating in them. We sent a questionnaire to government-designated Cancer Genomic Medicine Hospitals, including all 12 Core Hospitals, all 33 Designated Hospitals, and 117 of 188 Cooperative Hospitals. The questionnaire asked how much time physicians and nonphysicians spent on administrative work for cancer genomic medicine. For every CGP test, 7.6 h of administrative work was needed. Physicians spent 2.7 h/patient, while nonphysicians spent 4.9 h/patient. Time spent preparing for molecular tumor boards, called Expert Panels, was the longest, followed by time spent participating in Expert Panels. Assuming an hourly wage of ¥24,000/h for physicians and ¥2800/h for nonphysicians, mean labor cost was ¥78,071/patient. On a monthly basis, more time was spent on administrative work at Core Hospitals compared with Designated Hospitals and Cooperative Hospitals (385 vs. 166 vs. 51 h/month, respectively, p < 0.001). Consequently, labor cost per month was higher at Core Hospitals than at Designated Hospitals and Cooperative Hospitals (¥3,951,854 vs. ¥1,687,167 vs. ¥487,279/month, respectively, p < 0.001). Completing a CGP test for a cancer patient in Japan is associated with significant labor at each hospital, especially at Core Hospitals. Streamlining the exchange of information and simplifying Expert Panels will likely alleviate this burden.

Comprehensive Genome profile testing in head and neck cancer

ObjectiveHead and neck cancer (HNC) is a tumor occurring in various primary sites with limited chemotherapy options for its treatment. Recently, comprehensive genomic profiling (CGP) testing has become clinically widespread. In this study, we examined the utility of CGP in diagnosing and treating HNC. MethodsThis study included 29 patients with HNC who underwent CGP testing at the Gifu University Hospital between December 2019 and April 2022. We analyzed the types of gene mutations and tumor mutational burden (TMB) based on the CGP results. Squamous cell carcinoma accounted for 55.2%, and other cancers accounted for 44.8%. And we investigated the correlation of prognosis with gene mutations and TMB. ResultsGene mutations were detected in TP53(48.3%), CDKN2A (27.6%), CDKN2B (17.2%), NOTCH1 (17.2%), PIK3CA (17.2%), ARID1A (13.8%), and NF1 (13.8%). TP53, CDKN2A and CDKN2B mutations significantly decreased survival rate in HNC. Five cases (17.2%) were TMB-high and 82.8% were TMB-low. In SCC cases treated with immune checkpoint inhibitors, TMB-high had better Overall survival than TMB-low. And all patients with TMB-high were oropharyngeal cancer. ConclusionAlthough there were no cases in which effective treatment was actually performed based on the results of CGP, many gene mutations have been detected and several gene mutations correlated with prognosis. Furthermore, TMB can be used as a biomarker to predict the therapeutic effects of immune checkpoint inhibitors in cases of SCC.

Comprehensive Genomic Profiling Detects Hereditary Cancers and Confers Survival Advantage in Patients With Gynaecological Cancers.

The clinical benefits of comprehensive genomic profiling (CGP) of tumours in patients with gynaecological cancers remain unknown. We investigated the utility of CGP in assessing patient survival and its efficacy in detecting hereditary cancers in gynaecological patients. We retrospectively analysed the medical records of 104 gynaecological patients who underwent CGP between August 2018 and December 2022. The detection of actionable and accessible genomic alterations and administration of targeted therapy, as recommended by the molecular tumour board (MTB), were assessed. The overall survival (after second-line treatment in cervical and endometrial carcinomas and after platinum-resistant recurrence in ovarian carcinoma) was compared between patients with or without administration of MTB-recommended genotype-matched therapy. Germline findings were assessed using a variant allele frequency-tumour content graph. Among 104 patients, actionable and accessible genomic alterations were observed in 53 patients. Matched therapy was applied in 21 patients, comprising administration of repurposing itraconazole (n=7), immune checkpoint inhibitors (n=7), poly (ADP-ribose) polymerase inhibitors (n=5), and others (n=2). The median overall survival of patients receiving and not receiving matched therapy were 19.3 months and 11.2 months, respectively (p=0.036, hazard ratio=0.48). Among 12 patients with hereditary cancers, 11 patients were previously undiagnosed. Seven patients had hereditary breast and ovarian cancer, and five had other cancer. The implementation of CGP testing prolonged overall survival in gynaecological cancer as well as provided an opportunity for genetic counselling for newly-diagnosed patients with hereditary cancers and their families.

Budget impact analysis of comprehensive genomic profiling for untreated advanced or recurrent solid cancers in Japan

AimsIn Japan, the use of comprehensive genomic profiling (CGP) is only available for cancer patients who have no standard of care (SoC), or those who have completed SoC. This may lead to missed treatment opportunities for patients with druggable alterations. In this study, we evaluated the potential impact of CGP testing before SoC on medical costs and clinical outcome in untreated patients with advanced or recurrent biliary tract cancer (BTC), non-squamous non-small cell lung cancer (NSQ-NSCLC), or colorectal cancer (CRC) in Japan between 2022 and 2026.Materials and methodsWe constructed a decision-tree model reflecting the healthcare environment of Japan, to estimate the clinical outcome and medical costs impact of CGP testing by comparing two groups (with vs without CGP testing before SoC). The epidemiological parameters, detection rates of druggable alterations, and overall survival were collected from literature and claims databases in Japan. Treatment options selected based on druggable alterations were set in the model based on clinical experts’ opinions.ResultsIn 2026, the number of untreated patients with advanced or recurrent BTC, NSQ-NSCLC, and CRC was estimated to be 8600, 32,103, and 24,896, respectively. Compared with the group without CGP testing before SoC, CGP testing before SoC increased druggable alteration detection and treatment rate with matched therapies in all three cancer types. The medical costs per patient per month were estimated to increase with CGP testing before SoC in the three cancer types by 19,600, 2900, and 2200 JPY (145, 21, and 16 USD), respectively.LimitationsOnly those druggable alterations with matched therapies were considered in the analysis model, while the potential impact of other genomic alterations provided by CGP testing was not considered.ConclusionsThe present study suggested that CGP testing before SoC may improve patient outcomes in various cancer types with a limited and controllable increase in medical costs.

Abstract 3225: Real-world surveillance from cancer patients about their experience of comprehensive genomic profiling tests in Japan

Abstract Introduction: Over 40,000 cancer patients have taken comprehensive genomic profiling (CGP) tests under health insurance coverage in Japan since June 2019. However, the indication is limited only to cancer patients who have finished (or are expected to finish) standard treatments. The aim of this study is to evaluate patients’ outcomes, levels of understanding, and satisfaction of the patients who received CGP tests. Methods: We performed a nationwide surveillance of 933 cancer patients who examined CGP tests at 80 institutions in Japan under the approval of the institutional ethics committee. The responses to the questionnaire (either web-based or paper-based) were from patients (81.6%) or their families (18.4%). Results: The range of patients’ age was 70s at 29.6%, followed by 60s at 26.8%, and 50s at 20.8%. The level of understanding during informed consent for the CGP tests {11 scales from 0 (lowest) to 10 (highest)} were 7 or higher in 70.8%, and those about their test results were 7 or higher in 75.2 %. The information was predominantly provided by attending physicians (78.0%) or physicians specialized in genomic medicine (19.6%), and limitedly from cancer genome medical coordinators (11.4%) and nurses (10.4%). The patients underwent FoundationOne CDx® (56.3%), FoundationOne Liquid CDx® (11.6%), or a domestic tumor/normal paired panel (OncoGuideTM NCC Oncopanel System, 14.4%). 16.2% of the patients could not recall which CGP test they received. New treatments based on the CGP testing were suggested in 46.8%, and 20.8% of them were treated with a suggested treatment by an expert panel (i.e., molecular tumor board). The treatment type was (i) approved drugs, 70.3%, (ii) clinical trials, 16.5%, (iii) patient-proposed national basket trial, 3.2%, and (iv) off-label use, 1.1%. 77.4% of the patients requested disclosure of germline findings, 10.5% declined, and 11.4% did not remember their decision. Overall satisfaction scores (11 scales) were found to be 7 or higher at 64.6%. The reasons for satisfaction included having the opportunity to learn about cancer risks of relatives (21.0%), having received detailed explanation (19.7%), having received information on new therapies (18.4%), and having the opportunity to learn about their cancer in detail (15.9%). The reason for lower scores (6 or lower) was mainly due to not receiving recommendations to a genome-matched therapy (58.3%). Conclusion: Our surveillance highlighted the significance of drug accessibility, information from interdisciplinary collaboration team, and appropriate information about the test results. The opportunity to learn about their cancer in detail was valuable for the patients as well, even when the results of CGP testing did not lead to a novel therapy. Citation Format: Katsutoshi Oda, Hidenori Kage, Manabu Muto, Katsuya Tsuchihara, Natsuko Okita, Yusuke Okuma, Junko Kikuchi, Hidekazu Shirota, Hideyuki Hayashi, Toshio Kokuryo, Daisuke Sakai, Akira Hirasawa, Makoto Kubo, Hirotsugu Kenmotsu, Nana Akiyama, Hyangri Chang, Aya Shinozaki-Ushiku, Masahiko Tanabe, Tetsuo Ushiku, Kaori Muto, Kiyoshi Miyagawa, Yasuyuki Seto. Real-world surveillance from cancer patients about their experience of comprehensive genomic profiling tests in Japan [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3225.

The DNA integrity number and concentration are useful parameters for successful comprehensive genomic profiling test for cancer using formalin-fixed paraffin embedded tissue.

The acquisition of high-quality biospecimens and the appropriate handling of these materials are indispensable for successful clinical sequencing. We developed a cancer clinical sequencing system targeting 160 cancer genes: PleSSision-Rapid. Through the PleSSision-Rapid system, we have analyzed DNA quality evaluated by DIN (DNA integrity number) with 1329 formalin-fixed paraffin embedded (FFPE) samples including 477 prospectively collected tissues for genomic test (P) and 852 archival samples after routine pathological diagnosis (A1/A2). As a result, the samples with more than DIN 2.1 was 92.0% (439/477) in prospectively collected sample (P), while it was 85.6% (332/388) and 76.7% (356/464) in two types of archival samples (A1/A2). We performed the PleSSision-Rapid sequence using the samples with over DIN 2.1 and DNA concentration >10 ng/μL with which we were able to construct a DNA library, and the probability of sequence success was almost equivalent during all types of specimen processing, at 90.7% (398/439) in (P), 92.5% (307/332) in (A1) and 90.2% (321/356) in (A2), respectively. Our result indicated the clinical benefit to prepare the prospective collection of FFPE materials for indisputable clinical sequence, and that DIN ≥ 2.1 would be a solid parameter for sample preparation of comprehensive genomic profiling tests.

Comparison of genomic profiling of circulating tumor DNA inpancreaticobiliary malignancies in plasma and bile.

Obtaining sufficient pancreaticobiliary tumor tissue for genomic profiling has limitations. Liquid biopsies using plasma do not provide sufficient sensitivity. Thus, this study aimed to determine the effectiveness of liquid biopsy between bile and plasma for identifying oncogenic and drug-matched mutations. This study created a panel of 60 significantly mutated genes specific to pancreaticobiliary cancer (PBCA) and used it for genomic analysis of 212 deoxyribonucleic acid (DNA) samples (87 bile supernatant, 87 bile precipitate, and 38 plasma) from 87 patients with PBCA. The quantity of extracted DNA from bile and plasma was compared, as were genomic profiles of 38 pairs of bile and plasma from 38 patients with PBCA. Finally, we investigated 87 bile and 38 plasma for the ability to detect druggable mutations. The amount of DNA was significantly lower in plasma than in bile (p<.001). Oncogenic mutations were identified in 21 of 38 (55%) patients in bile and nine (24%) in plasma samples (p=.005). Bile was significantly more sensitive than plasma in identifying druggable mutations (p=.032). The authors detected 23 drug-matched mutations in combined bile and plasma, including five ERBB2, four ATM, three BRAF, three BRCA2, three NF1, two PIK3CA, one BRCA1, one IDH1, and one PALB2. Liquid biopsy using bile may be useful in searching for therapeutic agents, and using the obtained genomic information may improve the prognoses of patients with PBCA. Genomic profiling of formalin-fixed paraffin-embedded tissues may provide actionable targets for molecular and immuno-oncological treatment. However, most pancreaticobiliary malignancies are unresectable and formalin-fixed paraffin-embedded tissues cannot be obtained. Although comprehensive genomic profiling tests using plasma have been used in recent years, the utility of those using bile is not clear. Our study revealed that bile identified more drug-matched mutations than plasma in advanced pancreaticobiliary cancer patients. Bile may help widen the patient population benefiting from targeted drugs.

Integrated Genomic DNA/RNA Profiling vs Fluorescence in Situ Hybridization in the Detection of MYC and BCL2 (and BCL6) Rearrangements in Large B-Cell Lymphomas: Updates Amid the New WHO Classification of Lymphoid Neoplasms.

Large B-cell lymphomas (LBCLs) are a heterogeneous group of lymphoid neoplasms whose molecular and cytogenetic profile has predictive and prognostic implications. The concept of double-hit lymphomas (DHLs) was recently updated in the fifth edition of the World Health Organization classification, with the exclusion of MYC and BCL6 rearranged tumors from the group. Now, DHLs are referred to as diffuse large B-cell lymphoma/high-grade B-cell lymphoma with MYC and BCL2 rearrangements. Fluorescence in situ hybridization (FISH) is the current gold standard for detecting rearrangements in LBCLs, but comprehensive genomic profiling (CGP) has recently been suggested to be at least as accurate as FISH in classifying these neoplasms and providing additional genetic information. We analyzed a cohort of 131 patients in whom FISH and CGP studies were performed as part of our normal clinical workflow and compared the effectiveness of FISH and CGP in detecting these clinically relevant rearrangements. Our findings are in agreement with our previously published study, which analyzed a cohort of 69 patients, supporting our hypothesis that the best approach to maximize detection of DHLs while limiting waste seems to be a combination of CGP and MYC break-apart FISH testing, the latter to capture the presence of non-IGH::MYC events. Our study supports the combined use of FISH and GCP rather than either method alone to better detect MYC and BCL2 (and BCL6) gene rearrangements.

Utility of Comprehensive Genomic Profiling Tests for Patients with Incurable Pancreatic Cancer in Clinical Practice.

Although comprehensive genomic profiling (CGP) tests have been covered under the Japanese national health insurance program since 2018, the utility and issues of CGP tests have not been clarified. We retrospectively reviewed 115 patients with incurable pancreatic cancer (IPC) who underwent CGP tests in a Japanese cancer referral center from November 2019 to August 2021. We evaluated the results of CGP tests, treatments based on CGP tests, and survival time. Eight cases (6.9%) were diagnosed as tumor mutation burden-high (TMB-H) and/or microsatellite instability-high (MSI-H). The gene mutation rates of KRAS/TP53/CDKN2A/SMAD4 were 93.0/83.0/53.0/25.2%, respectively. Twenty-five patients (21.7%) had homologous recombination deficiency (HRD)-related genetic mutations. Four patients (3.5%) having TMB-H and/or MSI-H were treated with pembrolizumab, and only two patients (1.7%) participated in the clinical trials. Patient characteristics were not significantly different between patients with and without HRD-related gene mutations. The median OS was significantly longer in the HRD (+) group than in the HRD (-) group (749 days vs. 519 days, p = 0.047). In multivariate analysis, HRD-related gene mutation was an independent prognostic factor associated with favorable OS. CGP tests for patients with IPC have the potential utility of detecting HRD-related gene mutations as prognostic factors as well as a therapeutic search.

Clinical Utility of Comprehensive Genomic Profiling in Patients with Unresectable Hepatocellular Carcinoma.

The molecular mechanism of hepatocellular carcinoma (HCC) is partially demonstrated. Moreover, in the patients receiving multiple molecular-targeted therapies, the gene alternations are still unknown. Six molecular-targeted therapies of unresectable HCC (uHCC) and comprehensive genomic profiling (CGP) have been approved in clinical practice. Hence, the utility of CGP in patients with uHCC treated with multiple molecular-targeted agents is investigated. The data of the patients with uHCC who received CGP tests were collected, retrospectively, between February 2021 and May 2022. Gene alterations detected by foundation testing, excluding variants of unknown significance, were reported in all nine patients. The samples for CGP were derived from liver tumor biopsy (n = 2), surgical specimens of bone metastases (n = 2), and blood (n = 5). The median number of systemic therapies was four. Seven patients were candidates eligible for clinical trials. One patient with a high tumor mutation burden (TMB) could receive pembrolizumab after CGP. This study presented genomic alternations after receiving multiple molecular-targeted therapies. However, further investigation needs to be conducted to develop personalized therapies and invent newer agents for treating HCC.

Clinical Outcomes of Comprehensive Genomic Profiling Tests for Gastrointestinal Cancers: Experience from Tokushima University Hospital

In Japan, cancer genome profiling (CGP) for cancer patients without standard treatment has been covered by public insurance since June 2019. This study analyzed data of 122 patients with gastrointestinal tumors who underwent CGP to clarify cancer genome medicine's current status and possible problems at the Tokushima University Hospital. The major types of cancer included pancreatic (n=30), colorectal (n=25), biliary tract (n=15), gastric (n=11), and hepatocellular carcinoma (n=8). CGP tests included F1CDx in 70 patients (57%), F1LCDx in 36 (30%), TSO500 in 14 (11%), and NCC Oncopanel in 2 (2%). Actionable gene alterations were identified in 72 patients (59%), but only 5 patients (4%) were treated for pancreatic (n=1), colorectal (n=3), and small bowel cancers (n=1). The main reasons for not receiving genotype-matched therapy included the lack of appropriate drugs or clinical trials that matched the actionable gene alterations (n=40) and the inability to participate in clinical trials (n=10). There is still not a sufficient number of patients receiving genotype-matched treatment for gastrointestinal cancers. To promote cancer genome medicine in regional areas, attempts to improve access to genotype-matched therapies are required, as well as to promote the development of new molecular-targeted drugs and clinical trials for these drugs. J. Med. Invest. 70 : 154-159, February, 2023.

Implementation of Comprehensive Genomic Profiling in Ovarian Cancer Patients: A Retrospective Analysis.

Comprehensive genomic profiling (CGP) allows for the detection of driver alterations at high resolution, but the limited number of approved targeted therapies and their high costs have contributed to its limited clinical utilization. We retrospectively compared data of 946 women with ovarian cancer (11.4% were referred to CGP, and 88.6% served as control) to examine whether CGP provides a prognosis benefit. Patient baseline parameters were similar between the groups. Cox regression analysis adjusted for age, disease stage at diagnosis, and recurrence status showed statistically significantly longer median overall survival (mOS) in the CGP group versus the control (73.4 versus 54.5 months, p < 0.001). Fifty-four patients (52.9%) had actionable mutations with potential treatments; twenty-six (48.2%) were treated with matched targeted therapy, showing a trend for longer mOS than the eighty-six women in the CGP group who were not given a suggested treatment (105.5 versus 63.6 months, p = 0.066). None of the genomic alterations predicted metastasis location. CCNE1 amplification and KRAS mutations were associated with shorter mOS. Patients with tumor mutation burden ≥4 mutations/megabase had longer mOS. High loss of heterozygosity was associated with longer mOS (99.0 versus 48.2 months, p = 0.004). CGP testing may provide both prognostic and predictive insights for treatment of patients with ovarian cancer. Prospective studies of larger cohorts are warranted.

C-CAT: The National Datacenter for Cancer Genomic Medicine in Japan.

Since June 2019, under the umbrella of the national health insurance system, Japan has started cancer genomic medicine (CGM) with comprehensive genomic profiling (CGP) tests. The Ministry of Health, Labour and Welfare (MHLW) of Japan constructed a network of CGM hospitals (a total of 233 institutes as of July 1, 2022) and established the Center for Cancer Genomics and Advanced Therapeutics (C-CAT), the national datacenter for CGM. Clinical information and genomic data from the CGP tests are securely transferred to C-CAT, which then generates "C-CAT Findings" reports containing information of clinical annotation and matched clinical trials based on the CGP data. As of June 30, 2022, a total of 36,340 datapoints of clinical/genomic information are aggregated in C-CAT, and the number is expected to increase swiftly. The data are now open for sharing with not only the CGM hospitals but also other academic institutions and industries.