Patient survey on cancer genomic medicine in Japan under the national health insurance system.

In Japan, comprehensive genomic profiling (CGP) tests have been reimbursed under the national health care system for solid cancer patients who have finished standard treatment. More than 50,000 patients have taken the test since June 2019. We performed a nation-wide questionnaire survey between March 2021 and July 2022. Questionnaires were sent to 80 designated Cancer Genomic Medicine Hospitals. Of the 933 responses received, 370 (39.7%) were web based and 563 (60.3%) were paper based. Most patients (784, 84%) first learned about CGP tests from healthcare professionals, and 775 (83.1%) gave informed consent to their treating physician. At the time of informed consent, they were most worried about test results not leading to novel treatment (536, 57.4%). On a scale of 0-10, 702 respondents (75.2%) felt that the explanations of the test result were easy to understand (7 or higher). Ninety-one patients (9.8%) started their recommended treatment. Many patients could not receive recommended treatment because no approved drugs or clinical trials were available (102/177, 57.6%). Ninety-eight patients (10.5%) did not wish their findings to be disclosed. Overall satisfaction with the CGP test process was high, with 602 respondents (64.5%) giving a score of 7-10. The major reason for choosing 0-6 was that the CGP test result did not lead to new treatment (217/277, 78.3%). In conclusion, satisfaction with the CGP test process was high. Patients and family members need better access to information. More patients need to be treated with genomically matched therapy.

Leveraging non-coding regions to guarantee the accuracy of small-sized panel-based tumor mutational burden estimates.

Accurate estimation of tumor mutational burden (TMB) as a predictor of responsiveness to immune checkpoint inhibitors in gene panel assays requires an adequate panel size. The current calculations of TMB only consider coding regions, while most of gene panel assays interrogate non-coding regions. Leveraging the non-coding regions is a potential solution to address this panel size limitation. However, the impact of including non-coding regions on the accuracy of TMB estimates remains unclear. This study investigated the validity of leveraging non-coding regions to supplement panel size using the OncoGuide NCC Oncopanel System (NOP). The aim of this study was to evaluate test performance against orthogonal assays and the association with responsiveness to immune checkpoint inhibitors was not included in the evaluation. We compared TMB status and values between TMB calculated only from coding regions (NOP-coding) and from both coding and non-coding regions (NOP-overall) using whole exome sequencing (WES) and FoundationOne®CDx (F1CDx) assay. Our findings revealed that NOP-overall significantly improved the overall percent agreement (OPA) with TMB status compared with NOP-coding for both WES (OPA: 96.7% vs. 73.3%, n = 30) and F1CDx (OPA: 90.0% vs. 73.3%). Additionally, the mean difference in TMB values compared with WES was lower for NOP-overall (3.55 [95% CI: 0.98-6.13]) than for NOP-coding (6.22 [95% CI: 3.73-8.70]). These results exemplify the utility of incorporating non-coding regions to maintain accurate TMB estimates in small-sized panels.

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.

Guidelines for Handling of Cytological Specimens in Cancer Genomic Medicine.

Rapid advances are being made in cancer drug therapy. Since molecularly targeted therapy has been introduced, personalized medicine is being practiced, pathological tissue from malignant tumors obtained during routine practice is frequently used for genomic testing. Whereas cytological specimens fixed mainly in alcohol are considered to be more advantageous in terms of preservation of the nucleic acid quality and quantity. This article is aimed to share the information for the proper handling of cytological specimens in practice for genomic medicine based on the findings established in "Guidelines for Handling of Cytological Specimens in Cancer Genomic Medicine (in Japanese)" published by the Japanese Society of Clinical Cytology in 2021. The three-part practical guidelines are based on empirical data analyses; Part 1 describes general remarks on the use of cytological specimens in cancer genomic medicine, then Part 2 describes proper handling of cytological specimens, and Part 3 describes the empirical data related to handling of cytological specimens. The guidelines indicated proper handling of specimens in each fixation, preparation, and evaluation.

The Japanese Society of Pathology Practical Guidelines on the handling of pathological tissue samples for cancer genomic medicine.

Clinical cancer genomic testing based on next-generation sequencing can help select genotype-matched therapy and provide diagnostic and prognostic information. Pathological tissue from malignant tumors obtained during routine practice are frequently used for genomic testing. This article is aimed to standardize the proper handling of pathological specimens in practice for genomic medicine based on the findings established in "Guidelines on the handling of pathological tissue samples for genomic medicine (in Japanese)" published by The Japanese Society of Pathology (JSP) in 2018. The two-part practical guidelines are based on empirical data analyses; Part 1 describes the standard preanalytic operating procedures for tissue collection, processing, and storage of formalin-fixed paraffin-embedded (FFPE) samples, while Part 2 describes the assessment and selection of FFPE samples appropriate for genomic testing, typically conducted by a pathologist. The guidelines recommend that FFPE sample blocks be used within 3 years from preparation, and the tumor content should be ≥30% (minimum 20%). The empirical data were obtained from clinical studies performed by the JSP in collaboration with leading Japanese cancer genome research projects. The Japanese Ministry of Health, Labour, and Welfare (MHLW) recommended to comply with the JSP practical guidelines in implementing cancer genomic testing under the national health insurance system in over 200 MHLW-designated core and cooperative cancer genome medicine hospitals in Japan.

Detection of Lung Cancer Cells in Solutions Using a Terahertz Chemical Microscope.

Cancer genome analysis has recently attracted attention for personalized cancer treatment. In this treatment, evaluation of the ratio of cancer cells in a specimen tissue is essential for the precise analysis of the genome. Conventionally, the evaluation takes at least two days and depends on the skill of the pathologist. In our group, a terahertz chemical microscope (TCM) was developed to easily and quickly measure the number of cancer cells in a solution. In this study, an antibody was immobilized on a sensing plate using an avidin-biotin reaction to immobilize it for high density and to improve antibody alignment. In addition, as the detected terahertz signals vary depending on the sensitivity of the sensing plate, the sensitivity was evaluated using pH measurement. The result of the cancer cell detection was corrected using the result of pH measurement. These results indicate that a TCM is expected to be an excellent candidate for liquid biopsies in cancer diagnosis.

Cancer genomic medicine in Japan.

Advances in cancer research have revolutionized the way cancer is diagnosed and treated. Any cancer is now known to be an amalgamation of many subtypes, each carrying its specific cancer-causing gene or oncogene. It is also evident that a given oncogene is often present across a wide range of cancer subtypes, albeit at different frequencies. These lines of information have brought cancer genomic medicine (CGM) to the clinic, where genetic information is used to optimize therapeutic intervention. In 2017, the Expert Meeting for Cancer Genomic Medicine Promotion Consortium in the Ministry of Health, Labour and Welfare (MHLW) of Japan submitted a blueprint for the CGM platform in Japan. Accordingly, the MHLW designated a total of 206 hospitals that conduct cancer gene panel testing under the national health insurance system and established the Center for Cancer Genomics and Advanced Therapeutics to store genomic/clinical information of cancer patients. Since June 2019, the CGM officially started in Japan.

Japanese General Clinical Oncologists' Knowledge and Real-world Experiences of Cancer Genomic Medicine: A Nationwide Web-based Survey Study.

Introduction: In Japan, insurance began covering two cancer gene panel tests in 2019. However, the availability of these tests remains limited to 247 facilities (as of October 2023). This survey-based study assessed the knowledge and recognition of cancer genomic medicine by physicians involved in cancer treatment. Methods: Written requests for participation in a web-based questionnaire survey were sent to 14,579 affiliated general clinical oncologists certified by the Japanese Board of Cancer Therapy. The survey was conducted from July 1 to 31st, 2021. Data between physicians affiliated with cancer genome hospitals and noncancer genome hospitals and between regions of Japan were compared. Results: In total, 2,402 valid responses were analyzed. Of the respondents, 1,296 and 1,106 were physicians working at cancer and noncancer genome hospitals, respectively. Physicians working at cancer genome hospitals showed significantly higher results for both knowledge of cancer genomic medicine and experience in cancer gene panel test performance compared with those working at noncancer genome hospitals. There were no significant regional differences in the percentage of physicians who reported having performed cancer gene panel tests. Conclusions: The survey results suggest a disparity in the knowledge of cancer genomic medicine between physicians working at cancer genome hospitals and those working at noncancer genome hospitals; this disparity should be addressed by stakeholders. Closer collaboration between these facilities may be necessary to achieve national dissemination of cancer genomic medicine.

Explainable AI for Estimating Pathogenicity of Genetic Variants Using Large-Scale Knowledge Graphs.

BACKGROUND: To treat diseases caused by genetic variants, it is necessary to identify disease-causing variants in patients. However, since there are a large number of disease-causing variants, the application of AI is required. We propose AI to solve this problem and report the results of its application in identifying disease-causing variants. METHODS: To assist physicians in their task of identifying disease-causing variants, we propose an explainable AI (XAI) that combines high estimation accuracy with explainability using a knowledge graph. We integrated databases for genomic medicine and constructed a large knowledge graph that was used to achieve the XAI. RESULTS: We compared our XAI with random forests and decision trees. CONCLUSION: We propose an XAI that uses knowledge graphs for explanation. The proposed method achieves high estimation performance and explainability. This will support the promotion of genomic medicine.

The evolution of cancer genomic medicine in Japan and the role of the National Cancer Center Japan.

The journey to implement cancer genomic medicine (CGM) in oncology practice began in the 1980s, which is considered the dawn of genetic and genomic cancer research. At the time, a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells, which led to the development of molecular targeted therapies in the 2000s and beyond. Although CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients, the National Cancer Center (NCC) of Japan has already contributed considerably to CGM advancement for the conquest of cancer. Looking back at these past achievements of the NCC, we predict that the future of CGM will involve the following: 1) A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be developed. The quantity and quality of these samples will be compatible with omics analyses. All biobank samples will be linked to longitudinal clinical information. 2) New technologies, such as whole-genome sequencing and artificial intelligence, will be introduced and new bioresources for functional and pharmacologic analyses (e.g., a patient-derived xenograft library) will be systematically deployed. 3) Fast and bidirectional translational research (bench-to-bedside and bedside-to-bench) performed by basic researchers and clinical investigators, preferably working alongside each other at the same institution, will be implemented; 4) Close collaborations between academia, industry, regulatory bodies, and funding agencies will be established. 5) There will be an investment in the other branch of CGM, personalized preventive medicine, based on the individual's genetic predisposition to cancer.

Undifferentiated embryonal sarcoma of the liver occurring in an adolescent: a case report with genomic analysis.

BACKGROUND: Undifferentiated embryonal sarcoma of the liver (UESL) is a rare malignant mesenchymal tumor that usually occurs in children and is rarely diagnosed in adults. CASE PRESENTATION: The case was a female in her late 20s who presented with a huge liver mass found upon the examination of fever. Imaging analysis showed a well-defined mass measuring 9 cm in the largest dimension in the right posterior segment of the liver. The patient underwent right hemi-hepatectomy. Histopathological studies revealed that the circumscribed tumor was composed of a proliferation of atypical epithelioid to spindle-shaped cells with pleomorphic nuclei arranged in haphazard pattern. Histopathological features observed in immunohistochemical analyses confirmed a final diagnosis of UESL. Genome analysis using FoundationOne CDx revealed 11 somatic mutations including TP53 (R196*) and STK11 (F354L). Adjuvant chemotherapy with ifosfamide and etoposide was performed, and the case has been followed up without recurrence for 1 year after hepatectomy. CONCLUSIONS: A UESL should be considered in the differential diagnosis of large and well-defined solid liver lesions. Although the prognosis of UESL is extremely unfavorable, aggressive surgical resection with adjuvant chemotherapy and genomic analysis may be helpful for ensuring long-term survival.

[Roles of Pharmacists in Cancer Genomic Medicine].

The development of cancer genomic medicine has been embraced as an important new policy issue in "The 3rd Basic Plan to Promote Cancer Control Programs" formulated by the Japanese government. Cancer-associated gene panel testing has been recognized by the public health insurance system since July 2019, and is a critical component of the clinical implementation of genomic science. Because of this dynamic change in cancer medicine, pharmacists are now expected to acquire knowledge about genomic science, and to apply it to individualized and appropriate pharmacotherapies. This review outlines the roles of pharmacists in cancer genomic medicine.