OBJECTIVE:The prevalence of MSI-H and MLH1 promoter hypermethylation (MLH1-PHM) as well as Lynch syndrome in Japanese patients with endometrial cancer (EC) has not been fully revealed. There is also a recent report that the prognosis of MLH1-PHM is worse than MLH1 non-PHM in EC; however, no large-scale studies have been conducted in Japan. We investigated the prevalence of MSI-H, MLH1-PHM and Lynch syndrome in EC cases and characteristic and prognosis of them. METHODS:The 677 patients who were pathologically diagnosed with EC at the Saitama Cancer Center Hospital between 2013 and 2023 were investigated in this study. The MSI and abnormal DNA methylation of the MLH1 promoter were tested in all cases. Patients with MSI-H EC or a family history provided informed consent and examined germline testing for Lynch syndrome. RESULTS:Among the 677 ECs, 170 (25.1%) were MSI-high (MSI-H), and 105 were involved MLH1 hypermethylation. Two of 13 Lynch syndrome cases had MLH1-PHM in ECs. The MSI-H group had more G3 histology, but had a favorable prognosis with 5-year PFS and OS compared with the MSS group. The group with MLH1-PHM have more patients with G1/2 histology and more advanced disease. There was no difference in prognosis between MLH1-PHM and non-PHM groups. CONCLUSION:This study provides information on the prevalence of MSI-H and MLH1-PHM in EC in Japan. Besides, the prognostic of the MSI-H group is better than that of the MSS group, but no differences were found between the MLH1-PHM and MLH1 non-PHM groups.

APC and MUTYH are both well-known colorectal polyposis causative genes. However, 30–50

Background It is known that gene- and disease-specific evidence domains can potentially improve the capability of the ACMG/AMP classification criteria to categorize pathogenicity for variants. We aimed to include gene–disease-specific clinical, predictive, and functional domain specifications to the ACMG/AMP criteria with respect to MMR genes. Methods Starting with the original criteria (InSiGHT criteria) developed by the InSiGHT Variant Interpretation Committee, we systematically addressed specifications to the ACMG/AMP criteria to enable more comprehensive pathogenicity assessment within the ClinGen VCEP framework, resulting in an MMR gene-specific ACMG/AMP criteria. Results A total of 19 criteria were specified, 9 were considered not applicable and there were 35 variations of strength of the evidence. A pilot set of 48 variants was tested using the new MMR gene-specific ACMG/AMP criteria. Most variants remained unaltered, as compared to the previous InSiGHT criteria; however, an additional four variants of uncertain significance were reclassified to P/LP or LB by the MMR gene-specific ACMG/AMP criteria framework. Conclusion The MMR gene-specific ACMG/AMP criteria have proven feasible for implementation, are consistent with the original InSiGHT criteria, and enable additional combinations of evidence for variant classification. This study provides a strong foundation for implementing gene–disease-specific knowledge and experience, and could also hold immense potential in a clinical setting. ### Competing Interest Statement Becky Milewski previously had a role with the pilot variant classification efforts in 2020/2021. She was previously an employee of GeneDx, LLC. Lauren Currie is an employee of GeneDx, LLC Ester Borras is an employee and shareholder of Invitae Corporation. John Paul Plazzer has previously consulted as curator for an external diagnostic testing company. ### Funding Statement JPP was supported by the Alan Watt and Chris Geyer Oncology Fellowship through The Royal Melbourne Hospital Foundation and NIH PA-18-591 Administrative Supplements to Promote Data Sharing in Cancer Epidemiology Studies. ABS was supported by NHMRC Funding (APP1104808). Grant funding for MKC: Cancer Council NSW, RG19-1. In Spain, this study has been partially funded by Ministerio de Ciencia e Innovacion, which is part of Agencia Estatal de Investigacion (AEI), through the Retos Investigacion grant, number PID2019-111254RB-I00, and La Marato de TV3 (202028-30). We also thank CERCA Programme / Generalitat de Catalunya for institutional support. MG was supported by Italian Ministry of Health RC 2022. KA and GY was supported by Japan Agency Medical Research and Development (AMED) under grant JP 18kk0205004, JSPS KAKENHI Grant Number JP18K07339 and JP22K07266. We would like to thank Ms. Lubaina Koti for editing the manuscript for language, structure, and accuracy. We acknowledge Marissa Rose for analysis of an early draft of the criteria. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Data is available in published literature (Pubmed IDs are provided in the databases listed here) or online open-access databases including: ClinVar , LOVD , and InSiGHT classification websites: [https://www.insight-database.org/classifications/mmr\_integrative\_eval.html][1] and Curated evidence will be available on I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Variant classifications are published in ClinVar () and curated evidence is available on the ClinGen Evidence Repository (). * ACMG : American College of Medical Genetics and Genomics AMP : Association for Molecular Pathology B : Benign BA : Benign Stand-Alone BS : Benign Strong BP : Benign Supporting ClinGen : Clinical Genome Resource CMMRD : constitutional mismatch repair deficiency GI : gastrointestinal gnomAD : Genome Aggregation Database FDA : Food and Drug Administration (United States) HCI : Huntsman Cancer Institute HGVS : Human Genome Variation Society IARC : International Agency for Research on Cancer IHC : immunohistochemistry InSiGHT : International Society for Gastrointestinal Hereditary Tumours IVS : intervening sequence (intron) LB : likely benign LP : likely pathogenic LOVD : Leiden Open Variation Database LS : Lynch syndrome MANE : matched annotation from National Center for Biotechnology Information and European Molecular Biology Laboratory and European Bioinformatics Institute MMR : mismatch repair (genes) MSI : microsatellite instability NGS : next generation sequencing NMD : nonsense–mediated mRNA decay P : Pathogenic PVS : Pathogenic Very Strong PS : Pathogenic Strong PM : Pathogenic Moderate PP : Pathogenic Supporting SVI WG : Sequence Variant Interpretation Working Group VCEP : variant curation expert panel VUS : variant of uncertain significance [1]: https://www.insight-database.org/classifications/mmr_integrative_eval.html

Purpose: The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. Methods: Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene -specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. Results: The APC-specific criteria represented gene- and disease -informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). Conclusion: The APC-specific ACMG/AMP criteria preserved the classification of wellcharacterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use. (c) 2023 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY -NC -ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Microsatellite instability (MSI) testing, an established technique that has gained prominence in recent years for its predictive potential regarding the efficacy of immune checkpoint inhibitors, is used to evaluate DNA mismatch repair (MMR) deficiency (dMMR). As with other methods, the immunohistochemistry (IHC) of MMR proteins is also widely adopted. Although both techniques have been validated, their concordance rate remains unknown, particularly regarding non-colorectal cancer. Therefore, the aim of the present study was to explore and elucidate their concordance in the context of gastric cancer (GC). A total of 489 surgically resected primary GC tissues were analyzed to compare the results yielded by the MSI test and those from IHC. Of 488 GC cases, 56 (11.5%) exhibited a loss of MMR proteins, whereas 52 (10.7%) were classified as high-frequency MSI (MSI-H). The concordance rate between these two categories was 99.2%. The microsatellite markers BAT26 and MONO27 demonstrated 100% sensitivity and 99.5% specificity in detecting dMMR GC. In addition, histopathological analysis revealed that MSI-H was more prevalent in GCs exhibiting coexisting Tub2 and Por1 subtypes. However, four discordant cases were observed. All four cases were microsatellite-stable cases but exhibited loss of MLH1 protein expression with hypermethylation of the MLH1 promoter. The results of the present study highlight that while there is a strong concordance between MSI and IHC testing results for determining dMMR status, IHC testing may offer superior efficacy in detecting dMMR.

The prevalence of Lynch syndrome (LS)-associated DNA mismatch repair (MMR)-deficient bladder cancer (BC) has scarcely been investigated. Immunohistochemistry for four MMR proteins (MLH1, MSH2, MSH6, and PMS2) was performed in formalin-fixed paraffin-embedded (FFPE) sections prepared from the resected specimens of 618 consecutive newly diagnosed BC cases. Genetic/epigenetic analyses were performed in patients displaying the loss of any MMR proteins in the tumor. Of the 618 patients, 9 (1.5%) showed the loss of MMR protein expression via immunohistochemistry; specifically, 3, 3, 2, and 1 patients displayed the loss of MLH1/PMS2, PMS2, MSH6, and MSH2/MSH6, respectively. All nine patients were male with a median age of 68 years (63–79 years). One had been previously diagnosed as having LS with an MSH2 variant. Genetic testing demonstrated the presence of a pathogenic PMS2 variant (n = 1), a variant of uncertain significance in MSH2 (n = 1), and no pathogenic germline variants of the MMR genes (n = 1). One patient with MSH6-deficient BC did not complete the genetic testing because of severe degradation of DNA extracted from the FFPE specimen, but the patient was strongly suspected to have LS because of their history of colon cancer and MSH6-deficient upper urinary tract cancer. There remained a possibility that the remaining four patients who refused genetic testing had LS. The prevalence of LS-associated MMR-deficient BC was estimated to be 0.6–1.1% among unselected BC cases.

MET exon 14 skipping mutation, observed in 3–4% of non-small cell lung cancer (NSCLC), is emerging as a targetable alteration. In recent years, immune checkpoint inhibitors (ICI) have been effective in treating several NSCLCs. Our research aimed to investigate the characteristics of patients with NSCLCs harboring MET exon 14 mutations and their response to ICI in Japan. Among the 1954 consecutive NSCLCs diagnosed at Saitama Cancer Center between 2010 and 2019, MET exon 14 skipping mutations were detected in 68 (3.5%) NSCLCs. We evaluated their characteristics such as programmed cell death ligand 1 (PD-L1) expression. Median age of patients with NSCLCs harboring MET exon 14 skipping mutations was 73 years. PD-L1 was highly expressed in 17 (70.8%) of the 24 patients examined. Seven patients received ICI monotherapy, and three out of seven had a remarkable treatment response, resulted in objective response rate (ORR) of 42.9% and progression-free survival of 24.7 months. Three patients with donor splice-site mutations showed a long-term treatment response, despite the fact that two with acceptor splice-site mutations demonstrated no response and experienced early disease progression with ICI monotherapy. Our results indicated that patients with NSCLCs harboring MET exon 14 mutations presented with a high rate of positive PD-L1 expression. ICI treatment showed a high ORR and long-term efficacy for NSCLCs harboring MET exon 14 mutations. Variants of MET exon 14 splice-site mutations may be associated with ICI response.

Spindle cell carcinoma (SpCC) exhibits dual features of malignancy, with the histology of squamous cell carcinoma and sarcoma-like proliferation of spindle cells. SpCC development in the oral region has rarely been reported. Skin grafts are frequently applied to defects following superficial cancer resection. We encountered an extremely rare case of SpCC that developed in the central part of a skin graft, which was applied after superficial tongue cancer resection. SpCC may develop on skin grafts and is not limited to the oral mucosa in the oral cavity. Therefore, long-term observation should be done carefully because skin grafts change over time.

Microsatellite instability (MSI) is an effective biomarker for diagnosing Lynch syndrome (LS) and predicting the responsiveness of cancer therapy. MSI testing is conventionally performed by capillary electrophoresis, and MSI status is judged by visual assessment of allele size change. Here, we attempted to develop a quantitative evaluation model of MSI using next-generation sequencing (NGS). Microsatellite markers were analyzed in tumor and non-tumor tissues of colorectal cancer patients by NGS after a single multiplex polymerase chain reaction amplification. The read counts corresponding to microsatellite loci lengths were calculated independently of mapping against a reference genome, and their distribution was digitized by weighted mean. Weighted mean differences between tumor and non-tumor samples with different MSI status were assessed, and cut-off values for each marker in the discovery cohort were determined. Each microsatellite maker was defined as unstable if the weighted mean difference was greater than the cut-off value. In the discovery cohort, the evaluation model demonstrated sensitivity and specificity of 100% for all markers. In the validation cohort, MSI status determined by the new model was consistent with the outcome of the conventional method in 29/30 cases (97%). The single inconsistent case was classified as low-frequency MSI by the conventional method but considered MSI-high by NGS. Genetic testing for mismatch repair genes revealed a pathogenic variant in MSH6 in the discordant case. We successfully developed a quantitative evaluation method for determining MSI status using NGS. This is a robust and sensitive method and could improve LS diagnosis.

Lynch syndrome is an autosomal dominant hereditary cancer syndrome in which many cancers develop, the main one being colorectal cancer. Germline pathogenic variants in one of four mismatch repair (MMR) genes are known to be causative of this disease. Accurate diagnosis using genetic testing can greatly benefit the health of those affected. Recently, owing to the improvement of sequence techniques, complicated variants affecting the functions of MMR genes were discovered. In this study, we analyzed insertions of a retrotransposon-like sequence in exon 5 of the MSH6 gene and exon 3 of the MSH2 gene found in Japanese families suspected of having Lynch syndrome. Both of these insertions induced aberrant splicing, and these variants were successfully identified by mRNA sequencing or visual observation of mapping results, although a standard DNA-seq analysis pipeline failed to detect them. The insertion sequences were ~2.5 kbp in length and were found to have the structure of an SVA retrotransposon (SVA). One SVA sequence was not present in the hg19 or hg38 reference genome, but was in a Japanese-specific reference sequence (JRGv2). Our study illustrates the difficulties of identifying SVA insertions in disease genes, and that the possibility of polymorphic insertions should be considered when analyzing mobile elements.

Background The prevalence of Lynch syndrome and the use of universal tumor screening to identify Lynch syndrome among unselected patients with upper urinary tract urothelial carcinoma, which is associated with Lynch syndrome, have not been closely investigated yet. Methods A total of 166 tumors from 164 upper urinary tract urothelial carcinoma patients were tested for microsatellite instability and expression of mismatch repair proteins (MLH1, MHS2, MSH6 and PMS2) by immunohistochemistry. Genetic testing was performed for patients suspected of having Lynch syndrome. Clinicopathological factors, including familial and personal cancer history associated with mismatch repair deficiency, were evaluated. Results The frequency of high-level microsatellite instability and loss of at least one mismatch repair protein was 2.4% (4/164); the microsatellite instability and immunohistochemistry results showed complete concordance. Of these four patients, three were genetically proven to have Lynch syndrome, while the remaining one was highly suggestive for Lynch syndrome based on their personal cancer history. Univariate analysis showed that age<70 years (P = 0.04), ureter as the tumor location (P = 0.052), previous history/synchronous diagnosis of colorectal cancer (P < 0.01) and fulfillment of the criteria per the revised Bethesda guideline (P < 0.01) tended to be or were significantly associated with high-level microsatellite instability/mismatch repair loss. Conclusions The prevalence of Lynch syndrome among unselected upper urinary tract urothelial carcinoma patients was at least 1.8% in our study population. The screening efficacies of the microsatellite instability test and immunohistochemistry appear equivalent. Universal tumor screening may be a valid approach; however, selective screening methods that consider factors associated with mismatch repair loss/high-level microsatellite instability tumors require further investigation.

Background DKC1 (dyskerin pseudouridine synthase 1) is a causative gene for X-linked dyskeratosis congenita. Approximately 8% of patients with dyskeratosis congenita have malignancy, but information about the development of malignancy in patients with dyskeratosis congenita is limited. Case presentation A young Japanese patient with bone marrow failure developed metachronous rectal adenocarcinomas at the ages of 16 and 18 years. He had no family history of cancer. Microsatellite instability testing with rectal tumor tissue demonstrated low-level microsatellite instability. To clarify whether any cancer susceptibility genes were involved in the development of rectal cancer, RNA sequencing was performed. Cancer-related genes were assessed, and a c.361A>G (p.Ser121Gly) germline variant was detected in DKC1 . The same missense variant was previously reported in two patients with dyskeratosis congenita as a pathogenic variant, but those patients did not develop malignancies. Conclusions Our patient developed rectal cancer at an early age of onset compared with the previously reported typical onset age of patients with dyskeratosis congenita. DKC1 might be involved in predisposition to colorectal cancer in young adulthood; therefore, appropriate surveillance may be considered.

The proband was a 62-year-old man with ureter cancer. He had a history of metachronous colorectal and gastric cancer. Immunohistochemical staining showed the absence of both MSH2 and MSH6 proteins in the ureter cancer and other available cancer tissue specimens. Genetic testing was conducted to identify the causative genes of hereditary gastrointestinal cancer syndromes including mismatch repair genes. We detected a germline variant, c.2635-3delC, within the splice acceptor site of exon 16, in the MSH2 gene. To investigate whether this variant affected splicing of the gene, RNA sequencing was performed using blood samples. We observed a substantial amount of the transcripts that lacked proper splicing of intron 15 in the indexed case, whereas, a very low amount of such aberrant transcripts was detected in the controls, strongly indicating an association between the variant and splicing defect. These results indicate that MSH2 c.2635-3delC affects normal splicing and might be a cause of Lynch syndrome.