A Validated Highly Sensitive Microsatellite Instability Assay Accurately Identifies Individuals Harboring Biallelic Germline PMS2 Pathogenic Variants in Constitutional Mismatch Repair Deficiency.

BACKGROUND: Constitutional mismatch repair deficiency (CMMRD) is a rare and extraordinarily penetrant childhood-onset cancer predisposition syndrome. Genetic diagnosis is often hampered by the identification of mismatch repair (MMR) variants of unknown significance and difficulties in PMS2 analysis, the most frequently mutated gene in CMMRD. We present the validation of a robust functional tool for CMMRD diagnosis and the characterization of microsatellite instability (MSI) patterns in blood and tumors. METHODS: The highly sensitive assessment of MSI (hs-MSI) was tested on a blinded cohort of 66 blood samples and 24 CMMRD tumor samples. Hs-MSI scores were compared with low-pass genomic instability scores (LOGIC/MMRDness). The correlation of hs-MSI scores in blood with age of cancer onset and the distribution of insertion-deletion (indel) variants in microsatellites were analyzed in a series of 169 individuals (n = 68 CMMRD, n = 124 non-CMMRD). RESULTS: Hs-MSI achieved high accuracy in the identification of CMMRD in blood (sensitivity 98.5% and specificity 100%) and detected MSI in CMMRD-associated tumors. Hs-MSI had a strong positive correlation with whole low-pass genomic instability LOGIC scores (r = 0.89, P = 2.2e-15 in blood and r = 0.82, P = 7e-3 in tumors). Indel distribution identified PMS2 pathogenic variant (PV) carriers from other biallelic MMR gene PV carriers with an accuracy of 0.997. Higher hs-MSI scores correlated with younger age at diagnosis of the first tumor (r = -0.43, P = 0.011). CONCLUSIONS: Our study confirms the accuracy of the hs-MSI assay as ancillary testing for CMMRD diagnosis, which can also characterize MSI patterns in CMMRD-associated cancers. Hs-MSI is a powerful tool to pinpoint PMS2 as the affected germline gene and thus potentially personalize cancer risk.

Incidences of colorectal adenomas and cancers under colonoscopy surveillance suggest an accelerated "Big Bang" pathway to CRC in three of the four Lynch syndromes.

BACKGROUND: Colorectal cancers (CRCs) in the Lynch syndromes have been assumed to emerge through an accelerated adenoma-carcinoma pathway. In this model adenomas with deficient mismatch repair have an increased probability of acquiring additional cancer driver mutation(s) resulting in more rapid progression to malignancy. If this model was accurate, the success of colonoscopy in preventing CRC would be a function of the intervals between colonoscopies and mean sojourn time of detectable adenomas. Contrary to expectations, colonoscopy did not decrease incidence of CRC in the Lynch syndromes and shorter colonoscopy intervals have not been effective in reducing CRC incidence. The prospective Lynch Syndrome Database (PLSD) was designed to examine these issues in carriers of pathogenic variants of the mis-match repair (path_MMR) genes. MATERIALS AND METHODS: We examined the CRC and colorectal adenoma incidences in 3,574 path_MLH1, path_MSH2, path_MSH6 and path_PMS2 carriers subjected to regular colonoscopy with polypectomy, and considered the results based on sojourn times and stochastic probability paradigms. RESULTS: Most of the path_MMR carriers in each genetic group had no adenomas. There was no association between incidences of CRC and the presence of adenomas. There was no CRC observed in path_PMS2 carriers. CONCLUSIONS: Colonoscopy prevented CRC in path_PMS2 carriers but not in the others. Our findings are consistent with colonoscopy surveillance blocking the adenoma-carcinoma pathway by removing identified adenomas which might otherwise become CRCs. However, in the other carriers most CRCs likely arised from dMMR cells in the crypts that have an increased mutation rate with increased stochastic chaotic probabilities for mutations. Therefore, this mechanism, that may be associated with no or only a short sojourn time of MSI tumours as adenomas, could explain the findings in our previous and current reports.

Phenotype correlations with pathogenic DNA variants in the MUTYH gene.

MUTYH -associated polyposis (MAP) is an autosomal recessive disorder where the inheritance of constitutional biallelic pathogenic MUTYH variants predisposes a person to the development of adenomas and colorectal cancer (CRC). It is also associated with extracolonic and extraintestinal manifestations that may overlap with the phenotype of familial adenomatous polyposis (FAP). Currently, there are discrepancies in the literature regarding whether certain phenotypes are truly associated with MAP. This narrative review aims to explore the phenotypic spectrum of MAP to better characterise the MAP phenotype. A literature search was conducted to identify articles reporting on MAP-specific phenotypes. Clinical data from 2109 MAP patients identified from the literature showed that 1123 patients (53.2%) had CRC. Some patients with CRC had no associated adenomas, suggesting that adenomas are not an obligatory component of MAP. Carriers of the two missense founder variants, and possibly truncating variants, had an increased cancer risk when compared to those who carry other pathogenic variants. It has been suggested that somatic G:C>T:A transversions are a mutational signature of MAP, and could be used as a biomarker in screening and identifying patients with atypical MAP, or in associating certain phenotypes with MAP. The extracolonic and extraintestinal manifestations that have been associated with MAP include duodenal adenomas, duodenal cancer, fundic gland polyps, gastric cancer, ovarian cancer, bladder cancer and skin cancer. The association of breast cancer and endometrial cancer with MAP remains disputed. Desmoids and Congenital Hypertrophy of the Retinal Pigment Epithelium (CHRPEs) are rarely reported in MAP, but have long been seen in FAP patients, and thus could act as a distinguishing feature between the two. This collection of MAP phenotypes will assist in the assessment of pathogenic MUTYH variants using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) Variant Interpretation Guidelines, and ultimately improve patient care.

Tumor analysis of MMR genes in Lynch-like syndrome: Challenges associated with results interpretation.

BACKGROUND: Up to 70% of suspected Lynch syndrome patients harboring MMR deficient tumors lack identifiable germline pathogenic variants in MMR genes, being referred to as Lynch-like syndrome (LLS). Previous studies have reported biallelic somatic MMR inactivation in a variable range of LLS-associated tumors. Moreover, translating tumor testing results into patient management remains controversial. Our aim is to assess the challenges associated with the implementation of tumoral MMR gene testing in routine workflows. METHODS: Here, we present the clinical characterization of 229 LLS patients. MMR gene testing was performed in 39 available tumors, and results were analyzed using two variant allele frequency (VAF) thresholds (≥5% and ≥10%). RESULTS AND DISCUSSION: More biallelic somatic events were identified at VAF ≥ 5% than ≥10% (35.9% vs. 25.6%), although the rate of nonconcordant results regarding immunohistochemical pattern increased (30.8% vs. 20.5%). Interpretation difficulties question the current utility of the identification of MMR somatic hits in the diagnostic algorithm of suspected LS cases.

Open-Source Bioinformatic Pipeline to Improve PMS2 Genetic Testing Using Short-Read NGS Data.

The molecular diagnosis of mismatch repair-deficient cancer syndromes is hampered by difficulties in sequencing the PMS2 gene, mainly owing to the PMS2CL pseudogene. Next-generation sequencing short reads cannot be mapped unambiguously by standard pipelines, compromising variant calling accuracy. This study aimed to provide a refined bioinformatic pipeline for PMS2 mutational analysis and explore PMS2 germline pathogenic variant prevalence in an unselected hereditary cancer (HC) cohort. PMS2 mutational analysis was optimized using two cohorts: 192 unselected HC patients for assessing the allelic ratio of paralogous sequence variants, and 13 samples enriched with PMS2 (likely) pathogenic variants screened previously by long-range genomic DNA PCR amplification. Reads were forced to align with the PMS2 reference sequence, except those corresponding to exon 11, where only those intersecting gene-specific invariant positions were considered. Afterward, the refined pipeline's accuracy was validated in a cohort of 40 patients and used to screen 5619 HC patients. Compared with our routine diagnostic pipeline, the PMS2_vaR pipeline showed increased technical sensitivity (0.853 to 0.956, respectively) in the validation cohort, identifying all previously PMS2 pathogenic variants found by long-range genomic DNA PCR amplification. Fifteen HC cohort samples carried a pathogenic PMS2 variant (15 of 5619; 0.285%), doubling the estimated prevalence in the general population. The refined open-source approach improved PMS2 mutational analysis accuracy, allowing its inclusion in the routine next-generation sequencing pipeline streamlining PMS2 screening.

Germline NPAT inactivating variants as cause of hereditary colorectal cancer.

Two independent exome sequencing initiatives aimed to identify new genes involved in the predisposition to nonpolyposis colorectal cancer led to the identification of heterozygous loss-of-function variants in NPAT, a gene that encodes a cyclin E/CDK2 effector required for S phase entry and a coactivator of histone transcription, in two families with multiple members affected with colorectal cancer. Enrichment of loss-of-function and predicted deleterious NPAT variants was identified in familial/early-onset colorectal cancer patients compared to non-cancer gnomAD individuals, further supporting the association with the disease. Previous studies in Drosophila models showed that NPAT abrogation results in chromosomal instability, increase of double strand breaks, and induction of tumour formation. In line with these results, colorectal cancers with NPAT somatic variants and no DNA repair defects have significantly higher aneuploidy levels than NPAT-wildtype colorectal cancers. In conclusion, our findings suggest that constitutional inactivating NPAT variants predispose to mismatch repair-proficient nonpolyposis colorectal cancer.

Systematic large-scale application of ClinGen InSiGHT APC -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases.

Background: Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP). Methods: A streamlined algorithm using the APC -specific criteria was developed and applied to assess all APC variants in ClinVar and the InSiGHT international reference APC LOVD variant database. Results: A total of 10,228 unique APC variants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promising APC variants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic. Conclusions: The application of APC -specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.

SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population.

Accurate classification of genetic variants is crucial for clinical decision-making in hereditary cancer. In Spain, genetic diagnostic laboratories have traditionally approached this task independently due to the lack of a dedicated resource. Here we present SpadaHC, a web-based database for sharing variants in hereditary cancer genes in the Spanish population. SpadaHC is implemented using a three-tier architecture consisting of a relational database, a web tool and a bioinformatics pipeline. Contributing laboratories can share variant classifications and variants from individuals in Variant Calling Format (VCF) format. The platform supports open and restricted access, flexible dataset submissions, automatic pseudo-anonymization, VCF quality control, variant normalization and liftover between genome builds. Users can flexibly explore and search data, receive automatic discrepancy notifications and access SpadaHC population frequencies based on many criteria. In February 2024, SpadaHC included 18 laboratory members, storing 1.17 million variants from 4306 patients and 16 343 laboratory classifications. In the first analysis of the shared data, we identified 84 genetic variants with clinically relevant discrepancies in their classifications and addressed them through a three-phase resolution strategy. This work highlights the importance of data sharing to promote consistency in variant classifications among laboratories, so patients and family members can benefit from more accurate clinical management. Database URL: https://spadahc.ciberisciii.es/.

Uso de paneles de genes en pacientes con alto riesgo de cáncer digestivo hereditario: documento de posicionamiento de la AEG, SEOM, AEGH y consorcio IMPaCT-GENÓMICA / Use of multi-gene panels in patients at high risk of hereditary digestive cancer: position statement of AEG, SEOM, AEGH and IMPaCT-GENÓMICA consortium

Este documento de posicionamiento, auspiciado por la Asociación Española de Gastroenterología, la Sociedad Española de Oncología Médica, la Asociación Española de Genética Humana y el consorcio IMPaCT-Genómica, tiene como objetivo realizar recomendaciones para el uso de paneles de genes en la evaluación de individuos con alto riesgo de cáncer digestivo hereditario. Para medir la calidad de la evidencia y los niveles de recomendación se ha utilizado la metodología basada en el sistema Grading of Recommendations Assessment, Development and Evaluation (GRADE). Se obtuvo el consenso entre expertos mediante un método Delphi. El documento incluye recomendaciones sobre escenarios clínicos en los que se recomienda el uso de paneles de genes en cáncer colorrectal, síndromes polipósicos, cáncer gástrico y pancreático, así como los genes de los paneles a ser considerados en cada una de estas situaciones clínicas. También se establecen recomendaciones sobre la evaluación de mosaicismos, las estrategias de asesoramiento ante la ausencia de sujeto índice y, finalmente, el análisis constitucional tras identificación de variantes patogénicas tumorales. (AU)

This position statement, sponsored by the Asociación Española de Gastroenterología, the Sociedad Española de Oncología Médica, the Asociación Española de Genética Humana and the IMPaCT-Genómica Consortium aims to establish recommendations for use of multi-gene panel testing in patients at high risk of hereditary gastrointestinal and pancreatic cancer. To rate the quality of the evidence and the levels of recommendation, we used the methodology based on the GRADE system (Grading of Recommendations Assessment, Development and Evaluation). We reached a consensus among experts using a Delphi method. The document includes recommendations on clinical scenarios where multi-gene panel testing is recommended in colorectal cancer, polyposis syndromes, gastric and pancreatic cancer, as well as the genes to be considered in each clinical scenario. Recommendations on the evaluation of mosaicisms, counseling strategies in the absence of an index subject and, finally, constitutional analysis after identification of pathogenic tumor variants are also made. (AU)

Síndrome de poliposis hiperplásica: diversidad fenotípica y asociación a cáncer colorrectal / Hyperplastic polyposis syndrome: phenotypic diversity and association to colorectal cancer

Fundamento y objetivo: El síndrome de poliposis hiperplásica (SPH) es un cuadro poco frecuente caracterizado por la presencia de pólipos hiperplásicos (PH) ocasionalmente asociados a adenomas serrados (AS) o pólipos mixtos (PM), y definido por criterios clínicos (OMS/Cleveland). El SPH es heterogéneo con respecto al número, tamaño de los pólipos, asociación a cáncer colorrectal (CCR) e historia familiar. Se desconoce su base genética. Describimos aquellos individuos que cumplen criterios de SPH dentro de la serie de familias valoradas en nuestra Unidad de Consejo Genético por una poliposis colónica. Nuestro objetivo es identificar las características clínicas de este síndrome. Pacientes y método: Estudio retrospectivo de 197 familias con poliposis colónica (1998-2011), en que se identificaron aquellos individuos con criterios de SPH. Para saber el número total de pólipos, se tuvo en cuenta las polipectomías y/o el estudio histológico de las piezas quirúrgicas. Los pólipos se clasificaron en adenomas, lesiones serradas (PH y AS) y PM. Los estudios genéticos realizados fueron: inestabilidad de microsatélites (IMS), variantes del gen MUTYH (p.Tyr165Cys, p.Gly382Asp y p.Glu396GlyfsX43) y el gen APC. Resultados: Un total de 18 individuos, con una edad media de 51,1 años, cumplían criterios de SPH (11 varones y 7 mujeres). El número de PH osciló entre 14 y 100,coexistiendo con adenomas clásicos, AS y PM en 14 individuos (77,8%). La localización de pólipos fue: colon derecho e izquierdo en 13 individuos (72,2%) y solo colon izquierdo en 5 (27,8%). Se detectó CCR en 10/18 (55,6%) pacientes, 3 de ellos (30%) presentaban un doble CCR, una historia familiar de CCR en 3 pacientes (16,7%) y de SPH en uno. No se detectó IMS en 8 CCR ni en los 3 adenomas estudiados; se detectaron 2/13 mutaciones en heterocigosis en el gen MUTYH (p.Gly382Asp) y una variante de significado biológico desconocido en el gen APC (p.Ser926Pro). Conclusiones: La variabilidad fenotípica del SPH dificulta su identificación, por lo que es importante seguir los criterios clínicos establecidos para su clasificación, así como establecer pautas de cribado de CCR dada la elevada incidencia del mismo (AU)

Background and objective: Hyperplastic polyposis syndrome (HPS) is an uncommon disorder characterized by hyperplastic polyps (HP) occasionally associated with serrated adenomas (SA) or mixed polyps (MP) and defined by clinical criteria (OMS/Cleveland). HPS is heterogeneous regarding the number and size of polyps, and it is associated with colorectal cáncer (CRC) and a family history. Its genetic basis is unknow. We describe individuals with HPS criteria from a series of families assessed in our Unit of Genetic Advice for colonic polyposis. Our objective is to identify the clinical characteristics of this syndrome. Patients and methods: Retrospective study of 197 families with colonic polyposis (1998-2011), identifying patients with HPS criteria. To know the number of polyps, we took into account polypectomies and/or the histologic study of surgical samples. Polyps were classified into adenomas, serrated lesiones (HP and SA) and MP. Genetic studies revealed: microsatellite instability (MSI), MUTYH gene variants (p.Tyr165Cys, p.Gly382Asp and p.Glu396GlyfsX43) and APC gene. Results: Eighteen individuals, with a median age of 51.1 years, had criteria of HPS (11 M/7 F). Number of HP varied between 14 and 100 coexisting with classical adenomas, SA and MP in 14 individuals (77.8%). Localization of polyps: ascending and descending colon in 13 individuals (72.2%) and only descending colon in 5 (27.8%). A CRC was detected in 10/18 (55.6%) patients, and 3 of them had a double CRC, a family history in 3 patients (16.7%) and a history of HPS in one. IMS was not detected in 8 CRC nor in 3 adenomas studied; we detected 2/13 heterozygous mutations in the MUTYH gene(p.Gly382Asp) and one variant with an unknown biological significance in the APC gene (p.Ser926Pro). Conclusions: The phenotypic variability of HPS difficults its identification, hence it is important to adhere to the clinical criteria established for its classification as well as to establish screening guidelines for CRC on the basis of its high incidence (AU)

Implantación ortotópica de fragmentos sólidos de cáncer de páncreas exocrino humano en ratones atímicos / Orthotopic solid human pancreatic cancer fragment implants in athimic rats

Introducción: el desarrollo de modelos experimentales de cáncer de páncreas exocrino es esencial para un mejor conocimiento de la enfermedad. El objetivo del presente trabajo ha sido implantar y perpetuar carcinomas de páncreas exocrino humano en el páncreas del ratón atímico (implantación ortotópica), estudiar su patrón de diseminación y las alteraciones en genes implicados en la tumorigénesis. Material y Métodos: Se implantaron, de forma ortotópica, fragmentos sólidos de 11 carcinomas de páncreas exocrino humano. Se analizó la presencia de mutaciones en los genes K-ras y p53, tanto en tumores primarios como en los tumores perpetuados. Resultados: Siete de 11 tumores implantados (63 por ciento) crecieron como ortoimplantes. En 4 tumores se evidenció diseminación a distancia (metástasis hepáticas, diseminación peritoneal, o metástasis en los ganglios linfáticos). El patrón de diseminación fue específico para cada tumor y reproducible a lo largo de múltiples pases. Los tumores primarios y los perpetuados compartían el mismo genotipo. Conclusiones: La implantación ortotópica de fragmentos sólidos de carcinomas de páncreas exocrino humano permite la perpetuación de tumores con distinto genotipo y la reproducción de diferentes patrones de crecimiento local y a distancia

Identificación de dos familias con cáncer de colon hereditario no polipósico (CCHNP) y criterios de Amsterdam. Relevancia del árbol genealógico y las medidas de seguimiento / Identification of two families with hereditary nonpolyposis colorectal cancer and Amsterdam criteria. Relevance of family history and follow-up

El diagnóstico clínico del cáncer de colon hereditario no polipósico (CCHNIP) se basa en el cumplimiento de los criterios de Amsterdam 1 o los criterios de Amsterdam modificados 2, que incluye la presencia de neoplasias extracolónicas del síndrome de Lynch II. Muchas familias presentan patrones de agregación fuertes, sospechosos de un carácter hereditario y cuyo seguimiento puede conducir a que se beneficien de un protocolo de diagnóstico precoz. Se presenta una familia inicialmente con criterios de sospecha de CCHNP que se convirtió en una familia Amsterdam 1 (familia 1) y una familia con criterios de Amsterdam 2 (familia 2) que presenta un miembro afectado a una edad muy joven. Ambas recibieron consejo genético y las recomendaciones de seguimiento. La realización de una colonoscopia total de control a un miembro asintomático de la familia 1 permitió llegar al diagnóstico de un cáncer de colon en estadio inicial y a un tratamiento quirúrgico amplio ante el elevado riesgo de una segunda neoplasia metacrónica. El caso de la familia 2 demuestra que las recomendaciones de consejo genético deben ser las mismas cuando se cumplen los criterios de Amsterdam 2. Ambas familias ilustran la importancia de realizar un cuidadoso árbol genealógico cuando se sospechen criterios de agregación familiar. (AU)