IntroductionCerebral Palsy (CP) is characterized by permanent, non-degenerative motor function deficits with increasing evidence of genetic contributions. Although prenatal and perinatal risk factors are well recognized, the underlying etiopathology remains incompletely understood. This study aimed to improve diagnostic accuracy and elucidate the genetic architecture of CP and CP-like phenotypes through systematic genomic analyses.MethodsPatients with clinically confirmed CP or CP-like presentations were recruited, and biological samples were stored in the ACU-Biobank. Whole-exome and whole-genome sequencing data were analyzed using a validated in-house pipeline incorporating comprehensive variant filtering, prioritization, and re-phenotyping.ResultsPathogenic or likely pathogenic variants were identified in 36.4% (24/66) of patients, while variants of uncertain significance (VUS) were detected in 25.8% (17/66). Identified variants involved genes such as SPAST, KIF1A, PLA2G6, CTNNB1, L1CAM, and SYNGAP1. These results demonstrate a substantial contribution of rare monogenic variants to CP and CP-like phenotypes, reflecting extensive genetic heterogeneity.DiscussionOur findings support the increasing evidence that genetic factors contribute significantly to CP etiology and emphasize the importance of integrating genomic testing into clinical evaluation. The systematic use of exome and genome sequencing improves diagnostic yield and enables genotype-informed classification, aiding targeted management and genetic counseling for affected individuals.

Multigene panel testing (MGPT) is a powerful tool for identifying pathogenic variants (PVs) underlying hereditary cancers. However, the clinical interpretation of variants of uncertain significance (VUS) remains a major challenge, particularly in populations underrepresented in population genomic databases. In this study, we analyzed 25 cancer susceptibility genes in a Turkish cohort comprising 1293 breast cancer (BC) patients, 370 colorectal cancer (CRC) patients, and 914 cancer-free controls. Compared with our previous work, the expanded dataset enabled a more refined classification of germline variants. In total, we identified 217 distinct PVs and 494 distinct VUS. Among BC patients, PVs were enriched in BRCA1, BRCA2, PALB2, CHEK2, and ATM, while in CRC patients PVs were enriched in MLH1, MUTYH, MSH2, and CHEK2. Notably, CHEK2 was among the most frequently mutated genes, and harbored the highest number of distinct PVs and VUS per coding region. Given the underrepresentation of the Turkish population in public variant databases and the continuous accumulation of population and functional evidence, we systematically re-evaluated the 415 VUS reported 5 years ago in the initial freeze of this cohort. This reclassification resulted in 98 VUS being reclassified as benign and 16 as PVs, increasing positive test rates by 3.7

Advances in high-throughput sequencing have increased the detection of TP53 variations, many of which occur at low allelic fractions. Such variants may arise due to clonal hematopoiesis (CHIP) or constitutional mosaicism, complicating their clinical classification and management. Since guidelines recommend Li-Fraumeni syndrome (LFS)-like management for individuals carrying TP53 variations, accurately determining the origin of low variant allelic fraction (VAF) variants is essential for risk assessment and clinical decision-making. This study evaluates TP53 VAF in patients with suspected hereditary cancer predisposition, tested via multigene panels and emphasizes the importance of conducting a detailed investigation before making clinical decisions in patients with low-VAF. In retrospectively analyzed 1,520 cases, we identified 17 actionable TP53 variations in 16 cases (1

Germline pathogenic variants (PVs) in CBL are found in 15 % of juvenile myelomonocytic leukemia (JMML) cases. Here we report three siblings with CBL(NM_005188):c.1111T>C variation presenting a heterogenous JMML clinic and outcome. The index case was diagnosed at the age of seven, whereas the younger brother was 10 months old and the youngest was one month old. The hematopoietic stem cell transplantation was successful for the index and the youngest brother with event-free survival, but the middle brother showed severe graft versus host disease. This study shows the heterogeneity of JMML and how the outcome might differ even within the family.

Background:Leukemia is the most common cancer in children, and 10%-15% of patients with leukemia/lymphoma carry pathogenic germline cancer-predisposing variants. Identifying these variants is critical for understanding the genetic predisposition and optimizing clinical management. Methods:We performed germline short-read sequencing in 36 individuals from 20 families with suspected leukemia/lymphoma predisposition, including 20 index cases, 9 affected relatives, and 7 unaffected members. Results:We identified 13 clinically relevant germline variants in known cancer predisposition genes including TP53, ETV6, MSH6, MLH1, and BRCA1. Notably, we uncovered novel candidate variants in ATR, TNFRSF9, ETAA1, and KSR1, which was supported by segregation analysis, consanguinity patterns, and secondary malignancy phenotypes. Several index cases exhibited striking familial cancer syndromes involving both hematologic and solid tumors, with progression from ALL to AML or glioma. Deep clinical-genomic correlation enabled reclassification of variants and refined diagnostic and therapeutic decision-making in multiple cases. The patients were referred to genetic counseling for surveillance of carriers and risk assessment for various family members. Conclusion:These findings emphasize the clinical utility of germline testing in pediatric hematologic cancers by providing novel insights into the predisposition to leukemia/lymphoma and contributing to treatment regimens, donor selection, and diagnostic refinement, particularly in populations with high consanguinity.

Background/Objectives: An accurate evaluation of variant actionability is essential in cancer management. In Von Hippel–Lindau Syndrome (VHL), the interpretation of the germline variants is confounded by the presence of non-syndromic component tumors, such as clear cell renal cell carcinoma (ccRCC), hemangioblastoma, pheochromocytoma, and neuroendocrine tumors. These tumors frequently occur sporadically, without any association with VHL syndrome. The presence of these tumors in a patient with a germline VHL variant could lead to inaccurate attribution of these tumors to the germline variant and VHL syndrome. In our previous INT2GRATE (INTegrated INTerpretation of GeRmline And Tumor gEnomes) programs, we demonstrated that integrating tumor-derived and germline evidence offers a comprehensive approach for the accurate assessment of the germline variants in cancer syndromes. Methods/Results: Here, we present a novel INT2GRATE variant evidence framework (VEF) for evaluating the clinical actionability of the germline variants in VHL syndrome, offering an integrated approach that incorporates both constitutional and tumor data. We analyzed 2672 variants in the VHL gene and their associated tumors and clinical evidence to effectively distinguish between constitutional, sporadic, VHL differentials, and VHL allelic genetic conditions. The germline INT2GRATE variants, along with their comprehensive associated evidence, were made accessible in the first open-access INT2GRATE Variant data Portal. Conclusions: This novel and integrated approach to variant assessment and data sharing in hereditary cancer syndromes is essential in the clinical evaluation of genomic variants, advancing precision oncology, and improving patient care.

Objective: Fragile X Syndrome (FXS) is a complex neurodevelopmental condition characterised by delayed speech development, dysmorphic features, and impaired cognitive development. FXS, which results from CGG repeat expansion in the FMR1 gene, is one of the most commonly identified genetic cause of autism. Accurate diagnosis of FXS is crucial for effective management and treatment. This study aimed to evaluate the prevalence of FXS in individuals with Autism Spectrum Disorder (ASD). Material and Methods: We conducted a retrospective study involv-ing50 patients. Comprehensive fragment analysis of the FMR1 gene was performed, with repeat sequences classified according to the stringent guidelines established by American College of Medical Genetics and Genomics(ACMG), Clinical Molecular Genetics Society (CMGS) ve European Society of Human Genetics (ESHG). Results: FXS was identified in three individuals (6%) within the study cohort. This finding aligns with previous reports indicating prevalence rates between 2% and 8% among ASD populations, thereby confirming the significance of our results. Conclusion: The overlapping symptoms of FXS and idiopathic autism present diagnostic challenges, highlighting the importance of identifying FXS to implement targeted therapies. Family history is critical in identifying at-risk individuals, as FXS can lead to varied manifestations in family members, including ataxia and early menopause. Although this study provides valuable insights, the limited sample size underscores the need for larger-scale research. Advanced genetic investigations and comprehensive panels could further aid in identifying additional causes of autism.

ImportanceCHEK2 pathogenic and likely pathogenic variants (PVs) are common, and low-risk (LR) variants, p.I157T, p.S428F, and p.T476M, are even more common. Biallelic CHEK2 PVs are associated with specific cancer phenotypes, including early age at onset of breast cancers. Whether biallelic LR variants are associated with cancer predisposition is unknown.ObjectiveTo characterize the cancer phenotype among individuals with biallelic CHEK2 variants, specifically those that have been associated with lower cancer risk in the heterozygous state.Design, Setting, and ParticipantsThis retrospective observational cohort study examining cancer phenotype by CHEK2 genotype was conducted at a single diagnostic genetic testing laboratory. Of 36 821 individuals who underwent genetic testing, 3783 (10.3%) with CHEK2 PVs or LR variants were ascertained from July 1, 2012, to September 30, 2019. Analyses were conducted from September 2022 to January 2024.ExposuresCancer phenotype among individuals with 2 LR variants and those with 1 PV and 1 LR variant was compared with cancer phenotype among individuals with wild type (WT) (n = 33 034), single LR variant (n = 1566), single PV controls (n = 2167), and 2 PVs (n = 21). Cancer phenotypes were investigated for any cancer, multiple primary cancers, female breast cancer, and bilateral female breast cancers.Main Outcomes and MeasuresCancer phenotype of CHEK2 2 LRs and 1 PV and 1 LR.ResultsOf 36 821 individuals, 92.1% were female, and the median age at testing was 53 years (IQR, 44-63 years); 3787 (10.3%) were identified as having a CHEK2 PV or LR variant. There were 13 individuals with 2 LR variants and 20 with 1 PV and 1 LR variant. Among those with 2 LR variants, prevalence of any cancer (76.9%) and breast cancer (60.0%) were similar to those with WT (any cancer, 69.8%; breast cancer, 52.7%) and those with a single LR variant (any cancer, 70.9%; breast cancer, 57.5%). Among participants with 1 PV and 1 LR variant, 95.0% had a prior cancer diagnosis, a higher rate than among those with a single PV (76.8%), but the difference was not statistically significant. Among female individuals with 1 PV and 1 LR variant, 86.7% had a breast cancer diagnosis, compared with 67.1% with a single PV, although these differences were not statistically significant.Conclusions and RelevanceIn this cohort study, individuals with 2 LR variants in CHEK2 had a cancer phenotype similar to those with a single LR variant and similar to WT controls. Individuals with 1 PV and 1 LR variant may have a more penetrant cancer phenotype than individuals with a single PV. Future studies focused on CHEK2 LR variants will aid in better understanding whether these variants are genetic modifiers associated with cancer risk.

Abstract Objective Turkish genome is underrepresented in large genomic databases. This study aims to evaluate the effect of allele frequency in the Turkish population in determining the clinical utility of germline findings in breast cancer, including invasive lobular carcinoma (ILC), mixed invasive ductal and lobular carcinoma (IDC‐L), and ductal carcinoma (DC). Methods Two clinic‐based cohorts from the Umraniye Research and Training Hospital (URTH) were used in this study: a cohort consisting of 132 women with breast cancer and a non‐cancer cohort consisting of 492 participants. The evaluation of the germline landscape was performed by analysis of 27 cancer genes. The frequency and type of variants in the breast cancer cohort were compared to those in the non‐cancer cohort to investigate the effect of population genetics. The variant allele frequencies in Turkish Variome and gnomAD were statistically evaluated. Results The genetic analysis identified 121 variants in the breast cancer cohort (actionable = 32, VUS = 89) and 223 variants in the non‐cancer cohort (actionable = 25, VUS = 188). The occurrence of 21 variants in both suggested a possible genetic population effect. Evaluation of allele frequency of 121 variants from the breast cancer cohort showed 22% had a significantly higher value in Turkish Variome compared to gnomAD (p < 0.0001, 95% CI) with a mean difference of 60 times (ranging from 1.37–354.4). After adjusting for variant allele frequency using the ancestry‐appropriate database, 6.7% (5/75) of VUS was reclassified to likely benign. Conclusion To our knowledge, this is the first study of population genetic effects in breast cancer subtypes in Turkish women. Our findings underscore the need for a large genomic database representing Turkish population‐specific variants. It further highlights the significance of the ancestry‐appropriate population database for accurate variant assessment in clinical settings.

Download This Paper Open PDF in Browser Add Paper to My Library Share: Permalink Using these links will ensure access to this page indefinitely Copy URL Copy DOI

Background and Objectives:Checkpoint kinase 2 (CHEK2) is a tumor suppressor gene involved in DNA repair and cell cycle regulation. Pathogenic or likely pathogenic (P/LP) variants in CHEK2 are associated with increased cancer risk. Conversely, recent large cohort studies have identified certain variants that, despite being classified as P/LP by in silico analysis, are considered low risk. Thus, the genotype-phenotype correlations of CHEK2 require a better understanding. In this study, we aimed to characterize germline CHEK2 variants from a group of individuals who applied to cancer genetic clinics in the Marmara Region of Türkiye. We also aimed to assess the phenotypic impacts of these variants by using a new score of statistically significant in silico predictors (SSIPs). Methods: We analyzed 1707 individuals with high risk cancer predisposition, focusing on germline CHEK2 variants, using SSIP scores and population-specific data. Results:CHEK2 variants appeared in approximately 8% of cases. The SSIP scores indicated that the missense mutation, p.Arg117Gly, significantly impairs DNA repair. Almost half of the variants had higher allele frequencies than the variants listed in the Genome Aggregation Database (gnomAD), and three variants had significantly higher frequencies compared to the variants listed on the Turkish Variome database (p.Thr476Met, p.Arg137Gln, c.592+3A>T), emphasizing the importance of population-specific data. Conclusions: This comprehensive analysis of CHEK2 variants in the Turkish population provides crucial insights for cancer geneticists and oncologists. Our findings will help to enhance the evaluation and management of cancer predisposition associated with CHEK2 in Türkiye and other regions that have significant Turkish populations.

PurposeAs panel testing expands, more individuals with double pathogenic variants (DPVs) in cancer susceptibility genes are likely to be identified. Little is known about the effects of DPVs on cancer phenotype, though this information is crucial for genetic counseling and risk management. We sought to describe the cancer phenotype among individuals with DPVs in cancer susceptibility genes.MethodsA retrospective study of individuals with DPVs identified through a single testing laboratory from 2012-2017 was conducted. DPV combinations were enumerated. For DPV gene combinations that occurred >10 times, cancer histories of individuals with DPVs were compared to cancer histories of controls with a single PV matched by gene.ResultsAmong 644 individuals with DPVs, combinations that included the ATM, BRCA1, BRCA2, CHEK2 and PALB2 genes occurred >10 times. There were 8,883 matched controls for a single PV in these genes. The median age of first cancer diagnosis was younger with ATM+CHEK2 (43), compared to ATM (47, P=.016) or CHEK2 (47, P=.015) alone. Similar findings were observed when comparing age at first breast cancer (BC) for the ATM+CHEK2 vs. single gene controls. Individuals with two CHEK2 PVs also were younger at first cancer diagnosis (40) compared to single CHEK2 PV controls (47, P=.0038). This difference was not driven by age at first BC diagnosis among females.ConclusionIndividuals with ATM+CHEK2 or two CHEK2 PVs have a greater cancer burden than single gene controls. These findings can be used to counsel individuals with DPVs and their families and inform cancer screening recommendations.

Biliary tract cancer is a highly heterogeneous group of gastrointestinal cancers, and the only curative treatment is surgery, which is only applicable at early stages of the malignancy. ADJUBIL, a phase II trial (NCT05239169), aims to evaluate immunotherapy with durvalumab and tremelimumab with or without capecitabine in adjuvant situations for biliary tract cancers. A total of 40 prospective patients will be randomly assigned following surgery, consisting of a two-arm feasibility pilot part with a pick-the-winner design with durvalumab and tremelimumab in combination with or without capecitabine.

Pathogenic variations in the BRCA2 gene have been detected with the development of next-generation sequencing (NGS)-based hereditary cancer panel testing technology. It also reveals an increasing number of variants of uncertain significance (VUSs). Well-established functional tests are crucial to accurately reclassifying VUSs for effective diagnosis and treatment. We retrospectively analyzed the multi-gene cancer panel results of 922 individuals and performed in silico analysis following ClinVar classification. Then, we selected five breast cancer-diagnosed patients’ missense BRCA2 VUSs (T1011R, T1104P/M1168K, R2027K, G2044A, and D2819) for reclassification. The effects of VUSs on BRCA2 function were analyzed using comet and H2AX phosphorylation (γH2AX) assays before and after the treatment of peripheral blood mononuclear cells (PBMCs) of subjects with the double-strand break (DSB) agent doxorubicin (Dox). Before and after Dox-induction, the amount of DNA in the comet tails was similar in VUS carriers; however, notable variations in γH2AX were observed, and according to combined computational and functional analyses, we reclassified T1001R as VUS-intermediate, T1104P/M1168K and D2819V as VUS (+), and R2027K and G2044A as likely benign. These findings highlight the importance of the variability of VUSs in response to DNA damage before and after Dox-induction and suggest that further investigation is needed to understand the underlying mechanisms.

Germline pathogenic variants (PVs) in CDH1 cause hereditary diffuse gastric cancer. The management of CDH1 cases with a positive family history includes total prophylactic gastrectomy or intensive surveillance. In this study, we report a 16-year-old boy with intramucosal gastric signet ring cells in the setting of a germline CDH1 PV and a family history of early-onset gastric cancer. The approach to managing both the proband and their 9-year-old sister, who also had the CDH1 PV, presented a challenge to both clinicians and the family. Herein, we present the complexities of managing gastric cancer risk when a CDH1 PV is identified in childhood in the setting of a family history of early-onset gastric cancer.

Book Citations: Authors, Title, HemaSphere, 2023;7(S3):pages. The individual abstract DOIs can be found at https://journals.lww.com/hemasphere/pages/default.aspx. Disclaimer: Articles published in the journal HemaSphere exclusively reflect the opinions of the authors. The authors are responsible for all content in their abstracts including accuracy of the facts, statements, citing resources, etc. 4564 inheritance of cancer predisposing genes can also play a role in the etiology of childhood leukemias and/or lymphomas. There were also six alterations with the classification of variant of unknown significance (VUS). Variants were also confirmed in ancillary tissues where available.

e15097 Background: Personalized medicine is a life saving approach in oncology, but it still needs improvement in profiling, applicability and accessibility. The PLATON Network (PLATON, NCT05489250) is an interactive precision oncology network that aims to improve personalized medicine by interlinking scientists, allowing them to view/follow their patients’ clinical and molecular profiles and to recruit new patients for ongoing clinical trials and to implement substudies or to benefit from the BioDataBank within the Network. PLATON covers various tumor entities and can also be considered as an umbrella structure for subprojects, substudies and a screening tool for molecular driven trials. Methods: PLATON enrolls patients during or prior to first line treatment and collects information on routine clinical data (baseline data, histopathology reports, treatment decisions, etc.). During follow up, all anti tumor therapy lines, tumor response, survival and quality of life data are recorded. Importantly, PLATON is able to offer molecular testing e.g. Foundation CDx and CDx Liquid and provide reports and molecular pathologoy case discussions by its own board of pathology experts. PLATON also enrolls cases with compatible external NGS reports through an evaluation by the central review board of medical advisors. PLATON is conducted by the Institute of Clinical Cancer Research (IKF) in Frankfurt. Results: Up to date 188 patients (122 male (m) and 66 female (f)) with complete standardized data capture of NGS report results and clinical data are enroled in the PLATON Network, from 31 sites. The mean age is 65(m)/67(f) (min: 21(m)/24(f) and max: 88(m)/87(f)). Within the diagnostic cohorts 43 patients with esophagogastric cancer, 50 with intra-/extrahepatic cholangiocellular carcinoma together with 13 patients with gallbladder carcinoma, 35 patients with hepatocellular cancer and 47 patients with pancreatic cancer are included. The individual observational status is ongoing in 88 out of 188 enrolled patients, while 87 died within 10 to 726 days after recruitment. Out of all cases, 134 were discussed in the educational series of the PLATON project ”Molecular Pathology Case Discussion. In 87 of these patients, targeted therapies were recommended based on the respective molecular profile of the tumors. In total 2707 genetic alterations were detected 1640 of them are variants of unknown significance (VUS). A tumor mutational burden (TMB) over 10 up to 67 mutations/mb could be detected in 21 cases. Conclusions: This first analysis of PLATON data shows the feasibility of the network. The obtained molecular results not only provide patient specific therapy follow up but also can provide a baseline data for further projects and substudies. PLATON’s interactive, multicenter, prospective cohort provides a well annotated and managed BioDataBank for translational research. PLATON aims to grow through prospective studies and is open to participation.