Likely Pathogenic Research Articles

Prioritize Variant Reclassification in Pediatric Long QT Syndrome-Time to Revisit.

Congenital long QT syndrome (LQTS) is an inherited arrhythmia syndrome associated with sudden cardiac death. Accurate interpretation and classification of genetic variants in LQTS patients are crucial for effective management. All patients with LQTS with a positive genetic test over the past 18years (2002-2020) in our single tertiary pediatric cardiac center were identified. Reevaluation of the reported variants in LQTS genes was conducted using the American College of Genetics and Genomics (ACMG) guideline after refinement by the US ClinGen SVI working group and guideline by Walsh et al. on genetic variant reclassification, under multidisciplinary input. Among the 59 variants identified. 18 variants (30.5%) were reclassified. A significant larger portion of variants of unknown significance (VUS) were reclassified compared to likely pathogenic (LP)/pathogenic (P) variants (57.7% vs 9.1%, p < 0.001). The rate of reclassification was significantly higher in the limited/disputed evidence group compared to the definite/moderate evidence group (p = 0.0006). All LP/P variants were downgraded in the limited/disputed evidence group (p = 0.0057). VUS upgrades are associated with VUS located in genes within the definite/moderate evidence group (p = 0.0403) and with VUS present in patients exhibiting higher corrected QT intervals (QTc) (p = 0.0445). A significant number of pediatric LQTS variants were reclassified, particularly for VUS. The strength of the gene-disease association of the genes influences the reclassification performance. The study provides important insights and guidance for pediatricians to seek for reclassification of "outdated variants" in order to facilitate contemporary precision medicine.

Townes-Brocks Syndrome Revealed by Kidney Gene Panel Testing

Townes-Brocks syndrome (TBS), a rare autosomal dominant genetic condition associated with SALL1 (Spalt like Transcription Factor 1), is reported to be present in 1:238,000 individuals in the general population. TBS is characterized by the triad of anorectal malformations, dysplastic ears, with or without hearing impairment, and hand or thumb anomalies. Although kidney involvement is less common in TBS, the disease can progress to kidney failure. Here, we sought to characterize the incidence of SALL1 variants in individuals undergoing broad-based genetic testing with a kidney gene panel and to quantify the presence of (extra)renal features. A retrospective analysis of the genetic data from a 385-gene panel identified cases with a pathogenic (P) or likely pathogenic (LP) variant in SALL1. Data including age, features, and disease progression were collected. Of 35,044 samples, P or LP variants in SALL1 were identified in 22, yielding a prevalence of 1:1592 among patients tested for monogenic kidney disease, and 1:342 among cases identified with a monogenic kidney disease. Among this cohort, the median patient age was 23 years (range: 3 months-62 years) with chronic kidney disease (CKD) reported in 91% (20/22) of cases. Reported kidney features included renal agenesis/hypoplasia (7/22; 32%), focal segmental glomerulosclerosis (4/22; 18%), and kidney cysts (3/22; 14%). Confirmed extrarenal features included hearing loss and/or ear features (7/22; 32%), anorectal malformations (6/22; 27%) and hand or thumb abnormalities (4/22; 18%). Three patients (3/22; 14%) had both a priori TBS diagnoses and the traditional "triad." Traditionally, a molecular diagnosis was ascertained primarily in individuals presenting with cardinal features of TBS; therefore, individuals with mild or atypical presentations were often overlooked clinically. Our findings reveal that SALL1 P/LP variants could be a consequential contributor to monogenic kidney disease.

Functional analysis of cell lines derived from SMAD3-related Loeys-Dietz syndrome patients provides insights into genotype-phenotype relation.

Pathogenic (P)/likely pathogenic (LP) SMAD3 variants cause Loeys-Dietz syndrome type 3 (LDS3), which is characterized by arterial aneurysms, dissections and tortuosity throughout the vascular system combined with osteoarthritis. Investigate the impact of P/LP SMAD3 variants with functional tests on patient-derived fibroblasts and vascular smooth muscle cells (VSMCs), to optimize interpretation of SMAD3 variants. A retrospective analysis on clinical data from individuals with a P/LP SMAD3 variant and functional analyses on SMAD3 patient-derived VSMCs and SMAD3 patient-derived fibroblasts, differentiated into myofibroblasts. Individuals with dominant negative (DN) SMAD3 variant in the MH2 domain exhibited more major events (66.7% vs. 44.0%, P= 0.054), occurring at a younger age compared to those with haploinsufficient (HI) variants. The age at first major event was 35.0years [IQR 29.0-47.0] in individuals with DN variants in MH2, compared to 46.0years [IQR 40.0-54.0] in those with HI variants (P = 0.065). Fibroblasts carrying DN SMAD3 variants displayed reduced differentiation potential, contrasting with increased differentiation potential in HI SMAD3 variant fibroblasts. HI SMAD3 variant VSMCs showed elevated SMA expression and altered expression of alternative MYH11 isoforms. DN SMAD3 variant myofibroblasts demonstrated reduced extracellular matrix formation compared to control cell lines. Distinguishing between P/LP HI and DN SMAD3 variants can be achieved by assessing differentiation potential, and SMA and MYH11 expression. The differences between DN and HI SMAD3 variant fibroblasts and VSMCs potentially contribute to the differences in disease manifestation. Notably, myofibroblast differentiation seems a suitable alternative in vitro test system compared to VSMCs.

Prevalence and characteristics of genetic disease in adult kidney stone formers.

Molecular mechanisms of kidney stone formation remain unknown in most patients. Previous studies have shown a high heritability of nephrolithiasis, but data on the prevalence and characteristics of genetic disease in unselected adults with nephrolithiasis are lacking. This study was conducted to fill this important knowledge gap. We performed whole exome sequencing in 787 participants in the Bern Kidney Stone Registry, an unselected cohort of adults with one or more past kidney stone episodes [kidney stone formers (KSFs)] and 114 non-kidney stone formers (NKSFs). An exome-based panel of 34 established nephrolithiasis genes was analysed and variants assessed according to American College of Medical Genetics and Genomics criteria. Pathogenic (P) or likely pathogenic (LP) variants were considered diagnostic. The mean age of KSFs was 47±15years and 18% were first-time KSFs. A Mendelian kidney stone disease was present in 2.9% (23/787) of KSFs. The most common genetic diagnoses were cystinuria (SLC3A1, SLC7A9; n=13), vitamin D-24 hydroxylase deficiency (CYP24A1; n=5) and primary hyperoxaluria (AGXT, GRHPR, HOGA1; n=3). Of the KSFs, 8.1% (64/787) were monoallelic for LP/P variants predisposing to nephrolithiasis, most frequently in SLC34A1/A3 or SLC9A3R1 (n=37), CLDN16 (n=8) and CYP24A1 (n=8). KSFs with Mendelian disease had a lower age at the first stone event (30±14 versus 36±14years; P=.003), were more likely to have cystine stones (23.4% versus 1.4%) and less likely to have calcium oxalate monohydrates stones (31.9% versus 52.5%) compared with KSFs without a genetic diagnosis. The phenotype of KSFs with variants predisposing to nephrolithiasis was subtle and showed significant overlap with KSFs without diagnostic variants. In NKSFs, no Mendelian disease was detected and LP/P variants were significantly less prevalent compared with KSFs (1.8% versus 8.1%). Mendelian disease is uncommon in unselected adult KSFs, yet variants predisposing to nephrolithiasis are significantly enriched in adult KSFs.

Abstract 2408: Comprehensive genomic profiling of ctDNA reveals distinct genomic signatures and therapeutic implications for immunotherapy response in advanced head and neck cancer

Abstract Background: Head and Neck Cancer (HNC) is highly prevalent malignancy in Southeast Asia. We investigated comprehensive genomic profiling (CGP) of ctDNA, aimed to compare genomic landscapes between responders (R) and non-responders (NR) to immunotherapy among advanced HNC patients. Methods: An observational study, ctDNA was evaluated in 69 advanced HNC patients both at the baseline (BL) and during follow up (FL). OncoIndx® CGP was used to identify patient-specific genomic alterations in the ctDNA cohort. Raw sequence alignment and variant calling were performed using iCare® software. Progression-free survival (PFS) and overall survival (OS) were assessed using Kaplan-Meier statistics. Results: Total 250 mutations, encompassing pathogenic (P), likely pathogenic (LP), and variants of unknown significance (VUS), were identified at BL. In FL samples a slight decrease in the overall number of mutations was observed. Loss-of-function (LOF) KMT2C, MSH6 mutations, and activating HNF1α mutations were consistently present at comparable frequencies in BL and FL samples, exhibiting ubiquity across immunotherapy R and NR populations (F test, P 0.00063, OR 13). The variants did not demonstrate statistically significant association with PFS and OS. Most prevalent variants at follow-up emerged from tumor suppressor genes TP53, BRIP1, STAT5B, NF1, suggesting their potential role as therapy-resistant variants. PFS and OS were notably lower for patients with TP53 + BRCA pathway variants compared to their wild-type counterparts (median PFS TP53 + BRCA pathway mutated 2.7 months vs wt 9.1 months, HR = 4.1; median OS TP53 + BRCA pathway mutated 4.7 months vs 12.8 months for wt, HR 7.7). Similarly STAT5B carriers compared to the wild-type STAT5B-bearing population. Multivariate analysis further confirmed the independent role of TP53 + BRCA pathway and STAT5B variants as determinants for worst outcome (P 0.006, HR2.5). Population with prevalent TP53 and STAT5B LOF variants exhibited a strong negative correlation with the PD-L1 score compared to the population with their wild-type counterparts (P 0.03). Average scores for genome-wide homologous recombination deficiency (HRD), bTMB, and loss of LOH were low at BL and FL and did not correlate with the PD-L1 score. Interestingly, bTMB was low for the cohort, Tumor fraction (TF) emerged as an independent prognosticator for OS and PFS. Conclusions: ctDNA revealed distinct genomic signatures in R and NR populations at BL and FL. Significant prevalence of TP53, BRIP1, STAT5B, and NF1 in the NR population suggest a potential role in conferring immunotherapy resistance. Genomic signatures, TMB and TF impacted survival of immunotherapy responders. Integrating CGP into SOC protocol may help in identifying therapy resistance in advanced HNC patients who did not respond to initial treatment. Citation Format: Atul Bharde, Vanita Noronha, Mrunal Ratnaparkhi, Vijay Patil, Bhagwat Jadhav, Sangeeta Prajapati, Anuradha Choughule, Pratik Chandrani, Sumit Haldar, Fauzul Moubeen, Nandini Menon, Kanchan Hariramani, Madhura Basavalingegowda, Aarthi Ramesh, Jayant Khandare, Pankaj Chaturvedi, Gowhar Shafi, Kumar Prabhash. Comprehensive genomic profiling of ctDNA reveals distinct genomic signatures and therapeutic implications for immunotherapy response in advanced head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2408.

Abstract 6372: Germline pathogenic variants are enriched in pediatric central nervous system tumor patients and associate with somatic functional consequences

Abstract The genetic contribution of rare pathogenic germline variation to central nervous system (CNS) tumor formation in pediatric patients without a family history of cancer remains unclear. We sought to characterize the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in 838 patients profiled in the Pediatric Brain Tumor Atlas (PBTA) by whole genome sequencing (n=821) or whole exome sequencing (n=17). Rare variants in 214 CPGs were annotated as pathogenic (P) or likely pathogenic (LP) consistent with American College of Medical Genetics criteria using AutoGVP, our open-source automated pathogenicity assessment tool. To assess enrichment of P/LP variants in the PBTA, we compared the frequency of CPG P/LP variants in cases to a tumor-free control cohort from Penn Medicine BioBank (PMBB; n=6,295). Somatic alterations, mutational signatures, and gene set enrichment analyses from matched tumor sequencing were integrated to characterize functional consequences associated with germline pathogenic variation. We observed 215 germline P/LP variants within 76 distinct CPGs in 189 (22.6%) PBTA patients. CPG P/LP variants were most prevalent among patients with a plexiform neurofibroma diagnosis (9/14, 64.3%), and least prevalent among patients with craniopharyngioma (3/39, 7.8%). We detected syndrome-associated P/LP variants in 45/58 (77.6%) patients with a clinically reported cancer predisposition syndrome and incidentally in another 37 patients. CPG P/LP variants were significantly enriched in the PBTA cohort relative to the PMBB control cohort (OR=2.0, p=1.0E-12, CI=1.6-2.4), and NF1 harbored the most significant excess P/LP variant burden (OR=30.7, p=4.57E-13, CI=11.2-105.1). We observed a significant enrichment of mismatch repair (MMR) gene P/LP variants in patients with high-grade gliomas (HGG) and tumors from MMR P/LP carriers exhibited significantly higher MMR-deficiency mutational signature exposures relative to tumors from non-carrier HGG patients (SBS14: W=478, p=1.71E-05). Overall, 90/215 (41.9%) of identified germline P/LP variants co-occurred with at least one corresponding somatic alteration in matched tumors, including oncogenic SNV (n=5), copy number variation (n=28), loss of heterozygosity (n=54), differential gene expression (n=23), and proximal alternative splicing (n=19). In summary, rare germline P/LP variants are enriched in PBTA patients and are associated with somatic events in the same gene, resulting in gene- and pathway-specific functional consequences. Our work emphasizes a role for pathogenic germline variation in pediatric CNS tumor development and frequent under-identification of cancer predisposition syndromes, underscoring the importance of germline sequencing in personalized patient care strategies. Citation Format: Ryan J. Corbett, Rebecca Kaufman, Shelly W. McQuaid, Zalman Vaksman, Saksham Phul, Miguel A. Brown, Jennifer L. Mason, Heena Desai, Ryan Hausler, Ammar S. Naqvi, Antonia Chroni, Zhuangzhuang Geng, Bo Zhang, Chuwei Zhong, Yuankun Zhu, Allison P. Heath, Marilyn Li, Penn Medicine BioBank, Phillip B. Storm, Adam C. Resnick, Kara N. Maxwell, Miriam Bornhorst, Kristina A. Cole, Angela J. Waanders, Suzanne P. MacFarland, Jo Lynne Rokita, Sharon J. Diskin. Germline pathogenic variants are enriched in pediatric central nervous system tumor patients and associate with somatic functional consequences [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6372.

Abstract 6133: Genetic profiling landscape among gynecological and breast cancer patients in the borde city of Tijuana, Mexico: A comprehensive study

Abstract Background: Individuals in Tijuana have been identified as having multicultural and racial diversity. In Baja, California, Mexico, the prevalence and composition of cancer-predisposing germline variants in gynecologic cancers in Tijuana patients have not been evaluated. Aim and Methods: We aimed to evaluate the prevalence of pathogenic variants (PV) using a panel of 84 cancer-predisposing genes in breast, endometrial, and ovarian cancer from the General Hospital of Tijuana during the period of October 2021-October 2023, who were contacted and invited to participate in the evaluation. Pre- and post-test genetic counseling was given, and a questionnaire on personal, gyneco-obstetric, demographic, and lifestyle variables was conducted. Peripheral blood samples were obtained from all patients, and Next-generation sequencing (NGS) was performed on the Illumina commercial platform (Illumina, SD, USA). Variants were classified according to the American College of Medical Genetics and Genomics (ACMG). Data was collected and descriptive statistics was applied to describe the characteristics of the population. Results: A total of 51 patients were included in our cohort; 98.0% (50/51) were females and 2% (1/51) were males. Among study participants (mean age ±standard deviation: 46.1 ± 10.9), 49% reported a personal history of cancer (25/51). Diagnosis of breast cancer was present in 80.3% of the patients (41/51), 9% (5/51) with ovarian cancer, and 3.9% (2/51) with endometrial cancer. Twenty-five percent of participants (13/51) harbor a PV or likely pathogenic (LP) variant distributed among four cancer-risk genes (BRCA1, BRCA2, ATM, and TP53). The distribution by gene in the patients with a PV was: BRCA1 in 61% (8/13), BRCA2 in 23% (3/13), TP53 in 8% (1/13), and ATM in 8% (1/13). Whereas 39.2% (20/51) had variants of uncertain clinical significance in genes with ambiguous or non-well-established risk association for cancer (BARD1, AXIN2, GPC3, NF2, CEBPA, MSH3, ALK, DIS3L2, CDC73, BAP1, RAD51D, NF1, MSH2, BLM, NBN, BRCA2, BARD1, RUNX1, RECQL4, EGFR, PALB2, CASR, and POLD1), and 35.2% (18/51) had negative results for both; PV and VUS. Conclusion: Our findings show a diverse pathogenic variant composition among the recruited individuals of the gynecological cancer population in Tijuana, Mexico, consistent with being a high-risk population for genetic diseases, which warrants further investigation to adequately assess the burden of hereditary cancer and implement appropriate preventative programs. Disparities in access to testing have a significant impact on affected populations, due in part to underrepresentation in surveys of regional cancer etiology and in genomic variant databases. Citation Format: Jorge Alberto Guadarrama-Orozco, Paula Leal-Anaya, Eva Guerrero-Santillan. Genetic profiling landscape among gynecological and breast cancer patients in the borde city of Tijuana, Mexico: A comprehensive study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6133.

Abstract 7506: Comprehensive mutational profile of true single circulating tumor cells compared with CtDNA in advanced pancreatic adenocarcinoma

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDAC) is aggressive malignancy characterized by 5-year survival rate of &amp;lt;10%. Comprehending PDAC's mutational landscape through NGS-based assays, acquiring representative tumor tissue biopsies remains arduous. Single circulating tumor cell (sCTC) genomics could provide clinically relevant personalized diagnostics. Here we demonstrate comparative analysis of sCTCs genomics and ctDNA outcomes in paired advanced PDAC patients. Methods: Retrospectively, 25 live sCTCs and sCTC clusters were isolated from 10 advanced PDAC patients' blood using OncoRadar platform consisting glass beads conjugated with antiEPCam antibodies, tuned for releasing CTCs, without cell fixing, an assay in 96 well plate. Whole genomes from sCTCs were amplified using random degenerate primer-based PCR. Amplified genomes and paired ctDNA were subjected to CGP using clinical assay OncoIndx® to identify patient-specific genomic alterations in sCTC and paired ctDNA samples. The raw sequence alignment and variant calling was performed using iCare software®. Results: Live 25 sCTCs and 8 CTC clusters were isolated (≥2 CTCs). Mutational profiling revealed multiple pathogenic (P) and likely pathogenic (LP) variants. sCTCs exhibited at least twice as many P variants compared to paired ctDNA samples, with CHD4, FGFR2, and HNF1α being the most common. The mutational profile of sCTCs showed concordance with at least one variant in paired ctDNA, and was enriched in dysregulated cytoskeleton and cell migration machinery. Specifically, COL7A, KIF5B, and RHOA mutations were prevalent in almost all sCTCs, with exclusive mutations (KIF5B and RHOA) in some cases. KRAS P variants were exclusive to 50% of ctDNA samples, paired sCTCs exhibited NRAS P variants. RAS isoforms were observed in 70% of sCTCs. Gene amplification occurred in CCND1/2, FGFR2, and ERBB2 in 90% of sCTCs, with CCND1 amplification more prevalent in sCTC clusters. Mutations in epigenetic repressors (HDAC1, KDM2B) were ubiquitous in sCTCs, co-occurring with DDR pathway mutations (F test, P 0.003, OR 11). Loss-of-function BRCA mutations were detected in 60% of sCTCs, and were absent in paired ctDNA. Additionally, 70% of sCTCs exhibited therapy-resistant variants (NF1, STK11, ARID1A, and PIK3CA), contrasting with a 10% frequency in paired ctDNA. Conclusions: Genomic profile of sCTCs in advanced PDAC patients revealed a complex mutational landscape, providing additional clinically relevant insights that complemented ctDNA findings. sCTCs exhibited greater tumor mutational heterogeneity compared to paired ctDNA samples, and detected additional actionable pathogenic variants. Results suggest that sCTCs may offer therapeutically relevant molecular information for advanced PDAC patients for whom tissue is unavailable and ctDNA fails to provide actionable therapy options. Citation Format: Jayant Khandare, Atul Bharde, Ganesh Khutale, Saloni Andhari, Richa Deshpande, Kanchan Hariramani, Madhura Basavalingegowda, Vikas Jadhav, Mohan Uttarwar, Gowhar Shafi. Comprehensive mutational profile of true single circulating tumor cells compared with CtDNA in advanced pancreatic adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7506.

Chromosomal microarray testing yield in 829 cases of microcephaly: a clinical characteristics-based analysis for prenatal and postnatal cases

IntroductionMicrocephaly, characterized by abnormal head growth, can often serve as an initial indicator of congenital, genetic, or acquired disorders. In this study, we sought to evaluate the effectiveness of chromosomal microarray (CMA) testing in detecting abnormalities in both prenatal and postnatal cases of microcephaly.Materials and methodsCMA Testing: We conducted CMA testing on 87 prenatally-detected microcephaly cases and 742 postnatal cases at a single laboratory. We evaluated the CMA yield in relation to specific clinical characteristics.ResultsIn prenatal cases, pathogenic and likely pathogenic (LP) results were identified in 4.6% of cases, a significantly higher rate compared to low-risk pregnancies. The male-to-female ratio in this cohort was 3, and the CMA yield was not influenced by gender or other clinical parameters. For postnatal cases, the CMA yield was 15.0%, with a significantly higher detection rate associated with dysmorphism, hypotonia, epilepsy, congenital heart malformations (CHM), learning disabilities (LD), and a history of Fetal growth restriction (FGR). No specific recurrent copy number variations (CNVs) were observed, and the rate of variants of unknown significance was 3.9%.ConclusionsThe yield of CMA testing in prenatal microcephaly is lower than in postnatal cases (4.6% vs. 15%). The presence of microcephaly, combined with dysmorphism, hypotonia, epilepsy, CHD, LD, and FGR, significantly increases the likelihood of an abnormal CMA result.

Author Correction: Genetic variants identified in novel candidate genes for anorexia nervosa and analysis of molecular pathways for diagnostic applications.

Correction to: Eur Rev Med Pharmacol Sci 2023; 27 (6 Suppl): 77-88-DOI: 10.26355/eurrev_202312_34692 After publication and following some post-publication concerns, the authors have applied the following corrections to the galley proof. The conflict of interest section has been amended as follows: K. Donato is employee at MAGI EUREGIO and MAGISNAT. G. Marceddu is employee at MAGI EUREGIO. M. Bertelli is president of MAGI EUREGIO, MAGISNAT, and MAGI's LAB. M.C. Medori, A. Macchia, S. Cecchin, C. Micheletti, K. Dhuli, G. Madeo, G. Bonetti are employees at MAGI's LAB. M. Bertelli, M.R. Ceccarini, and P. Chiurazzi are patent inventors (US20220362260A11). M. Bertelli, P.E. Maltese, G. Marceddu, and S. Cecchin are patent inventors (US20230173003A1). M. Bertelli, K. Dhuli, and P.E. Maltese are patent inventors (WO2022079498A1). M. Bertelli, K. Donato, M.C. Medori, M.R. Ceccarini, T. Beccari, P. Chiurazzi, C. Micheletti, K. Dhuli, G. Bonetti, G. Marceddu are patent applicants (Application Number: 18/466.879). The remaining authors have no conflict of interest to disclose. Since the current study shares the same NGS panel for the genetic analysis as the study cited in Ref. 5 (Ceccarini MR, Precone V, Manara E, Paolacci S, Maltese PE, Benfatti V, Dhuli K, Donato K, Guerri G, Marceddu G, Chiurazzi P, Dalla Ragione L, Beccari T, Bertelli M. A next generation sequencing gene panel for use in the diagnosis of anorexia nervosa. Eat Weight Disord 2022; 27: 1869-1880), the authors amend the following sentence: "A subset comprising 163 genes from a dedicated Next-Generation Sequencing (NGS) panel was analyzed5" in "A subset comprising 163 genes from a dedicated Next-Generation Sequencing (NGS) panel, previously used in the study by Ceccarini et al5, was analyzed". The authors clarify that the analyzed patients of the two articles are completely independent. To clarify the data reported in Table II, the authors amend the following sentence: "Genetic variants identified in the AN population are reported in Table II." In "The genomic sequencing NGS was performed in all 135 patients recruited in the study. After obtaining the raw data, based on the ACMG guidelines (https://www.acmg.net/ACMG/Medical-Genetics-Practice-Resources/Practice-Guidelines.aspx), the results were filtered, and Table II reports the variants considered Pathogenic (P), likely pathogenic (LP), and Variable with Uncertain Significance (VUS), 61 patients in total". Consequently, to improve clarity, the legend of Table II has been amended as follows: Genetic variants identified in 61 patients out of the total 135 patients analyzed by NGS. There are amendments to this paper. The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/34692.

Mutational spectrum in patients with dominant non-syndromic hearing loss in Austria

PurposeHearing loss (HL) is often monogenic. The clinical importance of genetic testing in HL may further increase when gene therapy products become available. Diagnoses are, however, complicated by a high genetic and allelic heterogeneity, particularly of autosomal dominant (AD) HL. This work aimed to characterize the mutational spectrum of AD HL in Austria.MethodsIn an ongoing prospective study, 27 consecutive index patients clinically diagnosed with non-syndromic AD HL, including 18 previously unpublished cases, were analyzed using whole-exome sequencing (WES) and gene panels. Novel variants were characterized using literature and bioinformatic means. Two additional Austrian medical centers provided AD HL mutational data obtained with in-house pipelines. Other Austrian cases of AD HL were gathered from literature.ResultsThe solve rate (variants graded as likely pathogenic (LP) or pathogenic (P)) within our cohort amounted to 59.26% (16/27). MYO6 variants were the most common cause. One third of LP/P variants were truncating variants in haploinsufficiency genes. Ten novel variants in HL genes were identified, including six graded as LP or P. In one cohort case and one external case, the analysis uncovered previously unrecognized syndromic presentations.ConclusionMore than half of AD HL cases analyzed at our center were solved with WES. Our data demonstrate the importance of genetic testing, especially for the diagnosis of syndromic presentations, enhance the molecular knowledge of genetic HL, and support other laboratories in the interpretation of variants.

Genetic complexity of diagnostically unresolved Ehlers-Danlos syndrome

BackgroundThe Ehlers-Danlos syndromes (EDS) are heritable disorders of connective tissue (HDCT), reclassified in the 2017 nosology into 13 subtypes. The genetic basis for hypermobile Ehlers-Danlos syndrome (hEDS) remains unknown.MethodsWhole exome...

Chromosomal Microarray Analysis in Fetuses with Ultrasound Abnormalities.

To explore and evaluate the value of chromosomal microarray analysis (CMA) in prenatal diagnosis of fetuses with ultrasound abnormalities. A retrospective analysis was performed on 370 fetuses with ultrasound abnormalities received invasive prenatal diagnosis at Meizhou People's Hospital from October 2022 to December 2023. Fetal specimens were analyzed by CMA, and the detection rates of aneuploidy and pathogenic (P)/likely pathogenic (LP) copy number variations (CNVs) in ultrasound structural abnormalities (malformations of fetal anatomy) and non-structural abnormalities (abnormalities of fetal nonanatomical structure) were analyzed. There were 114 (30.8%) cases with isolated ultrasound structural abnormalities, 226 (61.1%) cases with isolated non-structural abnormalities (182 isolated ultrasound soft markers abnormalities, 30 isolated fetal growth restriction (FGR), and 8 isolated abnormalities of amniotic fluid volume), and 30 (8.1%) cases with both structural and non-structural abnormalities. The overall detection rate of aneuploidy and P/LP CNVs in isolated ultrasonic structural abnormalities was 5.3%, among which cardiovascular system abnormalities were the highest. In addition, the largest number of fetuses with non-structural abnormalities was nuchal translucency (NT) thickening (n = 81), followed by ventriculomegaly (n = 29), and nasal bone dysplasia (n = 24). The detection rate of chromosomal abnormalities of fetuses with abnormal ultrasound soft markers was 9.9%, and the detection rate in single abnormal ultrasound soft marker, and multiple ultrasound soft markers abnormalities was 9.7% (16/165) and 11.8% (2/17), respectively. Moreover, the detection rate of chromosomal abnormalities of fetuses with FGR and structural abnormalities combined with non-structural abnormalities was 6.7% (2/30), and 13.3% (4/30), respectively. The incidence of chromosomal abnormalities (aneuploidy and P/LP CNVs) varies among different fetal ultrasound abnormalities.

A case of enamel renal syndrome from a novel genetic mutation, multidisciplinary management and long-term prognosis.

The heterogeneous features of enamel renal syndrome (ERS) make diagnosis and treatment challenging. The main symptoms are disturbed amelogenesis and nephrocalcinosis. Bi-allelic likely pathogenic (LP) or pathogenic (P) variants in FAM20A have been associated with the syndrome since 2012. Affected patients often receive extensive dental treatment because of deviant orofacial morphology. However, knowledge about long-term prognosis and treatment guidelines are still lacking. The complex nature of ERS might endanger both dental and general health. The purpose of this article is to highlight the risks of overlooking the symptoms of the syndrome, and to discuss management strategies, surveillance and prognosis. We report the management of a case with suspected ERS after initial dental treatment elsewhere with no adjustment for the syndrome. Dental treatment was revised and followed for 8 years. Complementary medical examinations were conducted, and ERS was genetically confirmed, revealing homozygosity for a LP c.755_757del, p.(Phe252del) variant in FAM20A. The nephrological investigation revealed medullary calcium deposits, normal renal function and hypophosphatemia. Urine analysis revealed hypocitraturia and hypocalciuria. Accordingly, the patient now medicates with potassium citrate to decrease the risk of progressive renal stone formation. We herein describe a patient with confirmed ERS with an 8-year follow-up. Diagnostic delay until adulthood led to complicated dental treatment. The results of nephrological investigations are presented. The importance of dental and medical multidisciplinary management in syndromic disorders affecting the formation of the enamel is also exemplified. The dental prognosis after rehabilitation is likely affected by anatomical variations and patient cooperation. The prognosis for renal function seems to be good. However, lifelong surveillance of renal function is recommended. The ethics committee in Uppsala, Sweden, determined that ethical approval was not necessary in this case (2019-04835). Informed consent was obtained from the participant in writing and is documented in the medical records.

Diagnosis of Primary Ciliary Dyskinesia via Whole Exome Sequencing and Histologic Findings.

To assess the diagnostic potential of whole-exome sequencing (WES) and elucidate the clinical and genetic characteristics of primary ciliary dyskinesia (PCD) in the Korean population. Forty-seven patients clinically suspected of having PCD were enrolled at a tertiary medical center. WES was performed in all patients, and seven patients received biopsy of cilia and transmission electron microscopy (TEM). Overall, PCD was diagnosed in 10 (21.3%) patients: eight by WES (8/47, 17%), four by TEM. Among patients diagnosed as PCD based on TEM results, two patients showed consistent results with WES and TEM of PCD (2/4, 50%). In addition, five patients, who were not included in the final PCD diagnosis group, had variants of unknown significance in PCD-related genes (5/47, 10.6%). The most frequent pathogenic (P)/likely pathogenic (LP) variants were detected in DNAH11 (n=4, 21.1%), DRC1 (n=4, 21.1%), and DNAH5 (n=4, 21.1%). Among the detected 17 P/LP variants in PCD-related genes in this study, 8 (47.1%) were identified as novel variants. Regarding the genotype-phenotype correlation in this study, the authors experienced severe PCD cases caused by the LP/P variants in MCIDAS, DRC1, and CCDC39. Through this study, we were able to confirm the value of WES as one of the diagnostic tools for PCD, which increases with TEM, rather than single gene tests. These results will prove useful to hospitals with limited access to PCD diagnostic testing but with relatively efficient in-house or outsourced access to genetic testing at a pre-symptomatic or early disease stage.

Genetic epidemiology of monogenic dyslipidemia and statin-associated adverse drug phenotypes in Indian population from whole-genomes of 1029 self-declared healthy individuals

BackgroundMonogenic dyslipidemia is a group of inherited genetic disorders characterized by abnormal levels of lipids and lipoproteins in blood, contributing to a significant risk for coronary artery diseases (CAD) and stroke. There is a paucity of prevalence estimates and genetic epidemiology of monogenic dyslipidemia in South Asian populations. The availability of population-scale genome sequencing datasets could potentially enable a better understanding of the genetic epidemiology of the disease. MethodsWe analyzed whole-genome sequence data of 1029 healthy individuals from India to identify pathogenic variants in 24 genes associated with 26 primary monogenic dyslipidemias. The American College of Medical Genetics and Genomics (ACMG) guidelines was used to classify the variants. We also inferred statin-associated adverse drug phenotypes from SLCO1B1, ABCG2, and CYP2C9 genotypes/haplotypes. ResultsOur analysis identified 12 pathogenic (P) and 9 likely pathogenic (LP) variants in 10 different genes. Autosomal dominant monogenic dyslipidemia prevalence ranged from 0.1% to 0.9%, while autosomal recessive disorder ranged from 0.000005% and 0.0005%. An infrequent ε4/ε4 APOE genotype associated with hypercholesterolemia was found in 1% of samples. Our pharmacogenomic analysis revealed that 10% may require reduced dosage for most statins including atorvastatin, and 1.5% may require reduced dosage for rosuvastatin. ConclusionOur study emphasizes the need for population-scale screening to enable early diagnosis and appropriate treatment of monogenic dyslipidemia in India. By identifying variants and estimating prevalence, our findings can inform healthcare providers in developing targeted prevention and management strategies to reduce cardiovascular disease risk.

Clinical phenotype and genetic characteristics of SZT2 related diseases: A case report and literature review

PurposeSeizure threshold 2 protein homolog gene (SZT2, MIM: 615463) related diseases are extremely rare autosomal recessive disorders with a wide spectrum of clinical phenotypes ranging from mild intellectual impairment to severe developmental epileptic encephalopathy (DEE). Most SZT2 related diseases are accompanied by craniofacial malformation and corpus callosum malformation. This study attempts to analyze and summarize the clinical phenotype and genetic characteristics of SZT2 related diseases, providing a basis for early diagnosis, treatment, and prognosis. MethodWe analyzed the clinical characteristics of a Chinese child with pathogenic variants of SZT2. We also performed whole-exome sequencing (WES) on the patient. In addition, we conducted a literature review of previously reported patients with pathogenic mutations in the SZT2 gene. ResultThe proband was a boy aged 1 year and 9 months with severe global developmental delay, transient drug-controlled focal epilepsy, cluster epilepsy, autism spectrum disorder, craniofacial deformity, hypotonia, focal EEG discharge, corpus callosum malformation, and persistent cavum septum pellucidum. WES revealed that the patient carried the SZT2 gene c.7584dupA and c.6302A>C complex heterozygous variants; the former being Likely Pathogenic (LP) and the latter Uncertain Significance (VUS) according to ACMG classification guidelines. According to our literature review, 43 cases of SZT2 related diseases have been reported so far; these include 15 cases with homozygous variations and 28 cases with complex heterozygous variations. A total of 57 types of variation were found, including 47 genetic variants, 2 de novo variants, and 8 unknown genetic modes. In addition, 2 high-frequency variants were found (c.5949_5951delTGT and c.6553C>T). The main clinical manifestations of the 40 patients were global developmental delay (GDD) of varying degrees (38/40, 95.00%), seizures (36/40, 90.00%), cranial deformity (27/40, 67.50%), facial deformity (22/40, 55.00%), hypotonia (22/40, 55.00%), abnormal interseizure EEG discharge (26/40, 65.00%), slow background activity (20/40, 50.00%), corpus callosum deformity (18/40, 45.00%). There was also one case of sudden unexpected death in epilepsy (SUDEP) and 3 cases of death from infection. In addition, three fetuses with the same variant had hydrocephalus and encephalocele. ConclusionThe compound heterozygous mutation of c.7584dupA and c.6302A>C in the SZT2 gene is the genetic etiology of this patient, expanding the mutation spectrum of SZT2 related diseases. Early genetic testing is the best choice for clear diagnosis, treatment, and prognosis.

The diagnostic yield of exome sequencing in liver diseases from a curated gene panel

Exome sequencing (ES) has been used in a variety of clinical settings but there are limited data on its utility for diagnosis and/or prediction of monogenic liver diseases. We developed a curated list of 502 genes for monogenic disorders associated with liver phenotypes and analyzed ES data for these genes in 758 patients with chronic liver diseases (CLD). For comparison, we examined ES data in 7856 self-declared healthy controls (HC), and 2187 patients with chronic kidney disease (CKD). Candidate pathogenic (P) or likely pathogenic (LP) variants were initially identified in 19.9% of participants, most of which were attributable to previously reported pathogenic variants with implausibly high allele frequencies. After variant annotation and filtering based on population minor allele frequency (MAF ≤ 10–4 for dominant disorders and MAF ≤ 10–3 for recessive disorders), we detected a significant enrichment of P/LP variants in the CLD cohort compared to the HC cohort (X2 test OR 5.00, 95% CI 3.06–8.18, p value = 4.5e−12). A second-level manual annotation was necessary to capture true pathogenic variants that were removed by stringent allele frequency and quality filters. After these sequential steps, the diagnostic rate of monogenic disorders was 5.7% in the CLD cohort, attributable to P/LP variants in 25 genes. We also identified concordant liver disease phenotypes for 15/22 kidney disease patients with P/LP variants in liver genes, mostly associated with cystic liver disease phenotypes. Sequencing results had many implications for clinical management, including familial testing for early diagnosis and management, preventative screening for associated comorbidities, and in some cases for therapy. Exome sequencing provided a 5.7% diagnostic rate in CLD patients and required multiple rounds of review to reduce both false positive and false negative findings. The identification of concordant phenotypes in many patients with P/LP variants and no known liver disease also indicates a potential for predictive testing for selected monogenic liver disorders.

Correlation of TCR Repertoire Diversity with Myeloid Gene Mutations in Chronic and Advanced Phase Myeloproliferative Neoplasms

Introduction: Myeloproliferative neoplasms (MPN) are characterized by a chronic phase (CP), with indolent clinical behavior and, in 10-30% of cases, progression to advanced phases (AP), with aggressive behavior and compromised prognosis. Numerous factors have been associated with progression to AP, including the acquisition of mutations in recurrently mutated myeloid genes (1,2). On the other hand, decreased diversity in the T-cell receptor (TCR) repertoire has been associated with worse prognosis in solid tumors. The purpose of this work is to study the correlation between the acquisition of mutations in myeloid genes and the diversity of the TCR repertoire in chronic and advanced myeloproliferative neoplasms. Methods: Patients with chronic CP and AP myeloproliferative neoplasms were selected. The selected patients underwent an NGS panel of 48 myeloid genes. Only pathogenic (P) or likely pathogenic (LP) variants were considered. In parallel, the study of the TCR repertoire by NGS with the panel “AmpliSeq for Illumina Immune Repertoire Plus, TCR beta Panel” (Illumina™) was performed on the available samples. Finally, the obtained data were correlated. The study was approved by the local ethics committee. Results: A total of 22 patients were selected, 10 in CP and 12 in AP. Regarding diagnosis, 8 were polycythemia vera (PV), 4 essential thrombocythemia (ET), 6 secondary myelofibrosis (MFS) (1 to PV and 5 to ET), 2 systemic mastocytosis (MS) and 1 primary myelofibrosis (MFP). Eighty percent were male and the mean age was 68 years. The AP patients were significantly older (74 vs. 62 years of age, p&amp;lt;0,001). Regarding the myeloid NGS panel result, 41 mutations were found in 19 patients. Fourteen percent of the patients had no mutation, 36% had an isolated driver mutation and 50% had additional mutations. Of these, 9% were in CP and 81% were in AP. The most recurrently mutated genes were JAK2 (45.4%), CALR (18.2%), ASXL1, IDH2, SRSF2, IDH2 (all 13.6%), MPL and KIT (both 9.1%). Regarding the results of the TCR repertoire, it was possible to perform the study in 11 patients, 4 in CP and 7 in AP. Only 6/11 had results of sufficient quality to allow analysis. Of these 6 patients, 3 were in CP and 3 in AP. As can be seen in Figure 1, the diversity of the TCR between CP patients and PC patients was different. Thus, while the pattern of diversity in the CP phase shows the expected distribution, the diversity in AP shows a characteristic pattern. Conclusions: APs of MPNs show an abnormal TCR diversity pattern. This pattern may be related to the acquisition of myeloid gene mutations in AP. To our knowledge, this is the first study demonstrating an alteration in TCR diversity in AP and opens the door to future fields of research.

Del(20q) As a Somatic Gene Rescue in Adult Patients: Can Germline Mutations Other Than SBDS be Found in Affected Patients?

Deletions involving chromosome 20 (20q-) are present in up to 5-8% of myeloid neoplasms (MN) and have been associated with either myelodysplastic (MDS) or myeloproliferative (MPN) features, chiefly myelofibrosis. Theoretically, any chromosomal deletion may result in haploinsufficient expression of tumor suppressor genes (TSGs) or in loss of a protective allele in heterozygous carriers of germline (GL) variants or heterozygous somatic (SM) mutations. However, deletions have also been implicated as a maladaptive somatic gene rescue (SGR) event in carriers of GL bone marrow failure (BMF) genes such as SAMD9 and SBDS. The latter is found in Shwachman-Diamond syndrome whereby the upregulated EIF6 gene, responsible for hematopoietic dysfunction, is clonally removed by SM 20q deletion event. We identified an interesting 35-years-old patient with mild cytopenia and 20q- in which a cryptic homozygous SBDS c.A148T GL mutation was found. This prompted us to search in other adult patients with 20q deletion for: i) other cases with SBDS gene alteration (both hetero and homozygous), ii) other GL variants which could be clonally relieved by compensatory 20q- or, iii) disease-prone GL variants on 20q, whereby either disease-prone suppressive allele is included in the deleted region. Within a cohort of 5,308 cases with various MN, 215 patients with 20q- were identified. WES results were available for 350 patients. We applied a stringent bioanalytic algorithm to identify unique GL alterations (not deposited in SM databases) in genes expressed in hematopoietic tissues and involved in BMF and cancer, and a population allelic frequency of &amp;lt;1% which were classified as pathogenic (P), likely pathogenic (LP), and VUS with particular level of clinical suspicion (sVUS). In 76 of 215 patients with 20q-, 346 GL mutations in genes of potential interest were identified and further analyzed. No P/LP variants were detected on genes within commonly deleted region on chr.20q, and no additional carriers of SBDS variants were found. However, we identified 9 pathogenic GL variants in potentially pertinent genes including GL alterations in DDX41, STAG2 and TP53 which have been described in the context of MN. However, these gene variants were also present in patients with diploid 20q. The remaining 6 variants included heterozygous P/LP GL alterations in 3 different Fanconi anemia genes ( FANCA, FANCM, FANCD2), SUZ12, and TINF2. The latter, TINF2, a telosome gene, known to be mutated in dyskeratosis congenita (DC), carried an LOF c.605-1G&amp;gt;A in a patient with MDS/MPN with a family history of cancer who later developed 20q-. The patient did not show any symptoms of DC-like features, which usually present at an early age. Since FANCA LOF with SGR via overepression of EIF6 has previously been described 1, we investigated and did not identify any cases in our cohort of EIF6 SGR resultant overexpression. While occasional patients with no previously diagnosed SBDS can be found among MDS with 20q-, screening for SBDS genes demonstrates that such a genetic configuration among adult patients with 20q is very rare. In addition, only 9 out of 215 patients with 20q- carried other pathogenic GL variants in non-recurrent genes which appear to be likely coincidental. This suggests that del20q is not a SGR in response to a GL mutation, but rather a SGR due to other aforementioned mechanisms, which are currently being explored in our cohort of patients.