Targeted Next-generation Sequencing Panel Research Articles

Novel compound heterozygous variants in LTBP2 associated with relative anterior microphthalmos.

Relative anterior microphthalmos (RAM) is a rare congenital defect associated with severe vision impairment that is primarily caused by genetic alterations. The purpose of this study was to identify the causative genetic variants in two Chinese families with RAM with an autosomal recessive inheritance pattern. DNA samples were obtained from two probands and their family members. Targeted next-generation sequencing (NGS) was used to screen 425 genes associated with inherited eye diseases to identify possible disease-causing variants in the two patients. Sanger sequencing was subsequently used to validate the results in both families. The targeted NGS panel identified potentially causative novel variants of the latent transforming growth factor beta binding protein 2 (LTBP2) gene in the two RAM families: a missense variant (c.2771C > T; p.Ala924Val) and an intronic variant (c.4582 + 9A > G) in Family A and a different missense variant (c.5239C > A; p.Arg1747Ser) and a synonymous variant (c.951G > A; p.Pro317Pro) in Family B. These four novel variants all cosegregated with the disease phenotype. To our knowledge, this is the first study to report novel LTBP2 gene variants related to RAM. Considering the importance of LTBP2 in ocular development, we provide initial insights into the potential pathogenic mechanisms of LTBP2 in RAM.

Abstract 5058: Genomic alterations predictive of outcome in early staged cervical cancer: A translational investigation from the SENTICOL III trial

Abstract Background: The risk of relapse in patients with early-stage cervical cancer (ESCC) ranges from 4-14% (LACC study). Risk-factors for recurrence are mainly derived from histopathological factors. Senticol III is a large multicenter international randomized prospective study aims to validate sentinel lymph node biopsy in the surgical management of ESCC. Our objective is to characterize prognostic and actionable biomarkers in ESCC. Methods: FFPE-fixed tumoral slides of the first 150 randomized patients were analyzed based on SEDLIS criteria. We characterized TIL’s infiltration, PD-L1 expression and HPV status. Sequencing of tumor DNA was carried out using an in-house targeted next-generation sequencing panel (571 genes). Relapse-free survival (RFS) was defined as the time between randomization and relapse of any type. We performed Fisher’s exact test and Student’s t-test to compare distributions of categorical variables and Log Rank test. Results: The sequencing quality control criteria were met for 135 samples. PIK3CA was the most commonly altered gene (17%). Loss-of-function variants in KMT2-family genes (KTM2C 9%, KMT2D 6%, KMT2A 1%) were found in 16% of samples. The loss-of-function variant of ARID1A was mostly non-sense mutation (6%). Activations of ERBB2 (5%) were 3 focal amplifications and 4 hotspot missense mutations. Two samples were found to have microsatellite instability due to an alteration of MLH1. The Pik3/AKT/mTOR (26%) and the chromatin remodeling (23%) pathways were the most altered pathways. The median follow-up period was 20 months. There were 6 relapses, of which 80% were considered as low risk based on SEDLIS criteria. Recurrences were local and occurred 9-23 months following surgery. Multiparity was the only clinical feature associated with RFS (p < 0,001). Tumor size, histological subtypes, PD-L1 status, number of TIL’s, presence or absence of lymphovascular emboli and deep stromal invasion were not associated with RFS in our cohort.KMT2C (p=0,018) and ARID1A (p < 0,001) pathogen variants were significantly associated with RFS. The pathway chromatin remodeling (p=0,063) showed a trend toward association with RFS. We found 32% of genomic alterations actionable for a target therapy including mutations of PIK3CA, ERBB2, ARID1A, PTEN, BRCA2, KRAS, BRAF, CDK12, FGFR2, NF1, AKT1, BRCA1, TP53 and MSI-high. Conclusion: Our prospective, randomized and multicentric study suggests a genomic profile from a homogeneous cohort of 150 patients. We identified genes involved in chromatin remodeling (ARID1A and KMT2C) as prognostic biomarkers of clinical interest and suggesting the relevance of epidrugs in ESCC. Theranostic annotations of variants identify a matched to target therapy for 32% of alterations. Those targets represent multiple tracks for personalized therapy in ESCC. Citation Format: Maryame El Gani, Sabrina Ibadioune, Zakhia El Beaino, Abderraouf Hamza, Sophie Vacher, Emmanuelle Jeannot, Julien Masliah-Planchon, Anne Salomon, Alexandre Degnieau, Anne-Sophie Bats, Martin Koskas, Virginie Fourchotte, Estelle Wafo, Nicolas Bourdel, Raffaele Fauvet, Marie Plante, Patrice Mathevet, Maud Kamal, Fabrice Lecuru, Ivan Bièche. Genomic alterations predictive of outcome in early staged cervical cancer: A translational investigation from the SENTICOL III trial [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 5058.

Comprehensive genomic and clinical analyses identify APOBEC mutational signatures as a brain metastasis risk factor in lung adenocarcinoma patients

BackgroundLung adenocarcinoma is the most common source of brain metastasis (BM), resulting in significant morbidity and mortality. We aimed to identify patients with high BM risk who possibly benefit from brain-penetrant drugs, prophylactic cranial irradiation, or close brain magnetic resonance imaging surveillance. MethodsMetastatic lung adenocarcinoma patients with extracranial tumor samples profiled by a next-generation sequencing panel targeting 425 tumor-related genes were retrospectively enrolled between February 2008 and July 2021. We compared BM and non-BM patients’ genomic and clinical features and studied their associations with BM risk. Two external cohorts were used for result validation and molecular mechanisms investigation, respectively. ResultsWe included 174 eligible patients, including 90 having developed BM by the end of follow-up. Age≤60, EGFR activating mutations, and high-level apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) mutational signatures were associated with elevated BM risk. Similar findings in BM-free survival were obtained by fitting Fine-Gray subdistribution hazard models addressing competing risks. Increased BM risk related to APOBEC mutational signatures was validated in an external cohort (N = 440). RNA sequencing data analyses performed in another external cohort (N = 230) revealed that expressions of metastasis-related pathways such as transforming growth factor (TGF)β and epithelial-mesenchymal transition (EMT) were upregulated in the patients with high-level APOBEC mutational signatures. ConclusionAPOBEC mutational signatures related to upregulated TGFβ and EMT, could serve as an independent risk factor for BM and BM-free survival in metastatic lung adenocarcinoma patients. Further investigations are warranted to tailor personalized treatments to improve the susceptible patient's outcomes.

The development of a next-generation sequencing panel targeting cannabinoid synthase genes to distinguish between marijuana and hemp.

Hemp and marijuana, both derived from Cannabis sativa L. (C. sativa), are subject to divergent legal regulations due to their different Δ9-tetrahydrocannabinol (Δ9-THC) contents. Cannabinoid synthase genes are considered the key enzymes that determine the chemical composition or chemotype of a particular cultivar. However, existing methods for crop type differentiation based on previous synthase gene theories have limitations in terms of precision and specificity, and a wider range of cannabis varieties must be considered when examining cannabis-based genetic markers. A custom next-generation sequencing (NGS) panel was developed targeting all synthase genes, including Δ9-THC acid synthase, cannabidiolic acid synthase, and cannabichromenic acid synthase, as well as the pseudogenes across diverse C. sativa samples, spanning reference hemp and marijuana, commercial hemp derivatives, and seized marijuana extracts. Interpretation of NGS data revealed a relationship between genotypes and underlying chemotypes, with the principal component analysis indicating a clear distinction between hemp and marijuana clusters. This differentiation was attributed to variations in both synthase genes and pseudogene variants. Finally, this study proposes a genetic cannabis classification method using a differentiation flow chart with novel synthase markers. The flow chart successfully differentiated hemp from marijuana with a 1.3% error rate (n=147).

Genetic profiling of rat gliomas and cardiac schwannomas from life-time radiofrequency radiation exposure study using a targeted next-generation sequencing gene panel.

The cancer hazard associated with lifetime exposure to radiofrequency radiation (RFR) was examined in Sprague Dawley (SD) rats at the Ramazzini Institute (RI), Italy. There were increased incidences of gliomas and cardiac schwannomas. The translational relevance of these rare rat tumors for human disease is poorly understood. We examined the genetic alterations in RFR-derived rat tumors through molecular characterization of important cancer genes relevant for human gliomagenesis. A targeted next-generation sequencing (NGS) panel was designed for rats based on the top 23 orthologous human glioma-related genes. Single-nucleotide variants (SNVs) and small insertion and deletions (indels) were characterized in the rat gliomas and cardiac schwannomas. Translational relevance of these genetic alterations in rat tumors to human disease was determined through comparison with the Catalogue of Somatic Mutations in Cancer (COSMIC) database. These data suggest that rat gliomas resulting from life-time exposure to RFR histologically resemble low grade human gliomas but surprisingly no mutations were detected in rat gliomas that had homology to the human IDH1 p.R132 or IDH2 p.R172 suggesting that rat gliomas are primarily wild-type for IDH hotspot mutations implicated in human gliomas. The rat gliomas appear to share some genetic alterations with IDH1 wildtype human gliomas and rat cardiac schwannomas also harbor mutations in some of the queried cancer genes. These data demonstrate that targeted NGS panels based on tumor specific orthologous human cancer driver genes are an important tool to examine the translational relevance of rodent tumors resulting from chronic/life-time rodent bioassays.

Validation of targeted next-generation sequencing panels in a cohort of Polish patients with epilepsy: assessing variable performance across clinical endophenotypes and uncovering novel genetic variants.

Targeted Next-Generation Sequencing Panels (TNGSP) have become a standard in global clinical practice. Instead of questioning the necessity of next-generation sequencing in epilepsy patients, contemporary large-scale research focuses on factors such as the size of TNGSP, the comparative advantages of exome or genome-wide sequencing over TNGSP, and the impact of clinical, electrophysiological, and demographic variables on genetic test performance. This study aims to elucidate the demographic and clinical factors influencing the performance of TNGSP in 138 Polish patients with epilepsy, recognizing the pivotal role of genetic testing in guiding patient management and therapy. A retrospective analysis was conducted on patients from a genetic clinic in Poznań, Poland, who underwent commercial gene panel studies at Invitae Corporation (USA) between 2020 and 2022. Patient groups were defined based on the age of onset of the first epileptic seizures, seizure type, gender, fever dependence of seizures, presence of intellectual disability or developmental delay, abnormalities in MRI, and the presence of dysmorphic features or congenital malformations. Seizure classification followed the 2017 ILAE criteria. Among the 138 patients, 30 (21.7%) exhibited a pathogenic or likely pathogenic variant, with a distribution of 20.7% in males and 22.5% in females. Diagnostic performance correlated with the patient's age at the onset of the first seizure and the type of seizure. Predominant variants were identified in the SCN1A, PRRT2, CDKL5, DEPDC5, TSC2, and SLC2A1 genes. Additionally, 12 genes (CACNA1A, SCN2A, GRIN2A, KCNQ2, CHD2, DYNC1H1, NEXMIF, SCN1B, DDX3X, EEF1A2, NPRL3, UBE3A) exhibited single instances of damage. Notably, novel variants were discovered in DEPDC5, SCN1A, TSC2, CDKL5, NPRL3, DYNC1H1, CHD2, and DDX3X. Identified variants were present in genes previously recognized in both European and non-European populations. A thorough examination of Variants of Uncertain Significance (VUSs), specifically focusing on gene copy number changes, may unveil more extensive chromosomal aberrations. The relatively frequent occurrence of pathological variants in X chromosome-linked genes in girls warrants further investigation, challenging the prevailing notion of male predominance in X-linked epilepsy.

Abstract A010: Insights into the Impact of Fanconi Anemia Repair Genes on Immunotherapy Response in Solid Tumors

Abstract Title: Insights into the Impact of Fanconi Anemia Repair Genes on Immunotherapy Response in Solid Tumors Background: Fanconi anemia repair (FAR) genes have crucial involvement in determining immunogenicity of solid tumors due to their substantial involvement in DNA damage repair (DDR). Previous work has alluded to the significance of DDR pathways such as mismatch repair and homologous recombination genes in treatment guidance. Herein, we study the potential impact of FAR genes mutations on immunotherapy parameters in solid tumors. Methods: We used the MSK immunotherapy and Tumor Mutational Burden (TMB) dataset was used in our analysis, which includes mutational and clinical data for 1661 patients on immune checkpoint inhibitors (anti-PD-1/L1, anti-CTLA-4, or combinational therapy) from ten cancer types (bladder, breast, colorectal, esophagogastric, glioma, head and neck, melanoma, non- small cell lung, renal cell, and unknown primary cancer). All clinical ang genomic data was retrieved through the cBioPortal database. Patients were categorized into the FAR mutated group if they harbored a mutation in at least one of the FAR genes (FANCA, FANCC, BRCA2, BRIP1, PALB2, RAD51C, SLX4) included in the MSK-IMPACT targeted next-generation sequencing panel. The log rank test and the Wilcoxon test, Chi-squared test were used to compare overall survival (OS), continuous and categorical data between FAR mutated and wildtype groups. Results: The MSK TMB cohort included 220 (13%) patients with FAR mutations, of which melanoma comprised the highest percentage (26.4%) followed by non-small cell lung cancer (NSCLC; 19.6%). The most common altered FAR gene was BRCA2 (6%), followed by SLX4 (5%), while the least altered gene was RAD51C (0.7%). FAR mutated patients had significantly higher OS compared to the wildtype group (median OS (mOS): 29 vs 17 months, log rank p < 0.001). Among melanoma patients (n = 320), there was no significant difference in OS between the mutated and FAR groups, whereas the NSCLC (n = 350) and colorectal cancer (CRC, n = 110) subgroups had significantly higher OS in the FAR mutated groups (NSCLC - mOS: 19 vs 10 months, p = 0.0256, CRC – mOS: not reached vs 13 months, p &l; 0.001). TMB was significantly higher in the FAR mutated group (median TMB: 22.3 vs 5.2, p < 0.001). Notably, the most frequent co-mutations in the FAR mutated group included CTLA4, STK19, E2F3, CD276, MYCL. Conclusion: Our analysis highlights the potential role of FAR genes mutations in predisposing solid tumor patients to ICI benefit, specifically in NSCLC and CRC patients. Insights into the potential interactions between FAR genes and other DDR pathways as well as their impact on tumor immune microenvironment parameters are needed in future research to understand the drivers of ICI benefit in this subset of patients. Citation Format: Ahmed M. Ashour, Amro M. Al-Omari, Mohammad S. Bani Amer, Zaid R. Kamal. Insights into the Impact of Fanconi Anemia Repair Genes on Immunotherapy Response in Solid Tumors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A010.

Development of ion torrent-based targeted next-generation sequencing panel for identification of animal species in pet foods

Manufacturers may intentionally or unintentionally incorporate ingredients not specified on the label of canned pet foods. Including any unacknowledged ingredients in a food product is considered food fraud or misbranding. Contamination of pet foods may occur in the processing of the foods, including potential cross-contamination in packaging facilities.Of the methods available to identify meat species in food products, Sanger sequencing and several next-generation sequencing methods are available, but there are limitations including the number of targets analyzed at a time and the method specificity. In this study, we developed a targeted next-generation sequencing panel to detect meat species in canned pet foods using Ion Torrent technology.The panel contains multiple primers targeting mitochondrial genes from as many as 27 animal species, of which 7 major animal species were validated. The meat species targets could be identified from samples spiked with as low as 0.01% w/w of the contaminating meat species in a vegetarian food matrix material. Targeted NGS in the current study enriches species-specific multiple target areas in the mitochondrial genome of the target material, which gives high accuracy in the sequencing results.

The landscape of actionable genomic alterations in lung adenocarcinomas in India.

Lung adenocarcinoma (LUAD), the most prevalent form of non-small cell lung cancer (NSCLC), remains a leading cause of cancer-related death globally, including in India, with a 5-year survival rate below 10%. Despite these grim statistics, recent advances in the use of next-generation sequencing (NGS) for identifying genetic alterations and the emergence of targeted therapies have opened new possibilities for personalized treatment based on distinct molecular signatures. To understand the molecular pattern of NSCLC, a retrospective study was conducted with 53 Indian LUAD patient samples, using a targeted NGS panel of 46 cancer-relevant oncogenes to identify clinically relevant variants. Pathogenic or likely pathogenic variants were detected in 94% of the 53 cases. Non-synonymous mutations, rearrangements, copy number alterations, insertions, and deletions of functional relevance were observed in 31 out of 46 genes. The most frequently mutated genes included TP53 (52.8%) and EGFR (50.9%), followed by RET, PIK3CA and ERBB2; some patients had multiple alterations in the same gene. Gender-based enrichment analysis indicated that ALK and IDH2 alterations were more prevalent in females, while TP53 and PTEN were more common in males. No significant correlation was found between mutations and other clinicopathological attributes, such as age, stage, and subtype. A higher prevalence of EGFR, RET, PIK3CA, ERBB2 and ALK mutations were observed compared to previous LUAD genetic studies coupled with a lower frequency of KRAS mutations. Clinically actionable variants were annotated using OncoKB and categorized into the four therapeutic levels based on their clinical evidence. Seventy-nine percent of cases had at least one clinically actionable alteration. Most patients (39.6%) had the highest level of actionability (Level 1) wherein an FDA-approved drug is available specifically for the observed mutation in lung cancer patients. EGFR Exon19 in-frame deletions and EGFR L858R were the most frequent among targetable variants (20.7%). These findings emphasize the importance of a selective NGS panel in enabling personalized medicine approaches by identifying actionable molecular alterations and informing the choice of targeted therapy for more effective treatment options in Indian NSCLC patients.

The TiHoCL panel for canine lymphoma: a feasibility study integrating functional genomics and network biology approaches for comparative oncology targeted NGS panel design.

Targeted next-generation sequencing (NGS) enables the identification of genomic variants in cancer patients with high sensitivity at relatively low costs, and has thus opened the era to personalized human oncology. Veterinary medicine tends to adopt new technologies at a slower pace compared to human medicine due to lower funding, nonetheless it embraces technological advancements over time. Hence, it is reasonable to assume that targeted NGS will be incorporated into routine veterinary practice in the foreseeable future. Many animal diseases have well-researched human counterparts and hence, insights gained from the latter might, in principle, be harnessed to elucidate the former. Here, we present the TiHoCL targeted NGS panel as a proof of concept, exemplifying how functional genomics and network approaches can be effectively used to leverage the wealth of information available for human diseases in the development of targeted sequencing panels for veterinary medicine. Specifically, the TiHoCL targeted NGS panel is a molecular tool for characterizing and stratifying canine lymphoma (CL) patients designed based on human non-Hodgkin lymphoma (NHL) research outputs. While various single nucleotide polymorphisms (SNPs) have been associated with high risk of developing NHL, poor prognosis and resistance to treatment in NHL patients, little is known about the genetics of CL. Thus, the ~100 SNPs featured in the TiHoCL targeted NGS panel were selected using functional genomics and network approaches following a literature and database search that shielded ~500 SNPs associated with, in nearly all cases, human hematologic malignancies. The TiHoCL targeted NGS panel underwent technical validation and preliminary functional assessment by sequencing DNA samples isolated from blood of 29 lymphoma dogs using an Ion Torrent™ PGM System achieving good sequencing run metrics. Our design framework holds new possibilities for the design of similar molecular tools applied to other diseases for which limited knowledge is available and will improve drug target discovery and patient care.

Right ventricle hypertrophy in fetuses diagnosed with Noonan syndrome: Can ductus venosus agenesis represent a contributing cause?

Noonan syndrome (NS) is the most common genetic syndrome in fetuses with increased nuchal translucency (NT) and normal karyotype. NS patients present typical patterns of cardiac defects, such as pulmonary stenosis, polyvalvular dysplasia and hypertrophic cardiomyopathy. This study aims to evaluate onset and trend of cardiac disease in fetuses with molecular diagnosis of NS and to search for other cardiovascular sonographic markers of NS. We performed a fetal echocardiographic follow-up of pregnancies with increased NT in the first trimester. All the fetuses with normal Karyotype and Comparative Genomic Hybridizationarray underwent a targeted next-generation sequencing panel for RASopathies. Increased NT was the only finding up to the second trimester in half of the fetuses, while in the others ductus venosus agenesis was also observed. In all of them, during the late second trimester, a severe cardiopathy arouse.

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

Anorexia nervosa (AN) is a severe psychiatric disorder characterized by an intense fear of gaining weight, a relentless pursuit of thinness, and a distorted body image. Recent research highlights the substantial contribution of genetics to AN's etiology, with genes like BDNF, SLC6A4, and DRD2 implicated. However, a comprehensive genetic test for AN diagnosis is lacking. This study aims to elucidate the biological foundations of AN, examining variants in genes associated with syndromic forms, rare variants in AN patients, and candidate genes from GWAS studies, murine models, or established molecular pathways. The study involved 135 AN patients from Italy, diagnosed based on DSM-V criteria. A specialized Next-Generation Sequencing panel targeting 163 genes was designed. Sequencing was performed on an Illumina MiSeq System, and variants were analyzed using bioinformatics tools. Data on clinical parameters, exercise habits, and AN types were collected. The AN cohort, predominantly female, exhibited diverse clinical characteristics. Our analysis identified gene variants associated with syndromic forms of AN, such as STRA6, NF1, MAT1A, and ABCC6. Variants were also found in known AN-related genes (CD36, DRD4, GCKR, GHRL, GRIN3B, GPR55, LEPR) and in other 16 candidate genes (A2M, AEBP1, ABHD4, ACBD7, CNTNAP, GFRAL, GRIN2D, LIPE, LMNA, NMU, PDE3B, POMC, RYR1, TNXB, TYK2, VPS13B), highlighting the complexity of AN's genetic landscape. The endocannabinoid and dopamine pathways play crucial roles. Skeletal muscle-related genes and appetite-regulating hormones also revealed potential connections. Adipogenesis-related genes suggest AN's association with subcutaneous adipose tissue deficiency. This study provides comprehensive insights into the genetic underpinnings of AN, emphasizing the importance of multiple pathways. The identified variants contribute.

Perspectives on Myelodysplastic Neoplasm Diagnosis: A Comparative Analysis of the Latest World Health Organization Classifications and the International Concensus Classification

Introduction : Myelodysplastic neoplasm (MDS) is a category of clonal hematopoietic stem cell neoplasms, defined by cytopenias and morphologic dysplasia, characterized by progressively ineffective hematopoiesis and increased risk of acute myeloid leukemia (AML). The 5th edition of the World Health Organization (WHO 2022) classification grouped MDS entities into two families: those having defining genetic abnormalities and those that are morphologically defined. The former newly included biallelic TP53 inactivation (MDS-biTP53) and SF3B1 mutation, meanwhile the latter newly included hypoplastic MDS (h-MDS) and MDS with fibrosis (MDS-F). An independent proposal, the International Consensus Classification (ICC), was also published during the same period. This study aims to compare and analyze these two classifications, focusing on MDS's diagnostic criteria and entity definition. Herein, we describe the redistribution of the MDS according to the WHO 2022 classification and ICC and evaluated their significance in predicting patient's outcomes. Methods : This study included a total of 639 patients who were diagnosed with MDS based on the 4th edition of WHO classification in Seoul St. Mary's hospital from 2016 to 2022. As part of the study, all patients were reclassified using the updated WHO 2022 classification and ICC through a comprehensive review of bone marrow aspiration and biopsy, as well as the results of whole genetic studies, including cytogenetic analysis, fluorescence in situ hybridization, and targeted panel next-generation sequencing. Risk stratification was determined by using the International Prognostic Scoring System for MDS (IPSS-R, WPSS and IPSS-M). Results : Among the 639 patients, six were classified as ‘clonal cytopenia of undetermined significance’ by WHO 2022 and ICC. In the WHO 2022 classification, 22 patients were categorized as AML, whereas ICC only identified nine of them due to low blast count (<10%). Out of the newly defined MDS patients (n=611), 12.6% (n=77) were genetically defined MDS, and 87.4% (n=534) were morphologically defined MDS. Regarding the WHO 2022 categories, MDS-biTP53 and MDS-SF3B1 accounted for 5.4% (n=33) and 6.3% (n=39) of cases, respectively, whereas h-MDS and MDS-F accounted for 11.9% (n=73) and 1.8% (n=11), respectively. As for the ICC, MDS, not otherwise specified (NOS) accounted for 327 patients with 77 having single lineage dysplasia and 250 having multilineage dysplasia. The h-MDS was also included in these criteria. Of 33 MDS-biTP53 cased identified by the WHO 2022 classification, 25 were categorized as MDS-TP53 and 8 as MDS/AML-TP53 in the ICC, which included an additional four patients. Moreover, 72 patients were classified as MDS/AML by ICC, with 35 of them presenting genetic mutations and 9 exhibiting cytogenetic abnormalities. The median survival of the 611 patients were 86 months (95% confidence interval (CI): 65-111). The WHO 2022 classification demonstrated significant prognostic discrimination based on diagnosis subtype (P <0.001). MDS-biTP53 exhibited the worst outcome [hazard ratio (HR): 7.24, 95% CI: 2.87 to 18.22], followed by MDS-F (HR: 5.64, 95% CI: 1.44 to 22.08) and MDS-IB2 (HR: 2.76, 95% CI: 1.72 to 4.42), in comparison to MDS-LB. On the other hand, the ICC did not reveal significant prognostic significance. The distribution of IPSS-R, WPSS and IPSS-M was similar and also showed meaningful prognostic discrimination (P <0.001). Conclusions : The results validated the clinical relevance of updated WHO 2022 classification for MDS and indicated that the newly defined categories such as MDS-biTP53 and MDS-F are unique disease types evidenced by their particular prognostic significance.

Higher Mutational Burden Is an Independent Predictor of Shorter Time to First Treatment in Untreated Chronic Lymphocytic Leukemia Patients

Background. Recent advancements in next-generation sequencing (NGS) technologies have revolutionized the ability to comprehensively profile chronic lymphocytic leukemia (CLL), unveiling various molecular lesions. Complex mutational landscapes and diverse combinatorial patterns of genetic alterations lead to heterogeneity of clinical course and outcomes. The primary objective of this study was to identify patterns of co-occurrence (CO) and mutual exclusivity (ME) among mutations in CLL and their impact on time to first treatment (TTFT). Methods. The cohort included 795 treatment-naïve (TN) patients (pts) with CLL diagnosed according to iwCLL guidelines. The median follow-up time for the cohort was 3.91 years (range 0 - 42.8). The median time from diagnosis to mutational analysis was 6.6 months (26.50 - 33.27, 95% CI). Mutational screening was performed by a clinical targeted NGS panel, covering all or hotspot exons of 95 genes - the Rapid Heme Panel implemented by BWH (Kluk MJ, et al. J Mol Diagn. 2016;18(4):507-515). Standard protocols were applied to analyze IGHV gene mutational status, chromosomal aberrations by FISH with probes for 11q, 13q, 17p, and trisomy 12, and stimulated karyotype, where complex karyotype (CK) was defined as ≥3 abnormalities. CO and ME patterns were analyzed in pts with a higher mutational burden, determined as ≥2 distinct mutated genes, using Fisher's exact test ( p<.05). Control for false discovery rate was performed using the Benjamini, Krieger and Yekutieli method ( q=20%). TTFT was the time from diagnosis to initial treatment. Results. We detected 1798 mutations in 719 (90.4%) pts. No mutations were detected in 9.6% (n=76) patients, while a single mutated gene was found in 216 (27.2%) pts, 2 mutated genes in 206 (25.9%) pts, and mutations in 3 and ≥4 genes were found in 153 (19.2%) and 144 (18.1%) pts, respectively. The most mutated (≥10%) genes in the cohort were ATM (18.1%), NOTCH1 (17.7%), TP53 (13.2%), SF3B1 (12.3%), TET2 (10.2%), and DNMT3A (10.1%). A higher mutational burden was associated with clinical Rai stages 1-4 [ p=.003]; elevated (>3.5 mg/L) levels of baseline ß-2 microglobulin (B2M) [ p=.036] and established high-risk genomic features: del(17p) [ p<.001], del(11q) [ p=.021], CK [ p=.009], unfavorable ZAP70 [ p=.027] and unmutated IGHV (UM- IGHV) [ p<.001] (incidence of UM- IGHV cases is 48.4% (n=359) in cohort). At the same time, cases with 0-1 mutation were more likely to have del(13q) [ p=.006]. Sex and age >65 years at diagnosis were not associated with mutational burden. Otherwise, lack of any mutations was associated with absence of del(17p) (0% vs 11.1% [ p=.002]), lower rates of B2M >3.5 mg/L (3.9% vs 21.7% [ p<.001]), less frequent UM- IGHV (25.4% vs 50.9% [p<.001]), lower ratio of CK (7.0% vs 17.5% [p=.024] and age >65 years at diagnosis (21.1% vs 35.1% [ p=.014]). After controlling for multiple comparisons, no genes showed significant mutational co-occurrence. UM- IGHV cases were enriched in mutated ATM [ p=.003], NOTCH1 [ p<.00001], SF3B1 [ p=.0012] and XPO1 [ p<.00001]. Mutated NOTCH1 [ p<.00001], as well as KRAS [ p=.0012], occurred along with tri12. In contrast, UM- IGHV did not co-occur with mutations in MYD88 [ p<.00001], as previously reported. Del(13q) did not co-occur with mutated BRAF [ p=.0006] or BCOR [ p=.006]. Mutated TP53 [ p=.008] and SF3B1 [ p=.0013] were absent in tri12 positive cases. Increased mutational burden in ≥2 distinct mutated genes predicted a shorter TTFT than 0 or 1 mutated gene (HR 2.16; 95%CI 1.57 - 2.97; p<.001). Factors including Rai stages 1-4 (HR 2.63; 95%CI 1.88 - 3.7; p<0.001), UM- IGHV (HR 2.4; 95%CI 1.74 - 3.3; p<.001), CK (HR 1.47; 95%CI 1.07 - 2.0; p=.018), mutational burden in ≥2 genes (HR 1.57; 95%CI 1.14 - 2.2; p=.006) and del(17p) /TP53mut (HR 1.79; 95%CI 1.15 - 2.8; p=.01) were independently associated with worsened TTFT ( Figure 1). Neither mutated TP53 without del(17p) (HR 1.47; 95%CI 0.92 - 2.3; p=.104), or wild-type TP53 with del(17p) (HR 1.03; 95%CI 0.51 - 2.1; p=.932) were significant predictors of TTFT. Conclusions: Higher mutational burden is associated with worsened TTFT in CLL pts independently of other genomic events. In this cohort we did not see co-occurrence of specific mutations.

Identification of causative gene variants for patients with known monogenic diabetes using a targeted next-generation sequencing panel in a single-center study.

We aimed to verify the usefulness of targeted next-generation sequencing (NGS) technology for diagnosing monogenic diabetes in a single center. We designed an amplicon-based NGS panel targeting 34 genes associated with known monogenic diabetes and performed resequencing in 56 patients with autoantibody-negative diabetes mellitus diagnosed at < 50years who had not been highly obese. By bioinformatic analysis, we filtered significant variants based on allele frequency (< 0.005 in East Asians) and functional prediction. We estimated the pathogenicity of each variant upon considering the family history. Overall, 16 candidate causative variants were identified in 16 patients. Among them, two previously known heterozygous nonsynonymous single-nucleotide variants associated with monogenic diabetes were confirmed as causative variants: one each in the GCK and WFS1 genes. The former was found in two independent diabetes-affected families. Two novel putatively deleterious heterozygous variants were also assumed to be causative from the family history: one frameshift and one nonsynonymous single-nucleotide variant in the HNF4A gene. Twelve variants remained as candidates associated with the development of diabetes. Targeted NGS panel testing was useful to diagnose various forms of monogenic diabetes in combination with familial analysis, but additional ingenuity would be needed for practice. The online version contains supplementary material available at 10.1007/s13340-023-00669-3.

Identification of High-Risk Population in First-Line Follicular Lymphoma at Screening with a Next Generation Sequencing (NGS) Assay Using Plasma Circulating Tumor DNA (ctDNA): Initial Data from Gallium

Background Follicular lymphoma (FL) is an indolent disease with favorable outcome in patients (pt) treated with antibody-based immunochemotherapy. However, ca. 15% of the pt population experience disease relapse within 24 months or transformation to a more aggressive disease, representing a population with high unmet medical need. Available clinicogenetic risk scores show suboptimal performance for predicting early disease progression (Jurinovic, Blood 2016). Here we evaluated ctDNA at screening as a novel tool to identify high risk pt populations. Material and Methods Pre-treatment plasma samples from 221 selected pts diagnosed with advanced stage or bulky FL in need of systematic treatment from the GALLIUM trial (NCT 01332968) were analyzed. Pts were selected to be evenly distributed among chemo/antibody groups (50 Rituximab (R) -Bendamustine (Benda), 63 R-CHOP/CVP, 50 Gazyva (G) -Benda, 58 G-CHOP/CVP). Within each treatment group, 25 to 28 cases with good responses (progression-free survival (PFS) &amp;gt; 5 years) and 25 to 31 cases with early progression or transformation to an aggressive disease (median PFS: 352 days and 91.6% of these cases progressed within 24 months) were selected. Targeted NGS was performed using a modified version of the AVENIO ctDNA analysis workflow (Roche; Research Use Only) based on the previously described CAPP-Seq workflow (Kurtz, J Clin Oncol 2018). The targeted NGS panel was designed to cover ~314 kb in or near 466 genes associated with NHL. Potential germline derived variants were filtered out using a publicly available database and panel specific blacklist filtering; additionally, variants with allelic frequency (AF) &amp;gt;20% were excluded. ctDNA was quantified as mutant molecules per milliliter-of-plasma (MMPM) based on single nucleotide variants (SNV) in the sequenced genomic regions. The association of PFS with this classifier was evaluated by Kaplan-Meier methods and Cox proportional hazards model, and an optimal cut-off for MMPM high vs low was determined by using maximally selected rank statistics, validated by 10-fold cross validation. Results We detected a median of 107 (range 0-554) SNV at a median deduplicated depth of 3766x. A strong correlation between ctDNA at screening, measured as MMPM, and clinical prognostic markers was observed; higher levels of MMPM were associated with larger sum of the product of the diameters (SPD) (Mann-Whitney-U (MWU) P &amp;lt; 0.0001), higher FLIPI2 scores (MWU P &amp;lt; 0.0001) and m7-FLIPI (MWU P = 0.0001). Pts with long PFS had a significantly (MWU P &amp;lt; 0.0001) lower median MMPM (59.9) than those who progressed early (276.5). Using an optimal cut-off to predict pts at risk of early progression, MMPM high cases (n=96) showed significantly more total SNVs compared to MMPM low cases (n=125) (MWU P &amp;lt; 0.0001). MMPM high vs low was a stronger marker for PFS (cross-validated log-rank P &amp;lt; 0.0001; HR [95% CI] = 2.4 [1.6,3.5]) versus FLIPI2 (log-rank P = 0.0063; HR [95% CI] = 1.7 [1.2,2.4]) or tumor burden measured as SPD (log-rank P = 0.0009; HR [95% CI] = 1.9 [1.3,2.8]). In a multivariate Cox model, the association of high MMPM and worse PFS was still significant after correction for FLIPI2, SPD and m7-FLIPI, indicating that MMPM has an independent prognostic value (log-rank P &amp;lt; 0.0001; HR [95% CI] = 2.42 [1.6,3.8]) (Figure 1). Consistent with previous reports (Jurinovic, ASH 2021), also in this selected cohort m7-FLIPI was prognostic for CHOP/CVP (log-rank P = 0.0061; HR [95% CI] = 2.2 [1.2,3.8]) but not for Benda (log-rank P = 0.2274; HR [95% CI] = 1.5 [0.76,3.0]). Notably, the prognostic value of ctDNA at screening using MMPM was observed for both CHOP/CVP (log-rank P &amp;lt; 0.0001; HR [95% CI] = 2.9 [1.7,5.0]), and Benda (log-rank P &amp;lt; 0.0001; HR [95% CI] = 2.9 [1.7,5.1]). Conclusion Measurements of ctDNA at screening showed promising results as a biomarker to predict high risk populations for early treatment failure in untreated FL. MMPM at baseline, quantified using the AVENIO NHL assay, showed an independent prognostic value compared to FLIPI 2, m7-FLIPI and SPD. Notably, while known clinicogenetic risk scores had a prognostic value limited to CHOP/CVP regimen (Jurinovic, ASH 2019, Bolen, Blood 2021), MMPM prognostic value was maintained on CHOP/CVP and Benda chemotherapy. Overall, these initial results warrant additional analysis to investigate the value of the ctDNA as a treatment agnostic stratification tool for clinical research.

Alternative Tissue Fixation Protocols Dramatically Reduce the Impact of DNA Artifacts, Unraveling the Interpretation of Clinical Comprehensive Genomic Profiling

Formalin-fixed paraffin-embedded (FFPE) samples represent the cornerstone of tissue-based analysis in precision medicine. Targeted next-generation sequencing panels are routinely used to analyze a limited number of genes to guide treatment decision-making for advanced-stage patients. The number and complexity of genetic alterations to be investigated are rapidly growing; in several instances, a comprehensive genomic profiling analysis is needed. The poor quality of genetic material extracted from FFPE samples may impact the feasibility/reliability of sequencing data. We sampled 9 colorectal cancers to allow 4 parallel fixations: (1) neutral buffered formalin (NBF), (2) acid-deprived formalin fixation (ADF), (3) precooled ADF (coldADF), and (4) glyoxal acid free (GAF). DNA extraction, fragmentation analysis, and sequencing by 2 large next-generation sequencing panels (OCAv3 and TSO500) followed. We comprehensively analyzed library and sequencing quality controls and the quality of sequencing results. Libraries from coldADF samples showed significantly longer reads than the others with both panels. ADF-derived and coldADF-derived libraries showed the lowest level of noise and the highest levels of uniformity with the OCAv3 panel, followed by GAF and NBF samples. The data uniformity was confirmed by the TSO500 results, which also highlighted the best performance in terms of the total region sequenced for the ADF and coldADF samples. NBF samples had a significantly smaller region sequenced and displayed a significantly lower number of evaluable microsatellite loci and a significant increase in single-nucleotide variations compared with other protocols. Mutational signature 1 (aging and FFPE artifact related) showed the highest (37%) and lowest (17%) values in the NBF and coldADF samples, respectively. Most of the identified genetic alterations were shared by all samples in each lesion. Five genes showed a different mutational status across samples and/or panels: 4 discordant results involved NBF samples. In conclusion, acid-deprived fixatives (GAF and ADF) guarantee the highest DNA preservation/sequencing performance, thus allowing more complex molecular profiling of tissue samples.

A Comprehensive Genetic Study of Microtubule-Associated Gene Clusters for Male Infertility in a Taiwanese Cohort.

Advanced reproductive technologies are utilized to identify the genetic mutations that lead to spermatogenic impairment, and allow informed genetic counseling to patients to prevent the transmission of genetic defects to offspring. The purpose of this study was to identify potential single nucleotide polymorphisms (SNPs) associated with male infertility. Genetic variants that may cause infertility are identified by combining the targeted next-generation sequencing (NGS) panel and whole exome sequencing (WES). The validation step of Sanger sequencing adds confidence to the identified variants. Our analysis revealed five distinct affected genes covering seven SNPs based on the targeted NGS panel and WES data: SPATA16 (rs16846616, 1515442, 1515441), CFTR (rs213950), KIF6 (rs2273063), STPG2 (r2903150), and DRC7 (rs3809611). Infertile men have a higher mutation rate than fertile men, especially those with azoospermia. These findings strongly support the hypothesis that the dysfunction of microtubule-related and spermatogenesis-specific genes contributes to idiopathic male infertility. The SPATA16, CFTR, KIF6, STPG2, and DRC7 mutations are associated with male infertility, specifically azoospermia, and a further examination of this genetic function is required.

Single-centre experience with autosomal recessive limb-girdle muscular dystrophy: case series and literature review.

Limb-girdle muscular dystrophy (LGMD) is a group of myopathies that lead to progressive muscle weakness, predominantly involving the shoulder and pelvic girdles; it has a heterogeneous genetic etiology, with variation in the prevalence of subtypes according to the ethnic backgrounds and geographic origins of the populations. The aim of the present study was to analyze a series of patients with autosomal recessive LGMD (LGMD-R) to contribute to a better characterization of the disease and to find the relative proportion of the different subtypes in a Southern Brazil cohort. The sample population consisted of 36 patients with LGMD-R. A 9-gene targeted next-generation sequencing panel revealed variants in 23 patients with LGMD (64%), and it identified calpainopathy (LGMD-R1) in 26%, dysferlinopathy (LGMD-R2) in 26%, sarcoglycanopathies (LGMD-R3-R5) in 13%, telethoninopathy (LGMD-R7) in 18%, dystroglicanopathy (LGMD-R9) in 13%, and anoctaminopathy (LGMD-R12) in 4% of the patients. In these 23 patients with LGMD, there were 27 different disease-related variants in the ANO5, CAPN3, DYSF, FKRP, SGCA, SGCB, SGCG, and TCAP genes. There were different causal variants in different exons of these genes, except for the TCAP gene, for which all patients carried the p.Gln53* variant, and the FKRP gene, which showed recurrence of the p.Leu276Ile variant. We analyzed the phenotypic, genotypic and muscle immunohistochemical features of this Southern Brazilian cohort.

B-149 Next-generation Sequencing Via Targeted Metagenomics for Broad Antimicrobial Resistance Surveillance

Abstract Background Antimicrobial-resistant infections secondary to the overuse of antibiotics are a major public health threat. The standard of care for identifying resistance is antimicrobial susceptibility testing, the phenotypic characterization of minimum inhibitory concentrations (mic) for antibiotics in the presence of bacterial growth, but these methods are labor intensive, have long turnaround times, and face challenges with non-cultivable bacteria. Molecular methods for antimicrobial resistance (AMR) ascertainment are high-throughput, robust, and sensitive and have gained interest as a genotypic complement to traditional phenotypic methods. Since the COVID-19 pandemic, next-generation sequencing has emerged as the leading technology for tracking and surveillance of infectious diseases and antimicrobial resistance, emphasizing the need for flexible sequencing panels that are easily interchangeable and capable of detecting pathogens and AMR genes. Methods In a collaboration between Illumina, a national retail pharmacy, and Aegis Sciences Corporation, residual, self-collected nasal swab samples (n = 4390) submitted for COVID-19 testing from patients across the U.S. were sequenced using the Respiratory Pathogen ID/AMR Panel (RPIP, Illumina – For Research Use Only), a target capture-based next-generation sequencing panel targeting 282 respiratory pathogens and 2097 relevant AMR markers. Sequencing data was analyzed using the Explify RPIP Analysis app (BaseSpace, Illumina) and paired with self-reported patient data submitted via an online questionnaire. Data including pathogens and anti-microbial resistance (AMR) genes detected, age, race, gender, residing state of the patient, collection month, self-reported symptoms, and health risks were collated, imported into Microsoft PowerBI software, and used to create interactive visuals for a surveillance dashboard. Results In this cohort of sequenced specimens, 85.1% (n = 3576) had one or more viral, bacterial, or fungal pathogens present, 41% (n = 1816) had one or more AMR genes present, and 38.4% (n = 1685) had one or more pathogens and AMR genes co-detected. Twenty-six different AMR genes were identified with the most prevalent being Erm 23S ribosomal RNA methyltransferase (65.5%; n = 1115). Erm was identified in samples from all 50 US states and was co-detected with staphylococcus aureus (18.2%; n = 216) and streptococcus pneumoniae (4.9%; n = 57), among others. Following Erm in prevalence, this cohort of samples harbored genes for trimethoprim resistant dihydrofolate reductase (dfr = 27.9%), tetracycline-resistant ribosomal protection protein (tet = 21.0%), and macrolide phosphotransferase (MPH = 14.2%). The data also revealed AMR gene-pathogen co-detections listed as CDC serious threats, such as the mecA gene responsible for methicillin resistance in staphylococcal species. The mecA gene was co-detected in 5.3% (n = 28) of staphylococcus aureus positive samples in this cohort. Finally, although not classified as a serious threat, neuraminidase inhibitor resistance, associated with less susceptibility to anti-virals, was found in 12% (n = 15) of all influenza A (H3N2) infected samples (n = 112). Conclusions Completion of these studies demonstrated that next-generation sequencing using targeted metagenomics with RPIP is a cost effective, high-throughput option for large-scale surveillance of AMR genes in potential respiratory infections.