Next-generation Sequencing Multigene Panel Research Articles

Prognostic significance of actionable next-generation sequencing multigene panel in esophageal cancer treatment.

Next-generation sequencing (NGS) has been offered as a large-scale and effective genomic analyzing tool. In this research, we seek to examine the possible benefits of an actionable mutation panel in association with clinical and pathological features in the treatment of esophageal cancer. In our study, 85 cases whose diagnosis of carcinoma was confirmed histopathologically either by endoscopic biopsy or esophageal surgery between 2010 and 2020 were identified from the hospital database. In formalin-fixed, paraffin-embedded tumor samples, a total of 20 genes of AKT1, ALK, BRAF, DDR, EGFR, ERBB2, ERBB3, ESR1, FGFR1, KIT, KRAS, MAP2K1, MET, NRAS, NTRK, PDGFRA, PIK3CA, PTEN, RICTOR and ROS1 were analyzed via NGS for actionable mutations. Of 85 cases, 47 patients (55.3%) were men and 38 (44.7%) were women, and the mean age of the patients was 58.01±11.45 years. There were substantial distinctions in the variables of pathogenicity of variant, operation type, stage, and both lymphovascular and perineural invasion (p<0.05). Most of the primary tumors were situated in the lower thoracic esophagus (n=23; 27%). PIK3CA variant was the highest in number among the variant types (n=17) and was detected in 41.2% of the lower thoracic tumors. The increases in mutation numbers of >2 were especially concentrated in the lower thoracic esophageal carcinomas. The utility of an actionable multigene panel revealed the value of a well-designed NGS workflow in the practical use of clinical outcomes via the prediction of responsiveness to therapeutic agents or indications for novel treatment modalities in addition to the estimation of prognosis.

Clinical Assessment and Genetic Testing for Hereditary Polyposis Syndromes in an Italian Cohort of Patients with Colorectal Polyps.

Background: Hereditary polyposis syndromes are clinically and genetically heterogeneous conditions associated with increased colorectal cancer risk. They are classified based on polyp histology, inheritance mode, causal gene, and colonic and extracolonic manifestations. Their diagnosis is challenging due to overlapping and heterogeneous clinical presentations. Methods: A multigene next-generation sequencing panel was used to screen 75 index cases with colorectal polyps and a personal/family history of cancer for key hereditary polyposis-associated genes (APC, BMPR1A, MUTYH, PTEN, SMAD4, and STK11) in order to identify germline genetic variants. Results: In the screened index cases, we found 14 pathogenic variants involving APC, MUTYH, SMAD4, and STK11 and 6 variants of uncertain significance involving APC, BMPR1A, and SMAD4. In this cohort, four patients not fulfilling the recommended eligibility criteria of current National Comprehensive Cancer Network (NCCN) guidelines for genetic testing were molecularly diagnosed with a hereditary polyposis syndrome. Conclusions: Our findings indicate that stringent NCCN eligibility criteria for molecular screening may lead to missing some of the patients affected by hereditary polyposis syndromes. This highlights the need for a careful evaluation of patients' clinical manifestations, polyp number, age of polyp onset, and family history to select appropriate candidates for molecular diagnosis of these conditions.

Prevalence and spectrum of germline pathogenic variants in cancer susceptibility genes among mexican patients with exocrine pancreatic cancer

BackgroundAlthough universal germline genetic testing is recommended for patients with exocrine pancreatic cancer (PC), access to genetic testing remains limited in low- and middle-income countries. This study aims to narrow the gap in our understanding of the spectrum of germline pathogenic and likely pathogenic variants (PVs) in cancer susceptibility genes in the Mexican population. MethodsThe landscape of PVs in cancer susceptibility genes was identified by next-generation sequencing multigene panel assays among patients with PC who were enrolled in the Clinical Cancer Genomics Community Research Network prospective registry in Mexico City. ResultsFrom August 2019 to April 2023, 137 patients underwent genetic testing. The median age at diagnosis was 60 years (range 36–85), 58.4 % were women, and 38.7 % were metastatic at diagnosis. The frequency of germline PVs was 16 % (n = 22): ATM 36.4 % (n = 8), CDKN2A/p16INK4A 27.3 % (n = 6), BRCA2 9.1 % (n = 2), PALB2 9.1 % (n = 2), CHEK2 9.1 % (n = 2), TP53 4.5 % (n = 1), and NF1 4.5 % (n = 1). Additionally, 2 carriers of monoallelic germline variants in MUTYH were identified. No significant differences were observed between carriers and non-carriers in terms of family history of pancreatic cancer. ConclusionsWe identified a significant frequency of actionable germline PVs in Mexicans with PC, wherein the majority were in a broad spectrum of genes associated with the homologous recombination DNA repair mechanism. Most pancreatic cancer associated PVs were detected in non-BRCA genes, so our findings support the recommendation of multigene panel testing for genetic cancer risk assessment of Mexican individuals with PC.

Next-generation sequencing in pediatric-onset epilepsies: Analysis with target panels and personalized therapeutic approach.

The objective of this study is to report the results of the genetic analysis in a large and well-characterized population with pediatric-onset epilepsies and to identify those who could benefit from precision medicine treatments. In this retrospective observational study, we consecutively recruited patients with pediatric-onset epilepsy observed at a tertiary neurological center over a time span of 7 years, collecting clinical and laboratory findings. Following in-depth diagnostic process to exclude possible structural and metabolic causes of the disease, patients with a suspected genetically determined etiology underwent next-generation sequencing (NGS) screening with panels for the analysis of target genes causative of epilepsy. We detected likely pathogenic or pathogenic variants (classes IV and V) in 24% of the 562 patients who underwent genetic investigations. By the evaluation of patients' data, we observed that some features (onset of epilepsy before one year old, presence of neurological deficits, psychomotor delay/cognitive disability, and malformative aspects at brain MRI) were significantly associated with class IV or V variants. Moreover, statistical analysis showed that the diagnostic yield resulted higher for patients affected by Progressive Myoclonic Epilepsy (PME) and with early onset developmental and epileptic encephalopathies (DEE), compared with focal epilepsies, genetic generalized epilepsies, DEE with onset at/after 1 y.o., and unclassified epileptic syndromes. According to the results of the genetic screening, up to 33% of patients carrying class IV or V variants resulted potentially eligible for precision medicine treatments. The large-scale application of NGS multigene panels of analysis is a useful tool for the molecular diagnosis of patients with pediatric-onset epilepsies, allowing the identification of those who could benefit from a personalized therapeutic approach. The analysis of patients with pediatric-onset epilepsy using advanced technologies for the screening of all the implicated genes allows the identification of the cause of diseases in an ever-increasing number of cases. Understanding the pathogenic mechanisms could, in some cases, guide the selection and optimization of appropriate treatment approaches for patients.

Real-world cost-effectiveness of panel-based genomic testing to inform therapeutic decisions for metastatic colorectal cancer

BackgroundMutations in KRAS and NRAS are associated with a lack of response to cetuximab and panitumumab, two biologics used for third-line therapy of metastatic colorectal cancer (mCRC). In British Columbia, Canada, eligibility for cetuximab or panitumumab was first based on single-gene KRAS testing. OncoPanel, a multi-gene next-generation sequencing panel with both KRAS and NRAS, was introduced in 2016. Our objective was to estimate the real-world cost-effectiveness of OncoPanel versus to single-gene KRAS testing to inform eligibility for cetuximab or panitumumab in mCRC. MethodsUsing population-based administrative health data, we identified a cohort of mCRC patients who had received a KRAS or OncoPanel test, and completed prior chemotherapy in 2010–2019. We matched KRAS- and OncoPanel-tested patients (1:1) using genetic matching to balance baseline covariates. Mean and incremental 3-year costs, survival, and quality-adjusted survival were estimated using inverse-probability-of-censoring weighting and bootstrapping. We conducted scenario-based sensitivity analysis for key costs and assumptions. FindingsAll OncoPanel-tested cases (n=371) were matched to a KRAS-tested comparator. In the KRAS and OncoPanel groups, respectively, 55·8 % and 41·2 % of patients were potentially eligible for cetuximab or panitumumab based on mutation status. Incremental cost and effectiveness of OncoPanel were $72 (95 % CI: −6387, 6107), −0·004 life-years (95 % CI: −0·119, 0·113), and −0·011 quality-adjusted life-years (95 % CI: −0·094, 0·075). Reductions in systemic therapy costs were offset by increased costs in other resources. Results were moderately sensitive to time horizon and changes in testing or treatment cost. InterpretationThe use of OncoPanel resulted in more precise targeting of cetuximab and panitumumab, but there was no change in incremental cost or quality-adjusted survival. Understanding the balance of costs achieved in practice can provide insight into the effect of future changes in testing policy, test cost, treatment eligibility, or drug prices in this setting.

Tumor-Agnostic Genomic and Clinical Analysis of BRAF Fusions Identifies Actionable Targets.

Even though BRAF fusions are increasingly detected in standard multigene next-generation sequencing panels, few reports have explored their structure and impact on clinical course. We collected data from patients with BRAF fusion-positive cancers identified through a genotyping protocol of 97,024 samples. Fusions were characterized and reviewed for oncogenic potential (in-frame status, non-BRAF partner gene, and intact BRAF kinase domain). We found 241 BRAF fusion-positive tumors from 212 patients with 82 unique 5' fusion partners spanning 52 histologies. Thirty-nine fusion partners were not previously reported, and 61 were identified once. BRAF fusion incidence was enriched in pilocytic astrocytomas, gangliogliomas, low-grade neuroepithelial tumors, and acinar cell carcinoma of the pancreas. Twenty-four patients spanning multiple histologies were treated with MAPK-directed therapies, of which 20 were evaluable for RECIST. Best response was partial response (N = 2), stable disease (N = 11), and progressive disease (N = 7). The median time on therapy was 1 month with MEK plus BRAF inhibitors [(N = 11), range 0-18 months] and 8 months for MEK inhibitors [(N = 14), range 1-26 months]. Nine patients remained on treatment for longer than 6 months [pilocytic astrocytomas (N = 6), Erdheim-Chester disease (N = 1), extraventricular neurocytoma (N = 1), and melanoma (N = 1)]. Fifteen patients had acquired BRAF fusions. BRAF fusions are found across histologies and represent an emerging actionable target. BRAF fusions have a diverse set of fusion partners. Durable responses to MAPK therapies were seen, particularly in pilocytic astrocytomas. Acquired BRAF fusions were identified after targeted therapy, underscoring the importance of postprogression biopsies to optimize treatment at relapse in these patients.

Mutation landscape in Chinese nodal diffuse large B-cell lymphoma by targeted next generation sequencing and their relationship with clinicopathological characteristics

BackgroundDiffuse large B-cell lymphoma (DLBCL), an aggressive and heterogenic malignant entity, is still a challenging clinical problem, since around one-third of patients are not cured with primary treatment. Next-generation sequencing (NGS) technologies have revealed common genetic mutations in DLBCL. We devised an NGS multi-gene panel to discover genetic features of Chinese nodal DLBCL patients and provide reference information for panel-based NGS detection in clinical laboratories.MethodsA panel of 116 DLBCL genes was designed based on the literature and related databases. We analyzed 96 Chinese nodal DLBCL biopsy specimens through targeted sequencing.ResultsThe most frequently mutated genes were KMT2D (30%), PIM1 (26%), SOCS1 (24%), MYD88 (21%), BTG1 (20%), HIST1H1E (18%), CD79B (18%), SPEN (17%), and KMT2C (16%). SPEN (17%) and DDX3X (6%) mutations were highly prevalent in our study than in Western studies. Thirty-three patients (34%) were assigned as genetic classification by the LymphGen algorithm, including 12 cases MCD, five BN2, seven EZB, seven ST2, and two EZB/ST2 complex. MYD88 L265P mutation, TP53 and BCL2 pathogenic mutations were unfavorable prognostic biomarkers in DLBCL.ConclusionsThis study presents the mutation landscape in Chinese nodal DLBCL, highlights the genetic heterogeneity of DLBCL and shows the role of panel-based NGS to prediction of prognosis and potential molecular targeted therapy in DLBCL. More precise genetic classification needs further investigations.

Molecular Characterization of Advanced-Stage Melanomas in Clinical Practice Using a Laboratory-Developed Next-Generation Sequencing Panel.

Cutaneous melanoma is one of the most lethal tumors among skin cancers, characterized by complex genetic and molecular alterations that result in uncontrolled cell proliferation and metastatic spread. Next-generation sequencing (NGS) enables the simultaneous examination of numerous genes, making this molecular technique essential for melanoma diagnosis, prognostic stratification, and therapy planning. Herein, we present the experience with our laboratory-designed NGS panel for the routine assessment of advanced-stage melanoma. A total of 260 specimens of advanced-stage melanomas were evaluated utilizing a laboratory-developed multi-gene NGS panel, which allowed the investigation of 229 amplicons in 25 oncogene/oncosuppressor genes. The NGS panel proved to be a reliable tool, failing to produce results in only 1.2% of the samples tested. BRAF and TERT were the two more commonly altered genes in 44.0% and 59.9% of samples, respectively. In 59.3% of the mutated cases, at least two concomitant variants were detected. In eight cases, both primary lesion and metastatic disease were analyzed by NGS. In all specimens (8/8, 100%), a perfect concordance in variants harbored by the primary and recurrence lesions was observed. Finally, this study described the validity of a laboratory-developed multi-gene NGS panel built specifically for advanced-stage melanomas in ordinary clinical practice.

Real-World Experiences of Next-Generation Sequencing in Oncology: From an Indian Multicenter Registry and Collaborative Centers

Abstract Background The integration of next-generation sequencing (NGS) in guiding personalized therapy for oncology faces the challenges, primarily, of cost and drug accessibility. Limited data from Indian academic centers accentuate the need for comprehensive insights into the real-world applications of NGS in oncology. Methods The Network of Oncology Clinical Trials in India (NOCI), accessible at www.noci-india.com, compiled data on patients who underwent NGS for solid organ cancers from January 1, 2018, to December 31, 2021. This study aimed to elucidate the testing indications, sample types analyzed, and the resultant impact on patient care. Results Analysis of data from six centers included 278 subjects, with 24 specimens (9%) excluded due to quality test failure. Tissue constituted 59.7% of specimens, blood 38.5%, and both 1.8%. Predominantly, NGS was employed for identifying BRCA1/2 mutations (56%) and for targeted therapy in non-small-cell lung cancer (NSCLC; 28%). Only 41 (16%) patients with other cancers underwent multigene NGS panels in pursuit of targetable mutations. Among them, 13 exhibited targetable mutations, and 3 received treatment based on NGS findings. Conclusion This study underscores that the majority of NGS applications focused on screening for BRCA1/2 mutations and identifying targetable mutations in NSCLC. However, among those undergoing NGS for advanced cancers, only a limited number received personalized therapy. The findings underscore the challenges of utilizing NGS in off-label indications within resource-constrained settings.

Access, autonomy, and affordability: ethical and human rights issues surrounding multigene panel testing for cancer in Japan and Switzerland.

Introduction: Advancements in precision medicine and genomics have led to prospects in a wide range of clinical fields, including oncology. In particular, developments in next-generation sequencing multigene panel tests have led to the possibility of tailoring treatment to the specific genomic markers of a patient's cancer. However, findings from current literature suggest that the path to implementation and uptake of genomic medicine is not without uncertainties and challenges. Methods: To better understand the current challenges to the implementation of genomic medicine services, we investigated the current state of patient access to genomic medicine in Japan and Switzerland. In this investigation, we focused on equal access, patient autonomy, and healthcare affordability. Results: Results have shown that although multigene panel testing is in principle covered by health insurance in both countries, barriers exist in terms of where the tests are available, comprehensive information for patients, and the affordability of not only the test itself but the overall process from diagnosis to treatment. Discussion: These results suggest a need to continue examining a more diverse range of clinical landscapes for genomic medicine to reveal more nuanced understandings of barriers to implementation and thus better identify best practices for overcoming them.

Comprehensive Molecular Genetic Analysis in Glioma Patients by Next Generation Sequencing.

Glioma is caused by multiple genomic alterations. The evolving classification of gliomas emphasizes the significance of molecular testing. Next generation sequencing (NGS) offers the assessment of parallel combinations of multiple genetic alterations and identifying actionable mutations that guide treatment. This study comprehensively analyzed glioma patients using multi-gene NGS panels, providing powerful insights to inform diagnostic classification and targeted therapies. We conducted a targeted panel-based NGS analysis on formalin-fixed and paraffin-embedded nucleic acids extracted from a total of 147 glioma patients. These samples underwent amplicon capture-based library preparation and sequenced using the Oncomine Comprehensive Assay platform. The resulting sequencing data were then analyzed using the bioinformatics tools. A total of 301 mutations, were found in 132 out of 147 tumors (89.8%). These mutations were in 68 different genes. In 62 tumor samples (42.2%), copy number variations (CNVs) with gene amplifications occurred in 25 genes. Moreover, 25 tumor samples (17.0%) showed gene fusions in 6 genes and intragenic deletion in a gene. Our analysis identified actionable targets in several genes, including 11 with mutations, 8 with CNVs, and 3 with gene fusions and intragenic deletion. These findings could impact FDA-approved therapies, NCCN guideline-based treatments, and clinical trials. We analyzed precisely diagnosing the classification of gliomas, detailing the frequency and co-occurrence of genetic alterations and identifying genetic alterations with potential therapeutic targets by NGS-based molecular analysis. The high-throughput NGS analysis is an efficient and powerful tool to comprehensively support molecular testing in neurooncology.

ADCY5-related dyskinesia: a treatable inherited neurometabolic disorder

Case Report. A 40-year-old Brazilian man presented with long-standing loss of balance, dystonia, and choreoathetosis, with episodic paroxysmal worsening. Neuroimaging and cerebrospinal fluid analysis were both unremarkable. Quantitative urine organic acid analysis, plasma acylcarnitine quantitative profile, and quantitative analysis of plasma amino acids by high performance liquid chromatography were all within normal interval values. Multigene next-generation sequencing panel identified the heterozygous pathogenic variant c.1252C&gt;T (p.Arg418Trp) in the ADCY5 gene, defining a diagnosis of ADCY5-related dyskinesia. Oral caffeine was associated to clonazepam and provided marked improvement of motor symptoms. Conclusion. This report adds evidence to the safety and efficacy of caffeine in the treatment of genetically confirmed cases of ADCY5-related dyskinesia in the context of gain-of-function variants.

Increasing targeted therapy options for mCRPC patients using multigene NGS panel.

e17056 Background: Prostate cancer (PCa) represents the second most common malignancy in males, characterized by a high level of clinical and molecular heterogeneity. Eventually, many patients develop metastatic Castration Resistant Prostate Cancer (mCRPC). mCRPC refers to prostate cancer that has spread beyond the prostate gland and is associated with increased morbidity and mortality. Next Generation Sequencing (NGS) has led to the identification of genomic alterations that may represent actionable targets with therapeutic potential in mCRPC. Such alterations can be identified on the somatic or hereditary level and implicate a variety of cell cycle mechanisms, like the DNA repair mechanism (Homologous Recombination Repair genes and Mismatch Repair Genes), as well as the AR, mTOR/AKT/PI3K, PTEN, ERK/MEK/Raf/Ras and WNT signaling pathways. Methods: In this study, 75 samples of patients with mCRPC were successfully processed. An NGS panel, targeting 513 genes associated with molecular and immuno-checkpoint inhibitor therapies, was used for the detection of gene alterations and fusions. In addition, genetic markers such as TMB, MSI and %gLOH were calculated for a subset of patients. Results: At least one mutation was detected in almost 90% of the cases tested, including SNVs, CNVs and gene fusions in a broad spectrum of the tested genes. In our cohort, the most commonly altered gene was CDK12 (9.3%), followed by ATM (6.7%) and PIK3CA (5.3%). Mutations were also found in FANCA (2.7%) and PTEN (2.7%). TMB was calculated in 52 patients, out of which 9.5% were characterized as TMB high ( &gt; 10 muts/Mb). MSI status was high for 4.5% of patients and %gLOH was elevated in 37.5% of the tested cohort. A mutation in an HRR gene was found in 29% of patients, rendering them eligible for therapy with PARP inhibitors. In addition, 18.7% of the patients could benefit from off label treatment. The calculation of genetic biomarkers, like TMB, MSI, and LOH, led to an increase to the cohort of patients who could receive on label therapy, even in cases with no or non-targetable mutation on DNA or RNA level. Moreover, due to the continuous approval of new drug regimens, retrospective evaluation of tumor analysis results led to an increase of the percentage of patients that could benefit from targeted treatment by 20%. Conclusions: Our results indicate that tumor analysis is essential for the identification of actionable biomarkers in mCRPC, since more than half of the patients were positive for a biomarker related to either targeted therapy or immunotherapy. Hence, frequent re-evaluation of NGS results is essential due to continuous drug approvals.

Diagnostic utility of next generation sequencing for somatic variants in cancer: A seven year cumulative cohort.

e15060 Background: Next generation sequencing (NGS) makes it possible to identify the specific molecular biomarkers to define patient eligibility for targeted therapies via multigene panels. Since then, even though the interpretation of data is complex and not all tumors have genomic alterations within actionable genes, using somatic sequencing for cancer patients becomes a daily routine in clinical oncology. Thus, here we present the data derived from our experience in NGS testing of different cancer patients and biological samples over the course of 7 years in our genetic diagnosis center. Methods: The cohort was consisted of total 5511 cases. While 2590 (46.99%) of them were formalin fixed paraffin embedded (FFPE) tissues, 2906 (52.73%) were liquid biopsies and 15 (0.27%) were other types of biological samples. Total of 15 different cancers were classified (Table 1) and were sequenced using 3 different multigene NGS panels (additional Table 1, BRCAs’ testing for breast/ovarian cancer is not included). NGS was performed via GeneReader NGS System (Qiagen, Germany). Bioinformatics analyzes and variant classification were performed using QCI-Analyze and QCI-Interpret interfaces. Results: As a result, the cases of 93.36% (n = 5145) among all samples were successfully sequenced. The lung cancer group was the most frequent with 47.96% (n = 2643 patients), followed by 491 (%8.9) colorectal 288 (5.23%) and breast cancer patients respectively, while 781 cases (14.17%) grouped as other including many rare cancers. Overall positivity rate was 42.57% (n = 2346) and 366 samples (6.64%) were not sufficient enough to be sequenced. The distribution of positivity rates in relation to cancer type and biological samples used were listed in Table 1. Classification and diagnosis of all tested cases, specimens and Tier 1-2 variants included in this cohort are available on the Additional Table 2. Conclusions: This report is a comprehensive review of the aggregate data across the entire cohort of cancer patients referred to a genetics diagnosis center. While our findings highlight the importance of NGS testing in the somatic setting for cancer patients, also these data stress the importance of diagnosis, biological sample types tested and test results. [Table: see text]

Comprehensive genomic profiling and therapeutic implications for patients with advanced cancers: The experience of an academic hospital.

e15162 Background: Next generation sequencing (NGS) can be used to detect tumor-specific genomic alterations, with the aim to identify actionable genomic alteration and provide additional treatment options for patients with advanced cancer. While smaller sequencing panels are being applied broadly, controversy exists around the routine implementation of comprehensive genomic profiling with large multigene NGS panels. Indeed, there is an ongoing discussion about the indications as well as timing of comprehensive genomic profiling in patients with advanced solid tumors. Therefore, there is a need for more data to increase understanding of the potential indications and added clinical benefit of routine implementation of broad comprehensive genomic profiling. However, available studies have often been reporting on a small patient population, which complicates the interpretation and translation to the clinical setting. This study aims to describe the feasibility of performing broad NGS panels in patients with advanced cancer in an academic hospital setting, as well as the targetable alterations detected. Methods: In this retrospective study, we analysed genomic alterations in solid tumor biopsies of 464 patients with locally advanced or metastatic cancer. Next generation sequencing was performed using the Foundation Medicine assay (FoundationOneCDx). The therapeutic implications of the genomic alterations were determined using the OncoKB classification. Results: The FoundationOne CDx was successfully applied in 464/521 patients (89%) with a range of cancer types. The most common altered genes were TP53 (61%), followed by KRAS (20%), CDKN2A (20%), TERT (16%), APC (16%), PTEN (14%), PIK3CA (14%) and CDKN2B (14%). Among 419 patients with successfully analyzed tumor mutational burden (TMB), the median TMB was 2.52 (range 0 – 67) mutations/Mb (mut/Mb). Forty-three patients presented with a high-TMB ( &gt; = 10 mut/Mb) of which eight had microsatellite instability. Out of 126 patients with an actionable target (e.g. ERBB2, KRAS, PIK3CA, FGFR2), 40 patients received matched treatment (8.6%), of which 17 were included in clinical trials. Conclusions: This single-center retrospective study shows that broad application of NGS is feasible in an academic center, increases the detection of actionable genomic alterations, and opens opportunities to provide treatment with immune checkpoint inhibitors in case of high tumor mutational burden and microsatellite instability status regardless of tumor histology. The study brings to attention that strategies such as inclusion in clinical (basket) trials and development of new targeted drugs are necessary to improve matched treatment rates. Further research is needed to assess the possible clinical benefit of broad application of NGS and genotype matched treatment.

Multi-Gene Next-Generation Sequencing Panel for Analysis of BRCA1/BRCA2 and Homologous Recombination Repair Genes Alterations Metastatic Castration-Resistant Prostate Cancer.

Despite significant therapeutic advances, metastatic CRPC (mCRPC) remains a lethal disease. Mutations in homologous recombination repair (HRR) genes are frequent in mCRPC, and tumors harboring these mutations are known to be sensitive to PARP inhibitors. The aim of this study was to verify the technical effectiveness of this panel in the analysis of mCRPC, the frequency and type of mutations in the BRCA1/BRCA2 genes, as well as in the homologous recombination repair (HRR) genes. A total of 50 mCRPC cases were analyzed using a multi-gene next-generation sequencing panel evaluating a total of 1360 amplicons in 24 HRR genes. Of the 50 cases, 23 specimens (46.0%) had an mCRPC harboring a pathogenic variant or a variant of uncertain significance (VUS), whereas in 27 mCRPCs (54.0%), no mutations were detected (wild-type tumors). BRCA2 was the most commonly mutated gene (14.0% of samples), followed by ATM (12.0%), and BRCA1 (6.0%). In conclusion, we have set up an NGS multi-gene panel that is capable of analyzing BRCA1/BRCA2 and HRR alterations in mCRPC. Moreover, our clinical algorithm is currently being used in clinical practice for the management of patients with mCRPC.

Pompe disease ascertained through The Lantern Project, 2018-2021: Next-generation sequencing and enzymatic testing to overcome obstacles to diagnosis.

The Lantern Project is an ongoing complimentary diagnostic program for patients in the United States sponsored by Sanofi and implemented by PerkinElmer Genomics. It combines specific enzymatic, biomarker, and genetic testing to facilitate rapid, accurate laboratory diagnosis of Pompe disease and several other lysosomal storage diseases, and a multigene next-generation sequencing panel including Pompe disease, LGMD, and other neuromuscular disorders. This article reports data for Pompe disease collected from October 2018 through December 2021, including acid α-glucosidase (GAA) enzyme assay and GAA sequencing (standard or expedited for positive newborn screening [NBS] to rule out infantile-onset Pompe disease [IOPD]) and the Focused Neuromuscular Panel, which includes GAA. One hundred forty patients (12 received only GAA enzyme testing, 128 had GAA sequencing alone or in addition to enzyme assay) have been confirmed with Pompe disease in this project. Eight of the 140 had a variant of unknown significance, but GAA activity ≤2.10μmol/L/h, thus were confirmed with Pompe disease. Three diagnosed patients 0-2years old had cross-reactive immunologic material (CRIM)-negative GAA variants and thus IOPD. One additional infant with presumptive IOPD had a homozygous frameshift c.1846del, likely CRIM-negative; symptoms were not provided. Among the 128 patients with molecular results, the c.-32-13T>G splice variant was homozygous in 11, compound-heterozygous in 98, and absent in 19. Proximal muscle weakness (58 patients) was the most common sign reported at testing; elevated creatine kinase (29 patients) was the most common laboratory result. The most common symptom categories were muscular (73 patients), musculoskeletal (13 patients), and respiratory (23 patients). Clinical information was not available for 42 samples, and 17 infants had only "abnormal NBS" or "low GAA" reported. Cardiac symptoms in 7 included potentially age-related conditions in five c.-32-13T>G-compound-heterozygous adults (myocardial infarction, heart murmur/palpitations, congestive heart failure: 1 each; 2 with atrial fibrillation) and hypertrophic cardiomyopathy in 2 children (1 and 2years old) with presumptive IOPD. One novel GAA variant was observed in a patient with enzyme activity 0.31μmol/L/h: c.1853_1854ins49, a frameshift pathogenic variant. The Lantern Project demonstrates the combinatorial utility of enzyme assay, targeted single-gene testing, and a focused neuromuscular next-generation sequencing panel in diagnosing Pompe disease.

Commercial Gene Panels for Congenital Anterior Segment Anomalies: Are They All the Same?

We compared next generation sequencing multigene panels (NGS-MGP) from 5 commercial laboratories to inform ophthalmologists' decision making in diagnostic genetic testing for congenital anterior segment anomalies (CASAs). Comparison of commercial genetic testing panels. This observational study gathered publicly available information on NGS-MGP from 5 commercial laboratories for the following: cataracts, glaucoma, anterior segment dysgenesis (ASD), microphthalmia-anophthalmia-coloboma (MAC), corneal dystrophies, and Axenfeld-Rieger syndrome (ARS). We compared gene panel composition, consensus rate (genes covered by all the panels per condition, "concurrent"), dissensus rate (genes covered by only 1 panel per condition, "standalone"), and intronic variant coverage. For individual genes, we compared publication history and association with systemic conditions. Altogether, cataract, glaucoma, corneal dystrophies, MAC, ASD, and ARS panels tested 239, 60, 36, 292, and 10 discrete genes, respectively. The consensus rate varied between 16% and 50%, and the dissensus rate varied between 14% and 74%. After pooling concurrent genes from all conditions, 20% of these genes were concurrent in 2 or more conditions. For both cataract and glaucoma, concurrent genes had significantly stronger correlation with the condition than standalone genes. The genetic testing of CASAs using NGS-MGPs is complicated, owing to their number, variety, and phenotypic and genetic overlap. Although the inclusion of additional genes, such as the standalone ones, might increase diagnostic yield, these genes are also less well studied, indicating uncertainty over their role in CASA pathogenesis. Rigorous prospective diagnostic yield studies of NGS-MGPs will aid in making decisions of panel selection for the diagnosis of CASAs.

Clinical usefulness of NGS multi-gene panel testing in hereditary cancer analysis.

Introduction: A considerable number of families with pedigrees suggestive of a Mendelian form of Breast Cancer (BC), Ovarian Cancer (OC), or Pancreatic Cancer (PC) do not show detectable BRCA1/2 mutations after genetic testing. The use of multi-gene hereditary cancer panels increases the possibility to identify individuals with cancer predisposing gene variants. Our study was aimed to evaluate the increase in the detection rate of pathogenic mutations in BC, OC, and PC patients when using a multi-gene panel. Methods: 546 patients affected by BC (423), PC (64), or OC (59) entered the study from January 2020 to December 2021. For BC patients, inclusion criteria were i) positive cancer family background, ii) early onset, and iii) triple negative BC. PC patients were enrolled when affected by metastatic cancer, while OC patients were all submitted to genetic testing without selection. The patients were tested using a Next-Generation Sequencing (NGS) panel containing 25 genes in addition to BRCA1/2. Results: Forty-four out of 546 patients (8%) carried germline pathogenic/likely pathogenic variants (PV/LPV) on BRCA1/2 genes, and 46 (8%) presented PV or LPV in other susceptibility genes. Discussion: Our findings demonstrate the utility of expanded panel testing in patients with suspected hereditary cancer syndromes, since this approach increased the mutation detection rate of 15% in PC, 8% in BC and 5% in OC cases. In absence of multi-gene panel analysis, a considerable percentage of mutations would have been lost.

Molecular profiling of male breast cancer by multigene panel testing: Implications for precision oncology.

Compared with breast cancer (BC) in women, BC in men is a rare disease with genetic and molecular peculiarities. Therapeutic approaches for male BC (MBC) are currently extrapolated from the clinical management of female BC, although the disease does not exactly overlap in males and females. Data on specific molecular biomarkers in MBC are lacking, cutting out male patients from more appropriate therapeutic strategies. Growing evidence indicates that Next Generation Sequencing (NGS) multigene panel testing can be used for the detection of predictive molecular biomarkers, including Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI). In this study, NGS multigene gene panel sequencing, targeting 1.94 Mb of the genome at 523 cancer-relevant genes (TruSight Oncology 500, Illumina), was used to identify and characterize somatic variants, Copy Number Variations (CNVs), TMB and MSI, in 15 Formalin-Fixed Paraffin-Embedded (FFPE) male breast cancer samples. A total of 40 pathogenic variants were detected in 24 genes. All MBC cases harbored at least one pathogenic variant. PIK3CA was the most frequently mutated gene, with six (40.0%) MBCs harboring targetable PIK3CA alterations. CNVs analysis showed copy number gains in 22 genes. No copy number losses were found. Specifically, 13 (86.7%) MBCs showed gene copy number gains. MYC was the most frequently amplified gene with eight (53.3%) MBCs showing a median fold-changes value of 1.9 (range 1.8-3.8). A median TMB value of 4.3 (range 0.8-12.3) mut/Mb was observed, with two (13%) MBCs showing high-TMB. The median percentage of MSI was 2.4% (range 0-17.6%), with two (13%) MBCs showing high-MSI. Overall, these results indicate that NGS multigene panel sequencing can provide a comprehensive molecular tumor profiling in MBC. The identification of targetable molecular alterations in more than 70% of MBCs suggests that the NGS approach may allow for the selection of MBC patients eligible for precision/targeted therapy.