Academic literature on the topic 'Targeted resequencing panel'

Abstract Introduction: Acute myeloid leukemia (AML) is one of the most threatening malignancies in children and adolescents. The accumulation of mutations in leukemia stem cells (LSC) is believed to lead to the development of leukemia. Cyto- and molecular genetics already identified several aberrations which are relevant in leukemogenesis, prognosis and therapy. Nevertheless, the molecular landscape and clonal evolution of AML and its clinical relevance, especially for pediatric patients, is not yet well described. Next Generation Sequencing (NGS) as an emerging sequencing technology provides the possibility to generate sequence data of high quality and detect genetic aberrations in a minimum of time. The aim of this study was to apply amplicon based panel targeted resequencing by using the TruSight Myeloid Panel (Illumina) to identify variants in 54 genes. Methods Patients: In total 150 samples derived from pediatric patients diagnosed with AML at the time of initial diagnosis or relapse were analysed regarding their mutational profile. All patients treated according to the AML-BFM therapy protocols (n=103) were chosen to determine the potential impact in prognosis. Sequencing and analysis of variants Sequencing with the TruSight Myeloid panel (Illumina) was performed on a MiseqDX. The sequencing panel is designed to identify somatic mutations associated with myeloid malignancies in 54 genes. To define variants, we excluded intronic, synonymous and variants with an allele frequency below 5% and a read depth below 50 reads. False positive variants were excluded by including healthy donors and reference samples. Variants were detected and analysed using Variant studio (Illumina) and Sophia DDM (Sophia Genetics). Almost all variants were detectable in both software, although great insertions and deletions were detectable only by Sophia DDM. Results In the cohort of 150 patients, we detected 408 mutations in the 54 genes included in the panel (fig. 1). 26% of the patients showed more than 4, 24% 3, 24% 2, 17% 1 and 9% of the patients showed 0 mutations. Four and more mutations occurred mostly in AML FAB M1 (n=17) and patients with a complex karyotype (n=6). Treatment related AML show less mutations compared to primary AML. Within the group of patients treated according the 1st line AML-BFM protocol (n=103), CEBPA, FLT3, KIT, NRAS, KRAS, NPM1 or WT1 mutations did not have prognostic relevance. Interestingly, we were able to detect mutations in ZRSR2 in 21 patients in total (SNVs in 6, InDels in 9 and splice acceptor variants in 6 patients). 15 patients were part of the group of patients who were treated according to the 1st line AML-BFM protocol. ZRSR2 encodes an essential splicing factor and the encoded protein associates with the U2 auxiliary factor heterodimer and may play a role in network interactions during spliceosome assembly [RefSeq 2008]. The presence of a ZRSR2 mutation seems to be associated with better EFS and lower cumulative incidence of relapse, respectively (fig.2). Even if patients with favourable cytogenetics were excluded, patients with mutated ZRSR2 might have better EFS (fig.2). Conclusions: Amplicon based panel targeted resequencing with the TruSight Myeloid panel provides the possibility to detect mutations in 54 genes associated to myeloid malignancies within 3 days. This will enable a faster and possible more precise characterisation of pediatric AML, either for risk group stratification or the addition of more specific treatment options. Due to the limited number of patients, the results concerning the prognostic relevance of ZRSR2 need to be confirmed in a larger patient group. Table patient characteristics Table. patient characteristics Figure 1 Number of variants detected in 54 genes Figure 1. Number of variants detected in 54 genes Figure 2 Event-free survival (EFS) and cumulative incidence for relapse for patients showing no mutation (blue) or mutations (red) in ZRSR2. Figure 2. Event-free survival (EFS) and cumulative incidence for relapse for patients showing no mutation (blue) or mutations (red) in ZRSR2. Disclosures Reinhardt: Jazz Pharma: Other: Travel Accomodation; Celgene: Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Boehringer Ingelheim: Membership on an entity's Board of Directors or advisory committees.

The term hereditary ataxia (HA) refers to a heterogeneous group of neurological disorders with multiple genetic etiologies and a wide spectrum of ataxia-dominated phenotypes. Massive gene analysis in next-generation sequencing has entered the HA scenario, broadening our genetic and clinical knowledge of these conditions. In this study, we employed a targeted resequencing panel (TRP) in a large and highly heterogeneous cohort of 377 patients with a clinical diagnosis of HA, but no molecular diagnosis on routine genetic tests. We obtained a positive result (genetic diagnosis) in 33.2% of the patients, a rate significantly higher than those reported in similar studies employing TRP (average 19.4%), and in line with those performed using exome sequencing (ES, average 34.6%). Moreover, 15.6% of the patients had an uncertain molecular diagnosis. STUB1, PRKCG, and SPG7 were the most common causative genes. A comparison with published literature data showed that our panel would have identified 97% of the positive cases reported in previous TRP-based studies and 92% of those diagnosed by ES. Proper use of multigene panels, when combined with detailed phenotypic data, seems to be even more efficient than ES in clinical practice.

Tumor mutational burden (TMB) refers to the number of somatic mutations in a tumor per megabase and is a biomarker for response to immune checkpoint inhibitor therapy. Immune checkpoint inhibitors are currently approved for tumors with TMB greater than or equal to 10 mutations/megabase. Many laboratories are currently reporting TMB values based upon targeted resequencing panels with limited genomic coverage. Due to sampling variation, this leads to significant uncertainty in the assay’s TMB result, particularly at relatively low TMB levels near the 10 mutation per megabase therapeutic threshold. In order to allow clinicians and laboratorians to explore this uncertainty, we built a novel web application that allows a user to view the potential error of a TMB result given the sequencing panel size. This application also allows the user to explore the effect of incorporating knowledge of a specific tumor type’s typical TMB distribution on the error profile of the TMB result.

Introduction Congenital dyserythropoietic anemias (CDA) are rare inherited red cell disorders characterized by ineffective erythropoiesis and inappropriate reticulocytopenia. CDAs are usually difficult to diagnose due to variable phenotypes and overlapping bone marrow (BM) morphology with other disorders. Numerous implicated causal genes make Sanger sequencing a less likely approach and hence, the use of targeted resequencing can expedite molecular diagnosis. This study aimed at determining the genetic spectrum of CDAs and translating the results into patient care. Methods Twenty nine patients with clinical and laboratory evidence suggestive of CDA and 1 patient suggestive of CDA with thrombocytopenia by BM morphology were studied. Various biochemical and molecular tests were done to exclude common hemolytic anemias. Common SEC23B: p.Tyr462Cys variant in our patients with CDA was screened by Sanger sequencing. DNA libraries were prepared using TruSight One Sequencing Panel and TruSeq Custom Amplicon Panel and sequenced on Illumina platform. After data analysis variants were classified and the most likely disease-causing variants were validated by Sanger sequencing followed by pedigree analysis. Results Out of 27 patients of suspected CDA, SEC23B: p.Tyr462Cys variant was found in 10 patients. Rest of the remaining 17 patients were subjected to targeted resequencing. Data analysis revealed novel potentially pathogenic variants in compound heterozygosity in SEC23B in 4 patients and 1 patient had a heterozygous variant in SEC23B. There could be the possibility of intronic or large indel in her. The variants were distributed throughout the SEC23B gene. Notably, in 7 patients with suspected CDA, the final molecular diagnosis were hemolytic anemias. Of them, 4 showed likely pathogenic variants in PKLR gene and 1 each had probably causal variant in MTRR, SPTB and PIEZO1 genes. In the patient's with pyruvate kinase deficiency, screening by enzyme assays were normal. Except for the patient with MTRR gene defect all 6 had transfusion dependent anemia and BM showed dyserythropoiesis. One patient each of GATA1 gene variant (novel) and a known pathogenic variant p.Glu325Lys in KLF1 gene (CDA type IV) was detected. Of 17 cases subjected to targeted resequencing the diagnosis was achieved in ~76% (13/17) of cases. The phenotypes correlated with the genetic defects found in the SEC23B gene. The homozygous and compound heterozygous defects in this gene cause CDA type II. As anticipated GATA1 gene defect (p.Val205Leu) was found in a patient of X-linked thrombocytopenia with dyserythropoietic anemia. Patient with KLF1 had high levels of fetal hemoglobin along with features of dyserythropoiesis in BM compatible with the phenotype of variant p.Glu325Lys causing CDA type IV. Phenotype-genotype correlation was discrepant in 7 cases of CDA. In 4 cases pyruvate kinase deficiency (PKLR) was found and each case of hereditary xerocytosis (PIEZO1), membrane defect (SPTB) and MTRR defect was found. Conclusion(s) CDA showed a highly varied etiology. Our experience demonstrates a high diagnostic yield (~76%) of targeted resequencing for molecular diagnosis of suspected CDAs. Discrepancy was noted in 41% (7/17) cases with suspected CDA which were diagnosed as hemolytic anemia after molecular analysis. Establishing the correct diagnosis of pyruvate kinase deficiency led to an evidence-based decision of splenectomy that eliminated transfusion dependence. In the patient with MTRR defect change in therapy was suggested. Prenatal diagnosis was done for 2 families, where in 1 of the family both the SEC23B variants were novel and in compound heterozygosity. This study highlights the importance of genetic testing in patients under frequent blood transfusions and suspected CDAs, to provide accurate diagnosis and therapeutic interventions. Disclosures No relevant conflicts of interest to declare.

Background. Small cell lung cancer (SCLC) is an aggressive and invasive malignancy that presents at advanced clinical stage with no more effective treatments. Development of a method for its early detection would be useful, also new therapeutic target need to be discovered; however, there is a lack of information about its oncogenic driver gene mutations. Objectives. We aim to identify the SCLC-related genomic variants that associate with clinical staging and serum protein biomarkers observed in other types of lung cancer. Methods. We screened formalin-fixed paraffin-embedded (FFPE) biopsy tissues of 32 Chinese SCLC patients using the 303 oncogenic driver gene panel generated by Tiling PCR amplification sequencing (tPAS) and analyzed the patients’ corresponding serum protein levels of CYFRA21-1 CEA, NSE, and SCCA. Results. In total, we found 147 SCLC-related mutant genes, among these, three important genes (TP53, RB1, KMT2D) as well as five novel genes LRRK2, BRCA1, PTCH1, ARID2, and APC that altogether occurred in 90% of patients. Furthermore, increased mutations to 6 genes (WT1, NOTCH1, EPHA3, KDM6A, SETD2, ACVR1B) significantly associated with higher serum NSE levels ( P = 0.0016 ) and higher clinical stages II + III compared to stage I ( P = 0.06 ). Conclusions. Our panel is relatively reliable in detecting the oncogenic mutations of Chinese SCLC patients. Based on our findings, it may be possible to combine SCLC-related mutations and serum NSE for a simple detection of clinical staging.

Introduction: Next Generation Sequencing (NGS) has driven the rapid increase in the number of recognizable inborn errors of immune system development and/or function often hampered by the wide heterogeneity of the many genetically diverse but phenotypically overlapping diseases. NGS has also led to the discovery of new genes implicated in well-defined biological pathways, revisiting frequencies and broadening their phenotypic spectrum. Objectives: Identification of the genetic causes of already known and unknown immune-mediated diseases with immunedysregulation; improvement of our knowledge about clinically overlapping phenotypes through the genetic characterization of the corresponding patients; optimization of the diagnostic work-up in order to administer disease specific treatments to patients. Methods: A total of 150 patients, selected based on a clinical history highly evocative for immune-dysregulation (peripheral and/or central cytopenia and/or lymphoprolipheration and/or autoimmunity or autoinflammation) and/or immunodeficiency were submitted to 3 custom gene panels of 146, 315 and 58 genes and sequenced through the Ion Personal Genome Machine (PGM™) System. Based on the clinical phenotype, frequency and impact on the protein, variants were selected and validate by standard Sanger sequencing. Results: The mutation detection rates for these panels were 15/51 (29%), and 16/69 (23%) and 2/30 (6%), respectively, for a total of 35 pathogenic variants that correlate with the respective clinical phenotypes. The patients could be classified in: ALPS/ALPS-like (97, 26 of which diagnosed), cytopenia (33, 4 diagnosed), undefined autoinfiammatory (12, 2 diagnosed) and suspected immunodeficiency (8, 1 diagnosed). Moreover, variants of unknown significance (VUS) in potentially causative genes were also found in additional 14 patients (6/30; 4/51; 4/69). A number of variants, either pathogenic, likely pathogenic, or VUS have been detected in some cases at genes unexpected on the basis of the phenotypes, among which PRKCD, PIK3CD, IL7R, NCF1, TNFRSF13C, CASP8, thus confirming wide heterogeneity in the phenotypic spectrum associated with diseases sharing haemato-immune rheumatological features. Conversely, several clinically similar cases did not reveal any relevant mutation, thus reflecting a genetic heterogeneity that is far from being disclosed yet. Conclusion: The NGS approach has demonstrated excellent performances in the 1) evaluation of large genes and mutation detection, 2) overall timeliness of the gene panels, relying on continuous literature updates, and 3) identification of unexpected phenotypes for well-defined monogenic disease and definition of different disease clinical entities characterized by overlapping phenotypes. By contrast, due to the remarkable variability in clinical presentations, defining the appropriate list of genes for a given phenotype represents one key difficulty in the design of these panels. In the near future we will have to focus on the functional study of the many variants, especially VUS, that have emerged in a massive study like ours

The Hereditary ataxias (HAs) are a group of heterogenous neurological disorders associated with multiple genetic etiologies and encompassing a wide spectrum of phenotypes, where ataxia is the prominent feature. HAs are characterized by degeneration of Purkinje cell and/or spinocerebellar connections, often associated with defects in additional brain structures, and all patterns of inheritance may occur. Similar to other fields of medical genetics, Next Generation Sequencing (NGS) has entered the HA scenario widening our genetic and clinical knowledge of this condition, but routine NGS applications still miss genetic diagnosis in about two third of patients. In this doctoral study, we applied multi-gene panels to define the molecular basis in 259 patients with a clinical diagnosis of HA and negative to tests for pathological expansion in SCA1, 2, 3, 6, 7, 8, 12, 17 and FXN. We found a positive molecular diagnosis in 25% of patients, whereas a similar number of patients had an uncertain diagnosis due to the presence of either variants of uncertain significance or lack of biological samples to determine segregation among family members. Hence despite a higher positive diagnostic rate compared to similar studies described in literature, a half of patients lacked any indication of the genetic cause of their disease. Using exome sequencing as a second-tier approach in some families, refractory to multi-gene panel analysis, did not significantly improved our diagnostic yield. On the other hand, NGS analysis in our cohort indicated that familial cases were more easily diagnosed rather than sporadic cases, and also that combining massive sequencing with detailed clinical information and family studies increases the likelihood to reach a molecular diagnosis. Among positive patients, we could expand clinical and allelic information in a subgroup of genes offering original description of new mutations and corroborating genetic findings with functional investigations that took advantage of different in vitro or in vivo platforms. In particular, through functional studies in SPG7 knock-down models of Drosophila melanogaster, we remarked that SPG7, whose mutations cause spastic paraplegia type 7, has a critical role in neurons more than in skeletal muscle. The high frequency of p.Ala510Val mutation in SPG7 observed in our cohort as well in similar studies performed elsewhere moved us to develop a humanized knock-in fruit fly model harboring that specific mutation and prepare preliminary characterizations. Similar studies in fruit fly were performed silencing AFG3L2, the gene causing SPAX5 in a child in association with an unusual, relatively milder phenotype. Furthermore, combination of skin fibroblasts and Saccharomyces cerevisiae as models was employed in the genetic characterization of new mutations in a novel recessive HARS-related phenotype whereas primary human cells, yeast and Danio rerio models were used to functionally characterize new HA-related mutations in COQ4. Finally, we could expand the clinical presentation of rare causes of HAs describing new dominant mutations in STUB1 and biallelic variants in RFN216, COQ8A, and ATP13A2. Altogether, studies performed during this doctoral work further underlined the usefulness of NGS in HAs and highlighted how NGS technologies rely on the integrated use of family and clinical studies and different in vitro/in vivo platforms to substantiate molecular findings. The latter platform will be also a tool for future investigations to dissect pathogenesis and to improve therapies.