Clinical Next-generation Sequencing Research Articles

Towards Personalized Medicine in Melanoma: Implementation of a Clinical Next-Generation Sequencing Panel

Molecular diagnostics are increasingly performed routinely in the diagnosis and management of patients with melanoma due to the development of novel therapies that target specific genetic mutations. The development of next-generation sequencing (NGS) technologies has enabled to sequence multiple cancer-driving genes in a single assay, with improved sensitivity in mutation detection. The main objective of this study was the design and implementation of a melanoma-specific sequencing panel, and the identification of the spectrum of somatic mutations in a series of primary melanoma samples. A custom panel was designed to cover the coding regions of 35 melanoma-related genes. Panel average coverage was 2,575.5 reads per amplicon, with 92,8% of targeted bases covered ≥500×. Deep coverage enabled sensitive discovery of mutations in as low as 0.5% mutant allele frequency. Eighty-five percent (85/100) of the melanomas had at least one somatic mutation. The most prevalent mutated genes were BRAF (50%;50/199), NRAS (15%;15/100), PREX2 (14%;14/100), GRIN2A (13%;13/100), and ERBB4 (12%;12/100). Turn-around-time and costs for NGS-based analysis was reduced in comparison to conventional molecular approaches. The results of this study demonstrate the cost-effectiveness and feasibility of a custom-designed targeted NGS panel, and suggest the implementation of targeted NGS into daily routine practice.

Validation and Utilization of a Clinical Next-Generation Sequencing Panel for Selected Cardiovascular Disorders.

The development of high-throughput technologies such as next-generation sequencing (NGS) has allowed for thousands of DNA loci to be interrogated simultaneously in a fast and economical method for the detection of clinically deleterious variants. Whenever a clinical diagnosis is known, a targeted NGS approach involving the use of disease-specific gene panels can be employed. This approach is often valuable as it allows for a more specific and clinically relevant interpretation of results. Here, we describe the customization, validation, and utilization of a commercially available targeted enrichment platform for the scalability of clinical diagnostic cardiovascular genetic tests, including the design of the gene panels, the technical parameters for the quality assurance and quality control, the customization of the bioinformatics pipeline, and the post-bioinformatics analysis procedures. Regions of poor base coverage were detected and targeted by Sanger sequencing as needed. All panels were successfully validated using genotype-known DNA samples either commercially available or from research subjects previously tested in outside clinical laboratories. In our experience, utilizing several of the sub-panels in a clinical setting with 33 real-life cardiovascular patients, we found that 20% of tests requested were reported to have at least one pathogenic or likely pathogenic variant that could explain the patient phenotype. For each of these patients, the positive results may aid the clinical team and the patients in best developing a disease management plan and in identifying relatives at risk.

Evaluating the Calling Performance of a Rare Disease NGS Panel for Single Nucleotide and Copy Number Variants.

Variant detection protocols for clinical next-generation sequencing (NGS) need application-specific optimization. Our aim was to analyze the performance of single nucleotide variant (SNV) and copy number (CNV) detection programs on an NGS panel for a rare disease. Thirty genes were sequenced in 83 patients with hereditary spastic paraplegia. The variant calls obtained with LifeScope, GATK UnifiedGenotyper and GATK HaplotypeCaller were compared with Sanger sequencing. The calling efficiency was evaluated for 187 (56 unique) SNVs and indels. Five multiexon deletions detected by multiple ligation probe assay were assessed from the NGS panel data with ExomeDepth, panelcn.MOPS and CNVPanelizer software. There were 48/51 (94%) SNVs and 1/5 (20%) indels consistently detected by all the calling algorithms. Two SNVs were not detected by any of the callers because of a rare reference allele, and one SNV in a low coverage region was only detected by two algorithms. Regarding CNVs, ExomeDepth detected 5/5 multi-exon deletions, panelcn.MOPs 4/5 and only 3/5 deletions were accurately detected by CNVPanelizer. The calling efficiency of NGS algorithms for SNVs is influenced by variant type and coverage. NGS protocols need to account for the presence of rare variants in the reference sequence as well as for ambiguities in indel calling. CNV detection algorithms can be used to identify large deletions from NGS panel data for diagnostic applications; however, sensitivity depends on coverage, selection of the reference set and deletion size. We recommend the incorporation of several variant callers in the NGS pipeline to maximize variant detection efficiency.

Miniaturized Nanopore DNA Sequencing: Accelerating the Path to Precision Medicine.

On January 30, 2015, President Barack Obama announced the launch of a Precision Medicine Initiative—“a bold new research effort to revolutionize how we improve health and treat disease” (1). The success of this bold new initiative depends upon continued improvements in the genomics space. Arguably, the key technological player in precision medicine is next generation sequencing (NGS),2 an extremely powerful technology for detection of genetic variation. NGS has enabled a multitude of impressive research discoveries that have been translated toward more rapid, cost-effective, and comprehensive analyses for inherited conditions and cancer. However, despite its achievements, NGS analysis is still too expensive and time-consuming of a process to be carried out routinely on all patients. The technological platform and the clinical-grade reagents themselves are both costly, as is the scientific know-how to perform the benchwork, bioinformatics, and variant interpretation. Reducing the time, cost, and effort to perform clinical NGS is essential to achieve further adoption of personalized medicine. Current NGS sequencing technologies generally use expensive and slow optic-based measurements of short copies of PCR-amplified DNA. Additionally, 3 major groups of genomic variation that are important for clinical diagnostics cannot be efficiently detected by de novo assembly of sequencing data from short DNA strands. The first of these, and closest to clinical optimization, are the copy number alterations that remove or add single or multiple exons, such as those commonly encountered in Duchene muscular dystrophy. The next major class is the trinucleotide repeat disorders. The classical example here is Fragile X, whereby a repeating CGG motif expansion (growing to over thousands of nucleotides in some cases) causes disease. Finally, regions of low sequence complexity, known as pseudogenes, or highly related gene family members, like members of the CYP family of genes, can be challenging to detect a real pathogenic change from …

The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

ABSTRACTRecent advances in next‐generation sequencing (NGS) have given rise to new challenges due to the difficulties in variant pathogenicity interpretation and large dataset management, including many kinds of public population databases as well as public or commercial disease‐specific databases. Here, we report a new database development tool, named the “Clinical NGS Database,” for improving clinical NGS workflow through the unified management of variant information and clinical information. This database software offers a two‐feature approach to variant pathogenicity classification. The first of these approaches is a phenotype similarity‐based approach. This database allows the easy comparison of the detailed phenotype of each patient with the average phenotype of the same gene mutation at the variant or gene level. It is also possible to browse patients with the same gene mutation quickly. The other approach is a statistical approach to variant pathogenicity classification based on the use of the odds ratio for comparisons between the case and the control for each inheritance mode (families with apparently autosomal dominant inheritance vs. control, and families with apparently autosomal recessive inheritance vs. control). A number of case studies are also presented to illustrate the utility of this database.

A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors

Clinical next-generation sequencing (NGS) assay choice requires careful consideration of panel size, inclusion of appropriate markers, ability to detect multiple genomic aberration types, compatibility with low quality and quantity of nucleic acids, and work flow feasibility. Herein, in a high-volume clinical molecular diagnostic laboratory, we have validated a targeted high-multiplex PCR-based NGS panel (OncoMine Comprehensive Assay) coupled with high-throughput sequencing using Ion Proton sequencer for routine screening of solid tumors. The panel screens 143 genes using low amounts of formalin-fixed, paraffin-embedded DNA (20 ng) and RNA (10 ng). A large cohort of 121 tumor samples representing 13 tumor types and 6 cancer cell lines was used to assess the capability of the panel to detect 148 single-nucleotide variants, 49 insertions or deletions, 40 copy number aberrations, and a subset of gene fusions. High levels of analytic sensitivity and reproducibility and robust detection sensitivity were observed. Furthermore, we demonstrated the critical utility of sequencing paired normal tissues to improve the accuracy of detecting somatic mutations in a background of germline variants. We also validated use of the Ion Chef automated bead templating and chip loading system, which represents a major work flow improvement. In summary, we present data establishing the OncoMine Comprehensive Assay-Ion Proton platform to be well suited for implementation as a routine clinical NGS test for solid tumors.

Systematic STAT3 Mutation Testing Identifies Patients with Unsuspected T-Cell Large Granular Lymphocytic Leukemia

▪The initial clinical presentation of T-cell large granular lymphocytic leukemia (T-LGL) and myelodysplastic syndromes (MDS) can be similar, each characterized by unexplained peripheral cytopenias. However, these diseases are pathobiologically distinct and associated with stark differences in prognosis and therapy. T-LGL is a clonal lymphoid disorder defined by phenotypically abnormal cytotoxic T cells and an indolent clinical course, while MDS is a clonal disorder of hematopoietic stem cells defined by ineffective hematopoiesis, morphologic dysplasia, and an elevated risk of acute leukemia. Despite these differences, distinction between T-LGL and MDS can be challenging and misdiagnosis can significantly delay initiation of appropriate therapy. The recent identification of STAT3 mutations in LGL may facilitate this distinction: activating STAT3 mutations occur in 40-70% of T-LGL cases, primarily within the SH2 domain, but have not been reported in patients with MDS without concomitant T-LGL. STAT3 is included within our clinical next generation sequencing (NGS) panel, which is used to evaluate patients with known or suspected hematologic malignancies, primarily acute myeloid leukemia, MDS and myeloproliferative neoplasms, as well as various lymphocytic leukemias. We report the frequency and type of STAT3 mutations within our patient population and assess the impact of this information on diagnosis.Between 1/1/2015 and 6/30/2016, 3414 samples (primarily peripheral blood (PB) or bone marrow (BM)) from 2530 unique patients evaluated at Brigham and Women's Hospital and/or Dana-Farber Cancer Institute underwent clinical NGS with a custom, 95-gene, amplicon-based panel (PMID: 27339098). Exons 2-17 and 21-23 of the STAT3 gene were analyzed in each sample using reference transcript 1 (NM_139276).We identified 40 patients with 40 candidate STAT3 mutations (Figure 1). Based on domain localization, variant allele fraction, and population allele frequency, we classified these sequence variants as somatic SH2 domain mutations (n = 21), somatic non-SH2 domain mutations of unknown significance (n = 5) or germline variants (n = 14). Of the 21 patients with somatic SH2 domain mutations, 9 carried a prior diagnosis of T-LGL and 8 were concurrently diagnosed with T-LGL by conventional diagnostic criteria (clonal aberrant T cells in the setting of neutropenia, anemia, or lymphocytosis). The final 4 patients with STAT3 SH2 domain mutations were unexpected diagnoses of T-LGL. These 4 patients were initially referred from outside institutions for MDS based on the reported presence of unilineage erythroid dysplasia (n=2), unquantified ring sideroblasts (n=1), or pancytopenia with unspecified marrow findings (n=1). In 3 of these cases, the STAT3 mutation discovery prompted T-cell flow cytometric analysis of peripheral blood, which revealed an aberrant immunophenotype, and T-cell receptor gamma gene rearrangement studies, which were clonal; these tests are pending in the 4th case. BM evaluation was performed in 12 of 21 patients, including the 4 with suspected MDS; in all cases, the findings did not meet diagnostic criteria for MDS by expert hematopathology review and all showed a normal karyotype. Five additional cases demonstrated somatic non-SH2 domain STAT3 mutations of unknown pathobiologic significance: 3 myeloid neoplasms, 1 chronic lymphocytic leukemia, and 1 autoimmune hemolytic anemia. Additional non-STAT3 mutations were also frequently identified in tumors other than T-LGL.Our experience demonstrates that STAT3 sequencing is a critical component of the evaluation of unexplained cytopenias, and identification of a mutation can clarify ambiguous phenotypes thus averting the consequences of misdiagnosis or diagnostic delay. Notably, several series have reported that MDS and T-LGL can infrequently occur concurrently and thus identification of a STAT3 mutation and a clonal T-LGL population does not exclude the possibility of concomitant MDS. In our cohort, however, no T-LGL patient with a STAT3 mutation demonstrated pathologic evidence of MDS and the majority (19 of 21) showed no other myeloid-associated somatic mutations. In addition, 5 cases in our cohort had likely somatic, non-SH2 domain STAT3 mutations in the context of disparate clinical scenarios, suggesting that these mutations may have a pathogenic role in other hematologic malignancies, a subject of future study. [Display omitted] DisclosuresDeAngelo:Ariad: Consultancy; Pfizer: Consultancy; Novartis: Consultancy; Amgen: Consultancy; Baxter: Consultancy; Incyte: Consultancy; Celgene: Consultancy. Stone:Celator: Consultancy; Jansen: Consultancy; ONO: Consultancy; Agios: Consultancy; Novartis: Consultancy; Pfizer: Consultancy; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Juno Therapeutics: Consultancy; Amgen: Consultancy; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Consultancy; Merck: Consultancy; Roche: Consultancy; Seattle Genetics: Consultancy; Sunesis Pharmaceuticals: Consultancy; Xenetic Biosciences: Consultancy. Lindsley:MedImmune: Research Funding; Takeda Pharmaceuticals: Consultancy.

Mutational Shift in FLT3 and NPM1-Positive Acute Myeloid Leukemia (AML) Relative to Therapy and Disease Progression

Introduction:Clonal myeloid malignancies such as AML are often characterized and treated based on specific mutation profiles identified at diagnosis. Routine use of clinical cancer next-generation sequencing (NGS) in diagnosis and disease monitoring has resulted in sequential mutation profiles of individual patients. On NGS profiling at interval follow-ups, mutations identified at diagnosis may change, or shift, through disease course. Here we track FLT3 and NPM1 mutations in the context of therapy, disease progression, clinical course, and pathology.Methods:Patients with AML or MDS whose blood or marrow specimens were sequenced using the Penn hematological-NGS panel (68 genes with full exon coverage) on at least 2 occasions and found at least once to have FLT3 or NPM1 mutations were included. An R script was written to track mutations and allele frequencies over time. These data were integrated with corresponding pathology and clinical data to evaluate mutation profiles in relation to disease status, therapy and progression. This study was approved by the institutional review board.Results:Review of clinical NGS data identified 37 patients with pathogenic mutations in FLT3 (n=15), NPM1 (n=5), or FLT3 and NPM1 (n=17) in samples characterized as de novo AML (AML), recurrent AML (rAML), myelodysplastic syndrome (MDS), recurrent MDS (rMDS), AML transformed from MDS (tAML), or AML in remission (R). Patients were divided into 3 mutational groups: FLT3 only, FLT3 and NPM1, and NPM1 only. The average number of pathogenic mutations (including mutations in genes other than FLT3 or NPM1) at initial and second testing was 1.9/3.1; 3.5/3.4 and 3.2/1.8, respectively.Tracking of FLT3 and NPM1 allele frequencies (>10% change) revealed changes in populations of multiple subclones at different time points. In the FLT3 and FLT3 and NPM1 groups, the original FLT3 and/or NPM1 mutation often became undetectable at subsequent testing. This frequently coincided with the emergence of new clones with different mutations. Nineteen patients showed loss of an original FLT3 mutation at subsequent testing, with 11 of these patients showing emergence of a new FLT3 clone with a different mutation. All 11 patients with loss of an original NPM1 clone had a new NPM1 clone with a different mutation appear. The NPM1 only group did not show loss of the original NPM1 clone unless it was at remission. All five patients in the NPM1 only group (3 AML, 2 rAML at initial CPD testing) achieved clinical and histologic remission with concordant loss of NPM1 mutations. In four patients, the detectable mutations remaining at remission were exclusively from the original clone (DNMT3A, DNMT3A/TET2, DNMT3A/IDH2/TET2, IDH2). The fifth patient had a newly detected SRSF2 mutation in addition to the original IDH2 mutation. All five patients are alive, and do not have overt morphologic evidence of recurrent AML on bone marrow biopsies that were performed within the last year.In four AML patients with FLT3 mutations, of which three were on FLT3 inhibitor therapy, the loss of a FLT3 mutation was followed by the emergence of a new NRAS mutation. Three patients achieved remission, but two died soon after of complications from graft versus host disease. The fourth patient achieved remission and had a detectable mutation only in IDH2, but on subsequent NGS testing showed reemergence of the previous NRAS mutation and relapsed three months later.Conclusions:Monitoring of FLT3 and NPM1 mutations in AML patients by NGS rather than single gene assays is crucial due to the frequent findings of other pathogenic co-mutations, mutational shift in response to disease progression and to therapy, and emergence of new disease associated clones at recurrence. DisclosuresNo relevant conflicts of interest to declare.

Molecular Profiling of High-Risk Pediatric Acute Myeloid Leukemia

Background: Several landmark genomic profiling studies have dramatically advanced our understanding of the origin, progression and clonal evolution of adult acute myeloid leukemia (AML) and directly impacted clinical care. However, very little is known about the mutational landscape of pediatric AML, a distinct entity that shares few genetic and clinical characteristics with adult AML. To investigate potential drivers of high-risk pediatric AML, comprehensive genomic profiling was performed on high-risk AML samples as part of a prospective clinical next-generation sequencing program.Methods:Samples obtained from patients with known high-risk features at diagnosis or with refractory or relapsed AML were selected for molecular profiling. Comprehensive testing included whole-exome sequencing (WES) of matched tumor (bone marrow or chloroma tissue) and normal tissue (peripheral blood or buccal swab) samples and transcriptome analysis (RNAseq). Targeted sequencing of 467 cancer-associated genes was used when tumor tissue was limited. Sequencing was performed on Illumina's HiSeq 2500 with 150X and 500X average coverage for WES and targeted sequencing, respectively. Variants were filtered to select alterations in cancer-related genes or genes relevant for patient care.Results:Fifteen patients with AML (mean age 7.7 yrs; range 0.75-19 yrs) met high-risk criteria (high-risk features at diagnosis = 4, relapsed disease = 8, refractory disease = 3) and were selected for profiling. WES and RNAseq were performed on 11 samples, WES only on 3 samples and targeted DNA sequencing on 1 sample. The median number of variants was 60 (range 14- 5950) per case. After filtering, 54 mutations were identified in 35 genes with a mean of 3.6 mutated genes per patient sample (range 0-14); two samples only carried a fusion gene with no other genetic alterations. At least one driver genetic alteration was detected in each patient sample. Thirteen samples carried mutations in at least one gene known to be altered in AML (e.g. IDH1, WT1, TP53, NRAS) (mean, 2; range, 1-6) and 5 samples carried novel mutations in 15 genes not previously implicated in AML (e.g. CARD9, CHD9, Axin1). Mutations in 11 AML related genes were detected in more than one sample including NRAS in 4, TP53 in 3 and KRAS, PTPN11 PHF6, JAK3 in 2 samples each; genes not previously implicated in AML were only mutated in single patients. Of note, mutations in genes encoding members of the RAS pathway occurred in 60% of cases (9/15 samples). RNAseq identified gene fusions in 7/11 samples (63%). Four fusions involving KMT2A and core binding factor genes were also detected by FISH while three fusions were detected by RNAseq only: NUP98-NSD1 in two patients and CBFA2T3-GLIS2 in one patient. Samples carrying driver gene fusions had the lowest number of mutated genes (0-1) compared to samples lacking a gene fusion (1-5 mutated genes), with one exception of a patient with history of infant ALL who later developed KMT2A-AFF1AML with the highest number of mutated genes (n=14). There was no correlation between the number of mutated genes and age, clinical characteristics, initial risk classification at diagnosis or intensity of therapy prior to sequencing.Conclusion:Our study provides an initial overview of the genetic alterations that characterize high-risk, chemo-resistant pediatric AML. Analysis of the data highlights the overall low genetic complexity of high-risk AML despite the aggressive clinical behavior and exposure to intense chemotherapy, including stem cell transplant. Of interest, similar to adult AML, we found that mutations leading to aberrant activation of the RAS pathway were also very frequent in our cohort of pediatric high-risk AML, while genes typically mutated early in the process of leukemogenesis in adult AML, such as NPM1, DNMT3A, FLT3, IDH1, IDH2 were not affected. Such findings suggest that distinct, age-specific mechanisms of leukemogenesis might exist. Furthermore, our data also highlights the important role of RNA sequencing in complementing current standard diagnostic tools, allowing the identification of driver fusion genes in samples for which no other driver event is detected. Larger studies, preferably including diagnostic samples and utilizing broader approaches, are needed to better understand the mechanisms responsible for the initiation and progression of childhood AML. DisclosuresNo relevant conflicts of interest to declare.

Clonal Evolution Revealed By Exome Sequencing in a Case of Primary Myelofibrosis Associated with Subsequent Development of Aggressive Systemic Mastocytosis/Mast Cell Leukemia

A 77 year-old man initially presented in July 2013 with anemia, splenomegaly, and constitutional symptoms. A bone marrow biopsy revealed a hypercellular marrow with megakaryocytic hyperplasia and atypia and mild reticulin fibrosis, consistent with a diagnosis of primary myelofibrosis (PMF). Cytogenetics revealed a normal karyotype. JAK2 V617F testing was negative. Initiation of treatment with the JAK inhibitor ruxolitinib led to marked symptomatic improvement. The patient was then enrolled in a Phase 2 study with the anti-lysyl oxidase-like-2 (LOXL2) monoclonal antibody simtuzumab, administered via IV infusion every two weeks (while continuing ruxolitinib). He tolerated the simtuzumab infusions well initially, but with the 11th and 12th infusions experienced rigors, hypotension, and hypoxia. This occurred ~8 months after his initial PMF diagnosis. A repeat bone marrow biopsy revealed large aggregates of mast cells comprising 30-40% of the marrow cellularity (with 16% mast cells enumerated on the aspirate). A subset of the mast cells exhibited spindled morphology, and CD25 co-expression was demonstrated by flow cytometry in a subset of CD117-positive cells. Testing for the KITD816V mutation was positive. Tryptase levels were significantly elevated (375 ng/mL). These findings were consistent with a diagnosis of aggressive systemic mastocytosis with an associated hematologic non-mast cell lineage disorder (ASM-AHNMD).Compassionate-use approval for the KIT inhibitor midostaurin was obtained, and treatment with midostaurin (in addition to continuation of ruxolitinib) was initiated. The patient initially reported symptomatic improvement with midostaurin treatment, but after several months his symptoms began to worsen, with a corresponding increase in tryptase (875 ng/mL). A repeat bone marrow biopsy revealed overt evolution to mast cell leukemia (MCL) with > 90% mast cell involvement. Based on the presence of an IDH2mutation identified on a clinical next-generation sequencing assay, the patient was evaluated for a clinical trial with the mutant IDH2 inhibitor AG-221. Unfortunately, the patient decompensated and expired before he could enroll in the study.To identify contributing driver mutations and to delineate clonal hierarchy associated with disease initiation and progression in this unique case of PMF with concomitant ASM, exome sequencing was performed on serial samples obtained at the following disease stages:PMF diagnosis (pre-ruxolitinib) (Day 0)PMF on ruxolitinib (before ASM diagnosis) (Day 181)ASM diagnosis (post-anti-LOXL2 antibody, pre-midostaurin) (Day 394)Progression to MCL (on midostaurin) (Day 519)Matched skin (normal) sampleLikely driver mutations in IDH2 and SRSF2 were identified at ~40-50% variant allele frequency (VAF) in all samples and were therefore likely present in the founding clone. The KIT D816V mutation was found at 23% VAF at Day 0, then ~40% VAF in all other samples, suggesting it was present in a daughter subclone of the IDH2/SRSF2-containing clone that became dominant over time with disease progression. These findings also suggest that targeting KIT with midostaurin would be unlikely to eradicate the founding clone. Rather, selective targeting of IDH2 and/or SRSF2 could potentially ameliorate both diseases (PMF and ASM/MCL).To provide pre-clinical evidence of the potential utility of targeting IDH2, peripheral blood mononuclear cells obtained at the time of ASM diagnosis were plated in liquid culture in the presence or absence of the mutant IDH2 inhibitor AGI-6780. After 14 days in culture, the differentiation status of the cultured cells was examined by mass cytometry (CyTOF). Treatment with AGI-6780 resulted in a marked enhancement of myeloid differentiation (denoted by CD15 and CD66b expression) along with a corresponding decrease in CD34+ progenitor cells. These effects were not seen in cells cultured in the absence of AGI-6780. These results are consistent with prior studies in acute myeloid leukemia indicating that the beneficial effects of mutant IDH2 inhibition are likely related to inducing differentiation of primitive cells. In summary, this study highlights the capacity of serial genomic analysis to define the clonal architecture that drives disease initiation and evolution, and to distinguish founding vs subclonal mutations to identify the most promising targets for therapeutic intervention. DisclosuresOh:Janssen: Research Funding; CTI: Research Funding; Gilead: Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte Corporation: Membership on an entity's Board of Directors or advisory committees, Research Funding.

Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN.

Background: Targeted next generation sequencing (NGS) panels are increasingly being used in clinical genomics to increase capacity, throughput and affordability of gene testing. Identifying whole exon deletions or duplications (termed exon copy number variants, 'exon CNVs') in exon-targeted NGS panels has proved challenging, particularly for single exon CNVs. Methods: We developed a tool for the Detection of Exon Copy Number variants (DECoN), which is optimised for analysis of exon-targeted NGS panels in the clinical setting. We evaluated DECoN performance using 96 samples with independently validated exon CNV data. We performed simulations to evaluate DECoN detection performance of single exon CNVs and to evaluate performance using different coverage levels and sample numbers. Finally, we implemented DECoN in a clinical laboratory that tests BRCA1 and BRCA2 with the TruSight Cancer Panel (TSCP). We used DECoN to analyse 1,919 samples, validating exon CNV detections by multiplex ligation-dependent probe amplification (MLPA). Results: In the evaluation set, DECoN achieved 100% sensitivity and 99% specificity for BRCA exon CNVs, including identification of 8 single exon CNVs. DECoN also identified 14/15 exon CNVs in 8 other genes. Simulations of all possible BRCA single exon CNVs gave a mean sensitivity of 98% for deletions and 95% for duplications. DECoN performance remained excellent with different levels of coverage and sample numbers; sensitivity and specificity was >98% with the typical NGS run parameters. In the clinical pipeline, DECoN automatically analyses pools of 48 samples at a time, taking 24 minutes per pool, on average. DECoN detected 24 BRCA exon CNVs, of which 23 were confirmed by MLPA, giving a false discovery rate of 4%. Specificity was 99.7%. Conclusions: DECoN is a fast, accurate, exon CNV detection tool readily implementable in research and clinical NGS pipelines. It has high sensitivity and specificity and acceptable false discovery rate. DECoN is freely available at www.icr.ac.uk/decon.

Clinical Validation of a Next-Generation Sequencing Genomic Oncology Panel via Cross-Platform Benchmarking against Established Amplicon Sequencing Assays

Next-generation sequencing (NGS) genomic oncology profiling assays have emerged as key drivers of personalized cancer care and translational research. However, validation of these assays to meet strict clinical standards has been historically problematic because of both significant assay complexity and a scarcity of optimal validation samples. Herein, we present the clinical validation of 76 genes from a novel 1212-gene large-scale hybrid capture cancer sequencing assay (University of Chicago Medicine OncoPlus) using full-data comparisons against multiple clinical NGS amplicon-based assays to yield dramatic increases in per-sample data comparison efficiency compared with previously published validations. Using a sample set of 104 normal, solid tumor, and hematopoietic malignancy specimens, head-to-head NGS data analyses allowed for 6.8 million individual clinical base call comparisons, including 2729 previously confirmed variants, with 100% sensitivity and specificity. University of Chicago Medicine OncoPlus showed excellent performance for detection of single-nucleotide variants, insertions/deletions up to 52 bp, and FLT3 internal tandem duplications of up to 102 bp or larger. Highly concordant copy number variant and ALK/RET/ROS1 gene fusion detection were also observed. In addition to underlining the efficiency of NGS validation via full-data benchmarking against existing clinical NGS assays, this study also highlights the degree of performance similarity between hybrid capture and amplicon assays that is attainable with the application of strict quality control parameters and optimized computational analytics.

Next-generation sequencing in patients with advanced cancer: are we ready for widespread clinical use? A single institute's experience.

The next-generation sequencing (NGS) assay targeting cancer-relevant genes has been adopted widely for use in patients with advanced cancer. The primary aim of this study was to assess the clinical utility of commercially available NGS. We retrospectively collected demographic and clinicopathologic data, recommended therapy, and clinical outcomes of 30 patients with a variety of advanced solid tumors referred to Foundation Medicine NGS. The initial pathologic examination was performed at the pathology department of the referring hospital. The comprehensive clinical NSG assay was performed on paraffin-embedded tumor samples using the Clinical Laboratory Improvement Amendments-certified FoundationOne platform. The median number of genomic alterations was 3 (0-19). The median number of therapies with potential benefit was 2 (0-8). In 12 cases, a comprehensive clinical NGS assay did not indicate any therapy with potential benefit according to the genomic profile. Ten of the 30 patients received treatments recommended by genomic profile results. In six of the 10 cases, disease progressed within 2 months and four patients died within 3 months of treatment initiation. Three of the 30 patients benefited from a comprehensive clinical NGS assay and the subsequent recommended therapy. The median PFS was 12 weeks (95% confidence interval 10-57) in patients treated with molecularly targeted agents chosen on the basis of tumor genomic profiling versus 48 weeks (95% confidence interval 8-38) in the control group treated with physician choice therapy (P=0.12). Our study suggests that NGS can detect additional treatment targets in individual patients, but prospective medical research and appropriate clinical guidelines for proper clinical use are vital.

Multiplexed Reference Materials as Controls for Diagnostic Next-Generation Sequencing: A Pilot Investigating Applications for Hypertrophic Cardiomyopathy

Diagnostic next-generation sequencing (NGS)-based gene panels are increasingly used for prevalent disorders with genetic and clinical heterogeneity. Clinical development, validation, and quality management of these panels ideally includes reference samples containing prevalent pathogenic variants; however, clinical domain expertise to select appropriate variants may not be present, samples are often not publicly available, and their inclusion is associated with added cost. Expert-designed, multiplexed controls can remedy some of these challenges. One approach relies on spiking biosynthetic fragments carrying desired variants into human genomic DNA. We piloted the utility of this approach for hypertrophic cardiomyopathy. Data from >3000 previously sequenced probands were used to select 10 common pathogenic and/or technically challenging variants in the top hypertrophic cardiomyopathy genes. Multiplexed controls were constructed across a range of ideal and realistic allelic fractions for heterozygous germline variants. NGS was performed in quadruplicate, and results were compared with diagnostic NGS data for the source patient samples. Overall, results were indistinguishable from patient-derived data with variants being detected at or reasonably close to the targeted allelic fraction ratios. The exception was a common 25-bp deletion in MYBPC3, underscoring the importance of including such variants in test development. These controls may be an attractive addition to the repertoire of materials for development, validation, and quality monitoring of clinical NGS assays.

Variations in the Genome: The Mutation Detection 2015 Meeting on Detection, Genome Sequencing, and Interpretation.

The content of the 13th Mutation Detection meeting (Leiden, April 2015) is summarized in this report. Topics discussed at the meeting included current challenges of clinical NGS, advances in bioinformatics, data quality control, single cell analysis and RNA sequencing, among others. Social, ethical and regulatory challenges of genomic data handling and data sharing were the focus of an expert panel debate. The 14th International Symposium on Variants in the Genome will take place in Santiago de Compostela, June 5-8, 2017. http://isv.variome.org.

Molecular Testing in Breast Cancer: A Guide to Current Practices.

-Molecular diagnostics play a role in the management of many cancers, including breast cancer. -To provide an update on molecular testing in current clinical practice, targeted at practicing pathologists who are not breast cancer specialists. -This study is a narrative literature review. -In addition to routine hormone (estrogen and progesterone) receptor testing, new and recurrent tumors are tested for HER2 amplification by in situ hybridization or overexpression by immunohistochemistry. Intrinsic subtyping of tumors represents a fundamental advance in our understanding of breast cancer biology, but currently it has an indirect role in patient management. Clinical next-generation sequencing (tumor profiling) is increasingly used to identify potentially actionable mutations in tumor tissue. Multianalyte assays with algorithmic analysis, including MammaPrint, Oncotype DX, and Prosigna, play a larger role in breast cancer than in many other malignancies. Given that a proportion of breast cancers are familial, testing of nontumor tissue for cancer predisposition mutations also plays a role in breast cancer care.

Abstract 3650: Multi-pronged approach to establish control standards for somatic mutations in next generation sequencing (NGS) oncology test

Abstract In recent years, somatic mutation testing via Next Generation Sequencing (NGS) has emerged as a powerful tool to detect targetable mutations in diseases such as cancer. These include mutations such as BRAF V600E, which can lead to targeted drug therapy; therefore, improving the standard of care in cancer diagnostics. To generate clinically meaningful results, we need to define standards that can be applied to laboratories performing somatic testing on tumor samples. With ongoing debate about the use of positive or negative controls in somatic testing assays, we designed an experiment to test the concordance of clinically actionable mutations commonly seen in tumor testing. We use cell line controls and commercially engineered DNA to validate concordance of mutations at specific allelic ratios. Our results depict an experiment design to determine if a genomic test can detect actionable mutations with high levels of accuracy and precision. In this study, we designed a multi-pronged approach to evaluate the need for control standards by the ICG100 clinical NGS panel. To establish a baseline negative control, we performed concordance testing on the NA12878 cell line. We compared SNPs, insertions and deletions found using our methodology to the variants reports by NIST. We found our results to be concordant with NIST at a sensitivity of 92% and a specificity of 93%. To establish a baseline for positive controls, we utilized commercially engineered DNA which contains variants spiked-in at known allelic frequencies. This allowed us to determine if the ICG100 panel was able to retrieve specific somatic mutations. We were able to detect high confidence somatic mutations, such as BRAFV600E, as well as BRAF V600G which was spiked in at a lower expect allelic frequency of 4%. Moreover, we are able to detect with high confidence mutations such as ALK F1174L, EGFR G719S, PIK3CA H1047R, and MET Y1247D, and we were able to reproduce the results across multiple cell lines. Overall, our results show the need to utilize controls as standard protocol which can help assess the proficiency of a clinical assay. With rapid advances is NGS testing methodologies, there is a need for establishing standardized controls that asses the performance of a somatic tumor testing. Citation Format: Christopher Johnson, Sharanya Raghunath, Jackie Wayne, Aimee Shamo, Patrick Bradley, Moises Hernandez, David Loughmiller, Jason Gillman, Derrick Haslem, Gary Stone, Lincoln Nadauld, Pravin J. Mishra. Multi-pronged approach to establish control standards for somatic mutations in next generation sequencing (NGS) oncology test. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3650.

Abstract 1389: A unified and streamlined targeted sequencing system for the quantification of DNA mutations and RNA expression markers in lung cancer

Abstract Introduction: The promise of precision medicine relies on the identification of DNA and RNA markers that can individualize patient management. Methods such as next-generation sequencing (NGS) can deduce DNA or RNA sequences, but both types of nucleic acid have not been efficiently and effectively combined into a single NGS workflow. We describe a comprehensive methodology for targeted clinical NGS that reports DNA and RNA variants, provides a streamlined workflow, and accommodates low-input total nucleic acid (TNA) from challenging clinical specimens. Methods: Sample QC was performed using a novel qPCR assay that quantifies discrete populations of amplifiable DNA and RNA from TNA material. PCR-based target enrichment was performed using QuantideX® NGS reagents (Asuragen) and sequenced on the MiSeq® System (Illumina). Bioinformatic analyses were conducted using QuantideX® Reporter (Asuragen), a software suite that directly incorporates pre-analytical QC information into the variant calling. Results: Targeted DNA- and RNA-seq panels were developed that query 54 lung cancer DNA targets and 135 RNA targets, including >100 gene fusions and mRNA expression markers associated with clinical actionability. Gene-specific primers were formulated as multiplex PCR or RT-PCR reactions to independently interrogate DNA or RNA variants, respectively, from TNA or combined into a 189-plex RT-PCR to report multi-categorical nucleic acid variants. Integration of the bioinformatics pipeline and variant caller with wet-lab QC results enhanced mutation call sensitivity at <10% abundance, improved PPV for low-input specimens, and achieved absolute quantification of RNA. The NGS panels were assessed with cell-line and synthetic controls and a residual clinical cohort of 97 NSCLC FFPE specimens. Mutations were accurately detected from as few as 5-10 DNA templates and down to <5% abundance, and RNA translocations could be observed in sub-nanogram quantities of fusion-positive FFPE TNA. The unified DNA/RNA panel identified clinically-relevant DNA and RNA variants and maintained similar coverage uniformity to the separate DNA and RNA panels. Analysis of 61 lung adenocarcinoma and 36 squamous cell carcinoma specimens revealed mutation distributions in driver genes and RNA fusions consistent with the known spectrum of variants from each tumor type as previously reported by TCGA and other groups. Conclusions: QuantideX targeted NGS chemistries can unify the analysis of DNA and RNA markers associated with lung cancer and report SNVs, indels, fusions, and aberrantly expressed mRNA transcripts from a single NGS run. This novel technology offers reliable, accurate and comprehensive molecular characterizations of challenging tumor specimens by integrating wet-bench and dry-bench methods and improving the efficacy of routine laboratory testing. Citation Format: Gary J. Latham, Julie Krosting, Michael Dodge, Robert Zeigler, Liangjing Chen, Jason Plyler, Shobha Gokul, Junya Fujimoto, Vassiliki Papadimitrakopoulou, Ignacio Wistuba, Richard Blidner, Brian Haynes. A unified and streamlined targeted sequencing system for the quantification of DNA mutations and RNA expression markers in lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1389.

A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing.

-Most current proficiency testing challenges for next-generation sequencing assays are methods-based proficiency testing surveys that use DNA from characterized reference samples to test both the wet-bench and bioinformatics/dry-bench aspects of the tests. Methods-based proficiency testing surveys are limited by the number and types of mutations that either are naturally present or can be introduced into a single DNA sample. -To address these limitations by exploring a model of in silico proficiency testing in which sequence data from a single well-characterized specimen are manipulated electronically. -DNA from the College of American Pathologists reference genome was enriched using the Illumina TruSeq and Life Technologies AmpliSeq panels and sequenced on the MiSeq and Ion Torrent platforms, respectively. The resulting data were mutagenized in silico and 26 variants, including single-nucleotide variants, deletions, and dinucleotide substitutions, were added at variant allele fractions (VAFs) from 10% to 50%. Participating clinical laboratories downloaded these files and analyzed them using their clinical bioinformatics pipelines. -Laboratories using the AmpliSeq/Ion Torrent and/or the TruSeq/MiSeq participated in the 2 surveys. On average, laboratories identified 24.6 of 26 variants (95%) overall and 21.4 of 22 variants (97%) with VAFs greater than 15%. No false-positive calls were reported. The most frequently missed variants were single-nucleotide variants with VAFs less than 15%. Across both challenges, reported VAF concordance was excellent, with less than 1% median absolute difference between the simulated VAF and mean reported VAF. -The results indicate that in silico proficiency testing is a feasible approach for methods-based proficiency testing, and demonstrate that the sensitivity and specificity of current next-generation sequencing bioinformatics across clinical laboratories are high.

Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis

Advances in next-generation sequencing (NGS) have facilitated parallel analysis of multiple genes enabling the implementation of cost-effective, rapid, and high-throughput methods for the molecular diagnosis of multiple genetic conditions, including the identification of BRCA1 and BRCA2 mutations in high-risk patients for hereditary breast and ovarian cancer. We clinically validated a NGS pipeline designed to replace Sanger sequencing and multiplex ligation-dependent probe amplification analysis and to facilitate detection of sequence and copy number alterations in a single test focusing on a BRCA1/BRCA2 gene analysis panel. Our custom capture library covers 46 exons, including BRCA1 exons 2, 3, and 5 to 24 and BRCA2 exons 2 to 27, with 20 nucleotides of intronic regions both 5' and 3' of each exon. We analyzed 402 retrospective patients, with previous Sanger sequencing and multiplex ligation-dependent probe amplification results, and 240 clinical prospective patients. One-hundred eighty-three unique variants, including sequence and copy number variants, were detected in the retrospective (n=95) and prospective (n=88) cohorts. This standardized NGS pipeline demonstrated 100% sensitivity and 100% specificity, uniformity, and high-depth nucleotide coverage per sample (approximately 7000 reads per nucleotide). Subsequently, the NGS pipeline was applied to the analysis of larger gene panels, which have shown similar uniformity, sample-to-sample reproducibility in coverage distribution, and sensitivity and specificity for detection of sequence and copy number variants.