Detection of Gene Rearrangements in Targeted Clinical Next-Generation Sequencing

Abel, Haley J.; Al-Kateb, Hussam; Cottrell, Catherine E.; Bredemeyer, Andrew J.; Pritchard, Colin C.; Grossmann, Allie H.; Wallander, Michelle L.; Pfeifer, John D.; Lockwood, Christina M.; Duncavage, Eric J.

doi:10.1016/j.jmoldx.2014.03.006

Cited by 65 publications

(50 citation statements)

References 39 publications

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“…The test focuses on nonsynonymous somatic mutations because validated predictive and prognostic variants at present fall into this category. In the test described herein, rearrangements were not detected by NGS, although this capability has now entered the clinical space in our laboratory and others …”

Section: Discussionmentioning

confidence: 99%

Clinical next‐generation sequencing in patients with non–small cell lung cancer

Hagemann

Devarakonda²,

Lockwood³

et al. 2014

Cancer

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BACKGROUND: A clinical assay was implemented to perform next-generation sequencing (NGS) of genes commonly mutated in multiple cancer types. This report describes the feasibility and diagnostic yield of this assay in 381 consecutive patients with non-small cell lung cancer (NSCLC). METHODS: Clinical targeted sequencing of 23 genes was performed with DNA from formalin-fixed, paraffin-embedded (FFPE) tumor tissue. The assay used Agilent SureSelect hybrid capture followed by Illumina HiSeq 2000, MiSeq, or HiSeq 2500 sequencing in a College of American Pathologists-accredited, Clinical Laboratory Improvement Amendments-certified laboratory. Single-nucleotide variants and insertion/deletion events were reported. This assay was performed before methods were developed to detect rearrangements by NGS. RESULTS: Two hundred nine of all requisitioned samples (55%) were successfully sequenced. The most common reason for not performing the sequencing was an insufficient quantity of tissue available in the blocks (29%). Excisional, endoscopic, and core biopsy specimens were sufficient for testing in 95%, 66%, and 40% of the cases, respectively. The median turnaround time (TAT) in the pathology laboratory was 21 days, and there was a trend of an improved TAT with more rapid sequencing platforms. Sequencing yielded a mean coverage of 13183. Potentially actionable mutations (ie, predictive or prognostic) were identified in 46% of 209 samples and were most commonly found in KRAS (28%), epidermal growth factor receptor (14%), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (4%), phosphatase and tensin homolog (1%), and BRAF (1%). Five percent of the samples had multiple actionable mutations. A targeted therapy was instituted on the basis of NGS in 11% of the sequenced patients or in 6% of all patients. CONCLUSIONS: NGS-based diagnostics are feasible in NSCLC and provide clinically relevant information from readily available FFPE tissue. The sample type is associated with the probability of successful testing. Cancer 2015;121:631-9.

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Section: Discussionmentioning

confidence: 99%

Clinical next‐generation sequencing in patients with non–small cell lung cancer

Hagemann

Devarakonda²,

Lockwood³

et al. 2014

Cancer

Self Cite

202

160

View full text Add to dashboard Cite

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“…Sequence reads were mapped to the GRCh37 assembly of the reference human genome using the default parameters of the Burrows‐Wheeler Aligner (bio‐bwa.sourceforge.net). Then, structural variants (SV) were identified from discordant read pairs and/or split reads using Phrap (http://www.phrap.org/), BreakDancer (http://breakdancer.sourceforge.net/), and ClusterFAST . If the mapping read crossed the breakpoint with 20 or greater extra high‐quality unaligned bases or a contrary orientation, it was considered to be a potential output as a SV data set.…”

Section: Methodsmentioning

confidence: 99%

Relatively favorable prognosis for MLL‐rearranged childhood acute leukemia with reciprocal translocations

Liu

Ding

Liang

et al. 2018

Pediatric Blood & Cancer

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“…These strategies have shown to be accurate for targeted gene panel‐based next‐generation sequencing (Abel et al. ).…”

Section: Methodsmentioning

confidence: 99%

A novel molecular diagnostics platform for somatic and germline precision oncology

Cabanillas

Diñeiro

Castillo³

et al. 2017

Molec Gen & Gen Med

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BackgroundNext‐generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies.MethodsNext‐generation sequencing libraries enriched in the exons of 215 cancer genes (97 for therapy selection and 148 for predisposition, with 30 informative for both applications), as well as selected introns from 17 genes involved in drug‐related rearrangements, were prepared from 39 tumors (paraffin‐embedded tissues/cytologies), 36 germline samples (blood) and 10 cell lines using hybrid capture. Analysis of NGS results was performed with specifically developed bioinformatics pipelines.ResultsThe platform detects single‐nucleotide variants (SNVs) and insertions/deletions (indels) with sensitivity and specificity >99.5% (allelic frequency ≥0.1), as well as copy‐number variants (CNVs) and rearrangements. Somatic testing identified tailored approved targeted drugs in 35/39 tumors (89.74%), showing a diagnostic yield comparable to that of leading commercial platforms. A somatic EGFR p.E746_S752delinsA mutation in a mediastinal metastasis from a breast cancer prompted its anatomopathologic reassessment, its definite reclassification as a lung cancer and its treatment with gefitinib (partial response sustained for 15 months). Testing of 36 germline samples identified two pathogenic mutations (in CDKN2A and BRCA2). We propose a strategy for interpretation and reporting of results adaptable to the aim of the request, the availability of tumor and/or normal samples and the scope of the informed consent.ConclusionWith an adequate methodology, it is possible to translate to the clinical practice the latest advances in precision oncology, integrating under the same platform the identification of somatic and germline genomic alterations.

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Detection of Gene Rearrangements in Targeted Clinical Next-Generation Sequencing

Cited by 65 publications

References 39 publications

Clinical next‐generation sequencing in patients with non–small cell lung cancer

Clinical next‐generation sequencing in patients with non–small cell lung cancer

Relatively favorable prognosis for MLL‐rearranged childhood acute leukemia with reciprocal translocations

A novel molecular diagnostics platform for somatic and germline precision oncology

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