Comprehensive screening of target molecules by next-generation sequencing in patients with malignant solid tumors: guiding entry into phase I clinical trials

The global pandemic outbreak, SARS-COV-2, which causes COVID-19, has coerced numerous pharmaceutical companies to sprint for the vaccine and therapeutic biologics development. Most of the therapeutic biologics are common human IgG antibodies, which were identified by next-generation sequencing with the B cells from the convalescent patients in less than one-month post-infection. While the global public health emergency calls for medications urgently, it saves lives to expedite the clinical trials of biologics as much as possible, hence the biologics development strategies are unprecedentedly challenged. Since the advent of therapeutic biologics, transfection, and selection strategy has been continuously improving for developing more robust cell lines with greater productivity and efficiency. Next-generation sequencing (NGS) has also been implemented into cell bank testing for acceleration. These recent advances enable us to rethink and reshape the chemistry, manufacturing and controls (CMC) strategy against the pandemic outbreaks, to start supplying cGMP materials for the life-saving clinical trials as soon as possible. We elucidated an accelerated CMC workflow for biologics against pandemics, including using cGMP-compliant pool materials for Phase I clinical trials, selecting the final clone with similar product quality as Phase I materials for late-stage development and commercial production and matching product quality among different manufacturing stages.

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Next-Generation Sequencing and Phase I Clinical Trials in Cancer

Annals of Oncology ◽

10.1093/annonc/mdt042.17 ◽

2013 ◽

Vol 24 ◽

pp. i10

Author(s):

F. Janku

Keyword(s):

Clinical Trials ◽

Next Generation Sequencing ◽

Phase I ◽

Next Generation ◽

Phase I Clinical Trials ◽

Generation Sequencing

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Validation of a Next-Generation Sequencing Assay Targeting RNA for the Multiplexed Detection of Fusion Transcripts and Oncogenic Isoforms

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2018-0441-oa ◽

2019 ◽

Vol 144 (1) ◽

pp. 90-98 ◽

Cited By ~ 5

Author(s):

Robyn T. Sussman ◽

Amanda R. Oran ◽

Carmela Paolillo ◽

David Lieberman ◽

Jennifer J. D. Morrissette ◽

...

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Gold Standard ◽

University Hospital ◽

Fusion Partner ◽

Next Generation ◽

Fixed Tissue ◽

Fusion Transcripts ◽

Genetic Abnormalities ◽

Generation Sequencing

Context.— Next-generation sequencing is a high-throughput method for detecting genetic abnormalities and providing prognostic and therapeutic information for patients with cancer. Oncogenic fusion transcripts are among the various classifications of genetic abnormalities present in tumors and are typically detected clinically with fluorescence in situ hybridization (FISH). However, FISH probes only exist for a limited number of targets, do not provide any information about fusion partners, cannot be multiplex, and have been shown to be limited in specificity for common targets such as ALK. Objective.— To validate an anchored multiplex polymerase chain reaction–based panel for the detection of fusion transcripts in a university hospital–based clinical molecular diagnostics laboratory. Design.— We used 109 unique clinical specimens to validate a custom panel targeting 104 exon boundaries from 17 genes involved in fusions in solid tumors. The panel can accept as little as 100 ng of total nucleic acid from PreservCyt-fixed tissue, and formalin-fixed, paraffin-embedded specimens with as little as 10% tumor nuclei. Results.— Using FISH as the gold standard, this assay has a sensitivity of 88.46% and a specificity of 95.83% for the detection of fusion transcripts involving ALK, RET, and ROS1 in lung adenocarcinomas. Using a validated next-generation sequencing assay as the orthogonal gold standard for the detection of EGFR variant III (EGFRvIII) in glioblastomas, the assay is 92.31% sensitive and 100% specific. Conclusions.— This multiplexed assay is tumor and fusion partner agnostic and will provide clinical utility in therapy selection for patients with solid tumors.

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37. Clinical validation of somatic alterations in solid tumors by next generation sequencing

Cancer Genetics ◽

10.1016/j.cancergen.2018.04.098 ◽

2018 ◽

Vol 226-227 ◽

pp. 50

Author(s):

Xia Li ◽

Bryan Austin ◽

Michael Donovan ◽

Janet Orton ◽

Guang Liu

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Clinical Validation ◽

Next Generation ◽

Somatic Alterations ◽

Generation Sequencing

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Next generation sequencing-based gene panel tests for the management of solid tumors

Cancer Science ◽

10.1111/cas.13837 ◽

2018 ◽

Vol 110 (1) ◽

pp. 6-15 ◽

Cited By ~ 20

Author(s):

Masayuki Nagahashi ◽

Yoshifumi Shimada ◽

Hiroshi Ichikawa ◽

Hitoshi Kameyama ◽

Kazuaki Takabe ◽

...

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Gene Panel ◽

Next Generation ◽

Generation Sequencing

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Development and Validation of a Scalable Next-Generation Sequencing System for Assessing Relevant Somatic Variants in Solid Tumors

Neoplasia ◽

10.1016/j.neo.2015.03.004 ◽

2015 ◽

Vol 17 (4) ◽

pp. 385-399 ◽

Cited By ~ 126

Author(s):

Daniel H. Hovelson ◽

Andrew S. McDaniel ◽

Andi K. Cani ◽

Bryan Johnson ◽

Kate Rhodes ◽

...

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Next Generation ◽

Development And Validation ◽

Generation Sequencing

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Clinical Next-Generation Sequencing Assays for Solid Tumors

Advances in Molecular Pathology ◽

10.1016/j.yamp.2018.07.008 ◽

2018 ◽

Vol 1 (1) ◽

pp. 167-182

Author(s):

Susan J. Hsiao ◽

Dara L. Aisner ◽

Mark D. Ewalt

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Next Generation ◽

Generation Sequencing

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PATH-03. CLINICAL UTILITY OF NEXT GENERATION SEQUENCING IN IDH-WILDTYPE GLIOBLASTOMA: THE DANA-FARBER CANCER INSTITUTE EXPERIENCE

Neuro-Oncology ◽

10.1093/neuonc/noaa215.685 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii164-ii164

Author(s):

Mary Jane Lim-Fat ◽

Gilbert Youssef ◽

Mehdi Touat ◽

Bryan Iorgulescu ◽

Eleanor Woodward ◽

...

Keyword(s):

Clinical Trial ◽

Clinical Trials ◽

Next Generation Sequencing ◽

Immune Checkpoint Blockade ◽

Next Generation ◽

Single Nucleotide Variants ◽

Dana Farber Cancer Institute ◽

Clinical Records ◽

Ngs Data ◽

Generation Sequencing

Abstract BACKGROUND Comprehensive next generation sequencing (NGS) is available through many academic institutions and commercial entities, and is incorporated in practice guidelines for glioblastoma (GBM). We retrospective evaluated the practice patterns and utility of incorporating NGS data into routine care of GBM patients at a clinical trials-focused academic center. METHODS We identified 1,011 consecutive adult patients with histologically confirmed GBM with OncoPanel testing, a targeted exome NGS platform of 447 cancer-associated genes at Dana Farber Cancer Institute (DFCI), from 2013-2019. We selected and retrospectively reviewed clinical records of all IDH-wildtype GBM patients treated at DFCI. RESULTS We identified 557 GBM IDH-wildtype patients, of which 227 were male (40.7%). OncoPanel testing revealed 833 single nucleotide variants and indels in 44 therapeutically relevant genes (Tier 1 or 2 mutations) including PIK3CA (n=51), BRAF (n=9), FGFR1 (n=8), MSH2 (n=4), MSH6 (n=2) and MLH1 (n=1). Copy number analysis revealed 509 alterations in 18 therapeutically relevant genes including EGFR amplification (n= 186), PDGFRA amplification (N=39) and CDKN2A/2B homozygous loss (N=223). Median overall survival was 17.5 months for the whole cohort. Seventy-four therapeutic clinical trials accrued 144 patients in the upfront setting (25.9%) and 203 patients (36.4%) at recurrence. Altogether, NGS data for 107 patients (19.2%) were utilized for clinical trial enrollment or targeted therapy indications. High mutational burden (>17mutations/Mb) was identified in 11/464 samples (2.4%); of whom 3/11 received immune checkpoint blockade. Four patients received compassionate use therapy targeting EGFRvIII (rindopepimut, n=2), CKD4/6 (abemaciclib, n=1) and BRAFV600E (dabrafenib/trametinib, n=1). CONCLUSION While NGS has greatly improved diagnosis and molecular classification, we highlight that NGS remains underutilized in selecting therapy in GBM, even in a setting where clinical trials and off-label therapies are relatively accessible. Continued efforts to develop better targeted therapies and efficient clinical trial design are required to maximize the potential benefits of genomically-stratified data.

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