Next-Generation Sequencing Concordance Analysis of Comprehensive Solid Tumor Profiling between a Centralized Specialty Laboratory and the Decentralized Personal Genome Diagnostics elio Tissue Complete Kitted Solution

被引:8
作者
Deak, Kristen L. [1 ]
Jackson, Jennifer B. [2 ]
Valkenburg, Kenneth C. [2 ]
Keefer, Laurel A. [2 ]
Gerding, Kelly M. Robinson [2 ]
Angiuoli, Samuel V. [2 ]
Datto, Michael B. [1 ]
McCall, Shannon J. [1 ]
机构
[1] Duke Univ, Med Ctr, Dept Pathol, Durham, NC 27710 USA
[2] Personal Genome Diagnost Inc, Baltimore, MD USA
关键词
BLOCKADE; CANCER;
D O I
10.1016/j.jmoldx.2021.07.004
中图分类号
R36 [病理学];
学科分类号
100104 ;
摘要
Genomic tumor profiling by next-generation sequencing (NGS) allows for large-scale tumor testing to inform targeted cancer therapies and immunotherapies, and to identify patients for clinical trials. These tests are often underutilized in patients with late-stage solid tumors and are typically performed in centralized specialty laboratories, thereby limiting access to these complex tests. Personal Genome Diagnostics Inc., elio tissue complete NGS solution is a comprehensive DNA-to-report kitted assay and bioinformatics solution. Comparison of 147 unique specimens from >20 tumor types was performed using the elio tissue complete solution and Foundation Medicine's FoundationOne test, which is of similar size and gene content. The analytical performance of all genomic variant types was evaluated. In general, the overall mutational profile is highly concordant between the two assays, with agreement in sequence variants reported between panels demonstrating>95% positive percentage agreement for single-nucleotide variants and insertions/deletions in clinically actionable genes. Both copy number alterations and gene translocations showed 80% to 83% positive percentage agreement, whereas tumor mutation burden and microsatellite status showed a high level of concordance across a range of mutation loads and tumor types. The Personal Genome Diagnostics Inc., elio tissue complete assay is comparable to the FoundationOne test and will allow more laboratories to offer a diagnostic NGS assay in house, which will ultimately reduce time to result and increase the number of patients receiving molecular genomic profiling and personalized treatment.
引用
收藏
页码:1324 / 1333
页数:10
相关论文
共 22 条
  • [1] Signatures of mutational processes in human cancer
    Alexandrov, Ludmil B.
    Nik-Zainal, Serena
    Wedge, David C.
    Aparicio, Samuel A. J. R.
    Behjati, Sam
    Biankin, Andrew V.
    Bignell, Graham R.
    Bolli, Niccolo
    Borg, Ake
    Borresen-Dale, Anne-Lise
    Boyault, Sandrine
    Burkhardt, Birgit
    Butler, Adam P.
    Caldas, Carlos
    Davies, Helen R.
    Desmedt, Christine
    Eils, Roland
    Eyfjord, Jorunn Erla
    Foekens, John A.
    Greaves, Mel
    Hosoda, Fumie
    Hutter, Barbara
    Ilicic, Tomislav
    Imbeaud, Sandrine
    Imielinsk, Marcin
    Jaeger, Natalie
    Jones, David T. W.
    Jones, David
    Knappskog, Stian
    Kool, Marcel
    Lakhani, Sunil R.
    Lopez-Otin, Carlos
    Martin, Sancha
    Munshi, Nikhil C.
    Nakamura, Hiromi
    Northcott, Paul A.
    Pajic, Marina
    Papaemmanuil, Elli
    Paradiso, Angelo
    Pearson, John V.
    Puente, Xose S.
    Raine, Keiran
    Ramakrishna, Manasa
    Richardson, Andrea L.
    Richter, Julia
    Rosenstiel, Philip
    Schlesner, Matthias
    Schumacher, Ton N.
    Span, Paul N.
    Teague, Jon W.
    [J]. NATURE, 2013, 500 (7463) : 415 - +
  • [2] Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic
    Chan, T. A.
    Yarchoan, M.
    Jaffee, E.
    Swanton, C.
    Quezada, S. A.
    Stenzinger, A.
    Peters, S.
    [J]. ANNALS OF ONCOLOGY, 2019, 30 (01) : 44 - 56
  • [3] Microsatellite Instability: A Predictive Biomarker for Cancer Immunotherapy
    Chang, Liisa
    Chang, Minna
    Chang, Hanna M.
    Chang, Fuju
    [J]. APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY, 2018, 26 (02) : E15 - E21
  • [4] Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy
    Cristescu, Razvan
    Mogg, Robin
    Ayers, Mark
    Albright, Andrew
    Murphy, Erin
    Yearley, Jennifer
    Sher, Xinwei
    Liu, Xiao Qiao
    Lu, Hongchao
    Nebozhyn, Michael
    Zhang, Chunsheng
    Lunceford, Jared
    Joe, Andrew
    Cheng, Jonathan
    Webber, Andrea L.
    Ibrahim, Nageatte
    Plimack, Elizabeth R.
    Ott, Patrick A.
    Seiwert, Tanguy
    Ribas, Antoni
    McClanahan, Terrill K.
    Tomassini, Joanne E.
    Loboda, Andrey
    Kaufman, David
    [J]. SCIENCE, 2018, 362 (6411) : 197 - +
  • [5] High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis
    Hartmaier, Ryan J.
    Albacker, Lee A.
    Chmielecki, Juliann
    Bailey, Mark
    He, Jie
    Goldberg, Michael E.
    Ramkissoon, Shakti
    Suh, James
    Elvin, Julia A.
    Chiacchia, Samuel
    Frampton, Garrett M.
    Ross, Jeffrey S.
    Miller, Vincent
    Stephens, Philip J.
    Lipson, Doron
    [J]. CANCER RESEARCH, 2017, 77 (09) : 2464 - 2475
  • [6] Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden
    Hellmann, M. D.
    Ciuleanu, T. -E.
    Pluzanski, A.
    Lee, J. S.
    Otterson, G. A.
    Audigier-Valette, C.
    Minenza, E.
    Linardou, H.
    Burgers, S.
    Salman, P.
    Borghaei, H.
    Ramalingam, S. S.
    Brahmer, J.
    Reck, M.
    O'Byrne, K. J.
    Geese, W. J.
    Green, G.
    Chang, H.
    Szustakowski, J.
    Bhagavatheeswaran, P.
    Healey, D.
    Fu, Y.
    Nathan, F.
    Paz-Ares, L.
    [J]. NEW ENGLAND JOURNAL OF MEDICINE, 2018, 378 (22) : 2093 - 2104
  • [7] Comparison of Laboratory-Developed Tests and FDA-Approved Assays for BRAF, EGFR, and KRAS Testing
    Kim, Annette S.
    Bartley, Angela N.
    Bridge, Julia A.
    Kamel-Reid, Suzanne
    Lazar, Alexander J.
    Lindeman, Neal I.
    Long, Thomas A.
    Merker, Jason D.
    Rai, Alex J.
    Rimm, David L.
    Rothberg, Paul G.
    Vasalos, Patricia
    Moncur, Joel T.
    [J]. JAMA ONCOLOGY, 2018, 4 (06) : 838 - 841
  • [8] Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology
    Lindeman, Neal I.
    Cagle, Philip T.
    Aisner, Dara L.
    Arcila, Maria E.
    Beasley, Mary Beth
    Bernicker, Eric H.
    Colasacco, Carol
    Dacic, Sanja
    Hirsch, Fred R.
    Kerr, Keith
    Kwiatkowski, David J.
    Ladanyi, Marc
    Nowak, Jan A.
    Sholl, Lynette
    Temple-Smolkin, Robyn
    Solomon, Benjamin
    Souter, Lesley H.
    Thunnissen, Erik
    Tsao, Ming S.
    Ventura, Christina B.
    Wynes, Murry W.
    Yatabe, Yasushi
    [J]. JOURNAL OF THORACIC ONCOLOGY, 2018, 13 (03) : 323 - 358
  • [9] Genome sequencing and cancer
    Mardis, Elaine R.
    [J]. CURRENT OPINION IN GENETICS & DEVELOPMENT, 2012, 22 (03) : 245 - 250
  • [10] Estimation of the Percentage of US Patients With Cancer Who Benefit From Genome-Driven Oncology
    Marquart, John
    Chen, Emerson Y.
    Prasad, Vinay
    [J]. JAMA ONCOLOGY, 2018, 4 (08) : 1093 - 1098