Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform

Scott Morris, Janakiraman Subramanian, Esma Gel, George Runger, Eric Thompson, David Mallery, Glen Weiss

    Research output: Contribution to journalArticle

    Abstract

    Background Next generation sequencing tests (NGS) are usually performed on relatively small core biopsy or fine needle aspiration (FNA) samples. Data is limited on what amount of tumor by volume or minimum number of FNA passes are needed to yield sufficient material for running NGS. We sought to identify the amount of tumor for running the PCDx NGS platform. Methods 2,723 consecutive tumor tissues of all cancer types were queried and reviewed for inclusion. Information on tumor volume, success of performing NGS, and results of NGS were compiled. Assessment of sequence analysis, mutation calling and sensitivity, quality control, drug associations, and data aggregation and analysis were performed. Results 6.4% of samples were rejected from all testing due to insufficient tumor quantity. The number of genes with insufficient sensitivity make definitive mutation calls increased as the percentage of tumor decreased, reaching statistical significance below 5% tumor content. The number of drug associations also decreased with a lower percentage of tumor, but this difference only became significant between 1–3%. The number of drug associations did decrease with smaller tissue size as expected. Neither specimen size or percentage of tumor affected the ability to pass mRNA quality control. A tumor area of 10 mm2 provides a good margin of error for specimens to yield adequate drug association results. Conclusions Specimen suitability remains a major obstacle to clinical NGS testing. We determined that PCR-based library creation methods allow the use of smaller specimens, and those with a lower percentage of tumor cells to be run on the PCDx NGS platform.

    Original languageEnglish (US)
    Article numbere0196556
    JournalPLoS One
    Volume13
    Issue number4
    DOIs
    StatePublished - Apr 1 2018

    Fingerprint

    Tumors
    neoplasms
    Neoplasms
    sampling
    testing
    drugs
    Fine Needle Biopsy
    Tumor Burden
    Quality Control
    Pharmaceutical Preparations
    Needles
    quality control
    Quality control
    Tissue
    Mutation
    mutation
    Biopsy
    Testing
    Libraries
    Sequence Analysis

    ASJC Scopus subject areas

    • Biochemistry, Genetics and Molecular Biology(all)
    • Agricultural and Biological Sciences(all)

    Cite this

    Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform. / Morris, Scott; Subramanian, Janakiraman; Gel, Esma; Runger, George; Thompson, Eric; Mallery, David; Weiss, Glen.

    In: PLoS One, Vol. 13, No. 4, e0196556, 01.04.2018.

    Research output: Contribution to journalArticle

    Morris, Scott ; Subramanian, Janakiraman ; Gel, Esma ; Runger, George ; Thompson, Eric ; Mallery, David ; Weiss, Glen. / Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform. In: PLoS One. 2018 ; Vol. 13, No. 4.
    @article{21400350f7a74893bbc018e05b9eebe4,
    title = "Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform",
    abstract = "Background Next generation sequencing tests (NGS) are usually performed on relatively small core biopsy or fine needle aspiration (FNA) samples. Data is limited on what amount of tumor by volume or minimum number of FNA passes are needed to yield sufficient material for running NGS. We sought to identify the amount of tumor for running the PCDx NGS platform. Methods 2,723 consecutive tumor tissues of all cancer types were queried and reviewed for inclusion. Information on tumor volume, success of performing NGS, and results of NGS were compiled. Assessment of sequence analysis, mutation calling and sensitivity, quality control, drug associations, and data aggregation and analysis were performed. Results 6.4{\%} of samples were rejected from all testing due to insufficient tumor quantity. The number of genes with insufficient sensitivity make definitive mutation calls increased as the percentage of tumor decreased, reaching statistical significance below 5{\%} tumor content. The number of drug associations also decreased with a lower percentage of tumor, but this difference only became significant between 1–3{\%}. The number of drug associations did decrease with smaller tissue size as expected. Neither specimen size or percentage of tumor affected the ability to pass mRNA quality control. A tumor area of 10 mm2 provides a good margin of error for specimens to yield adequate drug association results. Conclusions Specimen suitability remains a major obstacle to clinical NGS testing. We determined that PCR-based library creation methods allow the use of smaller specimens, and those with a lower percentage of tumor cells to be run on the PCDx NGS platform.",
    author = "Scott Morris and Janakiraman Subramanian and Esma Gel and George Runger and Eric Thompson and David Mallery and Glen Weiss",
    year = "2018",
    month = "4",
    day = "1",
    doi = "10.1371/journal.pone.0196556",
    language = "English (US)",
    volume = "13",
    journal = "PLoS One",
    issn = "1932-6203",
    publisher = "Public Library of Science",
    number = "4",

    }

    TY - JOUR

    T1 - Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform

    AU - Morris, Scott

    AU - Subramanian, Janakiraman

    AU - Gel, Esma

    AU - Runger, George

    AU - Thompson, Eric

    AU - Mallery, David

    AU - Weiss, Glen

    PY - 2018/4/1

    Y1 - 2018/4/1

    N2 - Background Next generation sequencing tests (NGS) are usually performed on relatively small core biopsy or fine needle aspiration (FNA) samples. Data is limited on what amount of tumor by volume or minimum number of FNA passes are needed to yield sufficient material for running NGS. We sought to identify the amount of tumor for running the PCDx NGS platform. Methods 2,723 consecutive tumor tissues of all cancer types were queried and reviewed for inclusion. Information on tumor volume, success of performing NGS, and results of NGS were compiled. Assessment of sequence analysis, mutation calling and sensitivity, quality control, drug associations, and data aggregation and analysis were performed. Results 6.4% of samples were rejected from all testing due to insufficient tumor quantity. The number of genes with insufficient sensitivity make definitive mutation calls increased as the percentage of tumor decreased, reaching statistical significance below 5% tumor content. The number of drug associations also decreased with a lower percentage of tumor, but this difference only became significant between 1–3%. The number of drug associations did decrease with smaller tissue size as expected. Neither specimen size or percentage of tumor affected the ability to pass mRNA quality control. A tumor area of 10 mm2 provides a good margin of error for specimens to yield adequate drug association results. Conclusions Specimen suitability remains a major obstacle to clinical NGS testing. We determined that PCR-based library creation methods allow the use of smaller specimens, and those with a lower percentage of tumor cells to be run on the PCDx NGS platform.

    AB - Background Next generation sequencing tests (NGS) are usually performed on relatively small core biopsy or fine needle aspiration (FNA) samples. Data is limited on what amount of tumor by volume or minimum number of FNA passes are needed to yield sufficient material for running NGS. We sought to identify the amount of tumor for running the PCDx NGS platform. Methods 2,723 consecutive tumor tissues of all cancer types were queried and reviewed for inclusion. Information on tumor volume, success of performing NGS, and results of NGS were compiled. Assessment of sequence analysis, mutation calling and sensitivity, quality control, drug associations, and data aggregation and analysis were performed. Results 6.4% of samples were rejected from all testing due to insufficient tumor quantity. The number of genes with insufficient sensitivity make definitive mutation calls increased as the percentage of tumor decreased, reaching statistical significance below 5% tumor content. The number of drug associations also decreased with a lower percentage of tumor, but this difference only became significant between 1–3%. The number of drug associations did decrease with smaller tissue size as expected. Neither specimen size or percentage of tumor affected the ability to pass mRNA quality control. A tumor area of 10 mm2 provides a good margin of error for specimens to yield adequate drug association results. Conclusions Specimen suitability remains a major obstacle to clinical NGS testing. We determined that PCR-based library creation methods allow the use of smaller specimens, and those with a lower percentage of tumor cells to be run on the PCDx NGS platform.

    UR - http://www.scopus.com/inward/record.url?scp=85046095305&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=85046095305&partnerID=8YFLogxK

    U2 - 10.1371/journal.pone.0196556

    DO - 10.1371/journal.pone.0196556

    M3 - Article

    VL - 13

    JO - PLoS One

    JF - PLoS One

    SN - 1932-6203

    IS - 4

    M1 - e0196556

    ER -