Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation

Dror Hibsh, Kenneth Buetow, Gur Yaari, Sol Efroni

    Research output: Contribution to journalArticle

    Abstract

    The cancer genome is abnormal genome, and the ability tomonitor its sequence had undergone a technological revolution. Yet prognosis and diagnosis remain an expert-based decision, with only limited abilities to provide machine-based decisions. We introduce a heterogeneity-based method for stratifying and visualizing whole-genome sequencing (WGS) reads. This method uses the heterogeneity within WGS reads to markedly reduce the dimensionality of next-generation sequencing data; it is available through the tool HiBS (Heterogeneity-Based Subclassification) that allows cancer sample classification. We validated HiBS using >200 WGS samples from nine different cancer types from The Cancer Genome Atlas (TCGA).With HiBS, we show progress with two WGS related issues: (i) differentiation between normal (NB) and tumor (TP) samples based solely on the information structure of their WGS data, and (ii) identification of specific regions of chromosomal amplification/deletion and their association with tumor stage. By comparing results to those obtained through available WGS analyses tools, we demonstrate some of the novelties obtained by the approach implemented in HiBS and also show nearly perfect normal/tumor classification, used to identify known and unknown chromosomal aberrations. Finally, the HiBS index has been associated with breast cancer tumor stage.

    Original languageEnglish (US)
    Article numbere81
    JournalNucleic Acids Research
    Volume44
    Issue number9
    DOIs
    StatePublished - May 19 2016

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    Genome
    Neoplasms
    Breast Neoplasms
    Atlases
    Chromosome Aberrations

    ASJC Scopus subject areas

    • Genetics

    Cite this

    Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation. / Hibsh, Dror; Buetow, Kenneth; Yaari, Gur; Efroni, Sol.

    In: Nucleic Acids Research, Vol. 44, No. 9, e81, 19.05.2016.

    Research output: Contribution to journalArticle

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