Methods and compositions for diagnosis of glioblastoma or a subtype thereof

Abstract

An isoform-level gene panel is disclosed that can accurately classify a glioblastoma subtype from a tumor sample. Such an isoform level gene panel comprises the 121 to 214 target isoforms identified in Table 1. Also disclosed are reagents for quantitively detecting the expression or activity of the target isoforms of Table 1 in a patient sample. For example, such ligands can be PCR primer and probes sets. This isoform-level gene panel and reagents for detection of the isoforms are useful in an isoform-level assay for diagnosis of the molecular subtype of a glioblastoma in a patient. The assay employs algorithms and a novel computer program that performs the functions of FIG. 8. In one aspect, the assay is a high-throughput format.

1 : A method for diagnosis of the molecular subtype of a glioblastoma multiforme in a subject comprising
 (a) contacting a sample obtained from a subject that has or is suspected of having a glioblastoma with an isoform panel having target isoforms selected from Table 1, or a combination thereof, or with a reagent, kit, panel or microarray of ligands capable of specifically complexing with, binding to, or quantitatively detecting or identifying the level or activity of target isoforms of Table 1 or a combination thereof;   (b) analyzing the individual levels or activities of the target isoforms relative to a reference standard in an RNA sequence based protocol; and   (c) applying the results of (b) to a computer program performing the functions as described in  FIG. 8  and generating an isoform signature that permits a diagnosis or prediction of the subject's GBM molecular subtype.   
     
     
         2 : The method according to  claim 1 , further including in step (a) the ligands directed to the controls identified in Table 1. 
     
     
         3 : The method according to  claim 1 , comprising ligands capable of specifically complexing with, binding to, or quantitatively detecting or identifying the level or activity of all 121 signature target isoforms and the controls identified in Table 1, all 214 isoform targets of Table 1; or a combination of isoform targets selected from the 121 signature targets of Table 1 and the 93 additional isoform targets of Table 1. 
     
     
         4 : The method according to  claim 1 , wherein the diagnosis involves monitoring relapse after initial diagnosis and treatment, predicting clinical outcome or determining the best clinical treatment. 
     
     
         5 : The method according to  claim 1 , wherein the biological sample is selected from group consisting of GBM tumor tissue, a biopsy sample, whole blood, plasma, serum, circulating tumor cells, cerebrospinal fluid, ascites fluid, tumor secretome fluid, peritoneal fluid, and RNA isolated therefrom. 
     
     
         6 : The method according to  claim 1 , wherein the analyzing comprises performing a qRT-PCR assay or an Illumine HiSeq assay.