Abstract: Embodiments provide a user interface including an image panel for displaying a field of view corresponding to an image, or a portion of an image, of a biological specimen, and a biomarker panel for displaying thumbnail images for simultaneously viewing different aspects of a region within the field of view. Upon selection or update of the selected region of the field of view, the thumbnail images may be accordingly updated automatically to display the newly selected region. The image panel may include an interest region selection component for delineating a region within the field of view. The interest region selection component may be overlaid over a portion of the field of view displayed in the image panel, and may be used by a user to select or update the region within the field of view displayed in the biomarker panel. Images of interest may be saved to an electronic record.

Abstract: A method of analyzing a biological sample suspected of having classic Hodgkin lymphoma, comprising (1) detecting, in a single sample, for the expression of at least two biomarkers selected from CD30, CD15, CD20, CD45, CD3, Pax-5, CD79A, BOB1 and OCT-2; and (b) analyzing the sample based on the presence, absence and/or expression level of the at least two biomarkers. Also provided is a method wherein all the nine biomarkers are analyzed on a single sample. Further provided are method for diagnosing classical Hodgkin lymphoma, as well as system and kit that comprise the means for executing the novel methods.

Abstract: A method for providing a composite image of a single biological sample from a patient suspected of having lung cancer, comprising the steps of generating a first image of the biological sample, generating a second image of the biological sample, and generating a composite image that provides the relative location of both the targeted proteins. Also provided is a method of analyzing a biological sample, comprising providing a composite image of the biological sample according to the method for providing a composite image, and analyzing the expression of the protein of interest from the composite image. Further provided are method for classification of lung cancer, as well as system and kit that comprise the means for executing the novel methods.

Abstract: A method for providing a composite image of a single biological sample from a patient suspected of having classical Hodgkin lymphoma, comprising the steps of generating a first image of the biological sample including the presence, absence and/or expression level of a first biomarker, generating a second image of the biological sample including the presence, absence and/or expression level of a second biomarker, and generating a composite image that provides the relative location or expression of both biomarkers. Also provided is a method of analyzing a biological sample, comprising providing a composite image of the biological sample according to the method for providing a composite image, and analyzing the expression of the biomarkers of interest from the composite image. Further provided are method for diagnosing classical Hodgkin lymphoma, as well as system and kit that comprise the means for executing the novel methods.

Abstract: Methods of using TLE3 as a marker for predicting the likelihood that a patient's cancer will respond to chemotherapy. Methods of using TLE3 as a marker for selecting a chemotherapy for a cancer.

Abstract: A method for providing a composite image of a single biological sample, comprising the steps of generating a first image of the biological sample, generating a second image of the biological sample, and generating a composite image that provides the relative location of both the target protein and the target nucleic acid. Also provided is a method of analyzing a biological sample, comprising providing a composite image of the biological sample according to the method for providing a composite image, and analyzing the expression of the protein and the nucleic acid sequences of interest from the composite image. Further provided are system and kit that comprise the means for executing the novel methods.

Abstract: A method for generating an image of a region of interest in a biological sample comprising the steps of: generating a first image including the region of interest of the biological sample having undergone a first protocol but not a second protocol; and generating a second image including the region of interest of the biological sample after having undergone a second protocol; wherein the region of interest is smaller than said sample. Also provided is a method of analyzing a biological sample, comprising providing an image of the biological sample according to the method for generating an image of a region of interest in a biological sample, and analyzing the biological sample from the image. Further provided are system and kit that comprise the means for executing the novel methods.

Abstract: The present invention provides a method of detecting for the presence of a mutation in the ABL gene coding for the ABL T315I mutation, the method comprising: (a) providing a sample comprising an mRNA transcript encoding the ABL T315I mutation; (b) performing a reverse-transcription reaction to generate a cDNA sequence from the mRNA transcript; and (c) amplifying a cDNA sequence generated in step (b); wherein the reverse-transcription reaction in step (b) is selective for reverse transcription of the mRNA transcript encoding the ABL T315I mutation over a corresponding alternative ABL transcript that does not contain the mutation.

Abstract: A method of selectively producing and amplifying a cDNA sequence of a target allele of a gene, wherein the target allele is a mutant allele or is a specific allele of a polymorphic gene, the method comprising: (a) providing a sample comprising an mRNA transcript of the target allele; (b) performing a reverse-transcription reaction to generate a cDNA sequence from the mRNA transcript, and (c) amplifying the cDNA of the target allele; wherein the reverse-transcription reaction is selective for reverse transcription of the mRNA transcript of the target allele over an mRNA transcript of an alternative allele of the same gene.

Abstract: Methods of using TLE3 as a marker for predicting the likelihood that a patient's cancer will respond to chemotherapy. Methods of using TLE3 as a marker for selecting a chemotherapy for a cancer.

Abstract: Methods and reagents for classifying HER2+ breast tumors and for identifying new HER2+ breast tumor classes and subclasses. Methods for correlating tumor class or subclass with therapeutic regimen or outcome, for identifying appropriate (new or known) therapies for particular classes or subclasses, and for predicting outcomes based on class or subclass. New therapeutic agents and methods for the treatment of HER2+ breast cancer.

Abstract: Methods and reagents for classifying tumors and for identifying new tumor classes and subclasses. Methods for correlating tumor class or subclass with therapeutic regimen or outcome, for identifying appropriate (new or known) therapies for particular classes or subclasses, and for predicting outcomes based on class or subclass. New therapeutic agents and methods for the treatment of cancer.

Abstract: Methods and reagents for classifying tumors and for identifying new tumor classes and subclasses. Methods for correlating tumor class or subclass with therapeutic regimen or outcome, for identifying appropriate (new or known) therapies for particular classes or subclasses, and for predicting outcomes based on class or subclass. New therapeutic agents and methods for the treatment of cancer.

Abstract: Methods of using TLE3 as a marker for predicting the likelihood that a patient's cancer will respond to chemotherapy. Methods of using TLE3 as a marker for selecting a chemotherapy for a cancer.

Abstract: Methods and reagents for classifying tumors and for identifying new tumor classes and subclasses. Methods for correlating tumor class or subclass with therapeutic regimen or outcome, for identifying appropriate (new or known) therapies for particular classes or subclasses, and for predicting outcomes based on class or subclass. New therapeutic agents and methods for the treatment of cancer.