Abstract: Systems and methods are provided for identifying a set of highly-correlated genes for use in classifying both a first type of biological sample and a second type of biological sample as to a phenotypic characterization, where the first type of biological sample and the second type of biological sample are a sample type selected from the group consisting of a fresh biological sample, a frozen biological sample, a biological sample that has been preserved with a non-crosslinking preservative, and a fixed biological sample that has been fixed with a crosslinking agent, and where the first type of biological sample and the second type of biological sample are sample types that are not the same sample type. The invention also relates to computer systems and methods for use in training a classifier using the highly-correlated genes, and using the trained classifier to classify biological samples that are of the same sample type as the first type of biological sample or the second type of biological sample.

Abstract: The present invention provides probes and methods of use thereof in the diagnosis and/or prognosis of certain types of cancers, particularly human papillomavirus (HPV)-associated cancers. The probes are designed for hybridization with genomic material in a manner indicative of one or more aberrations in the genetic material present in the test sample. The identified aberrations are biomarkers of HPV-associated cancer. The methods of the invention comprise contacting a sample to one or more probes, allowing any genetic material in the sample to hybridize to the genomic regions provided in the probes, analyzing the hybridizations, and analyzing the hybridizations to identify detected aberrations as biomarkers indicative of HPV-associated cancer progression.

Abstract: The present invention provides probes and methods of use thereof in the diagnosis and/or prognosis of certain types of cancers, particularly human papillomavirus (HPV)-associated cancers. The probes are designed for hybridization with genomic material in a manner indicative of one or more aberrations in the genetic material present in the test sample. The identified aberrations are biomarkers of HPV-associated cancer. The methods of the invention comprise contacting a sample to one or more probes, allowing any genetic material in the sample to hybridize to the genomic regions provided in the probes, analyzing the hybridizations, and analyzing the hybridizations to identify detected aberrations as biomarkers indicative of HPV-associated cancer progression.

Abstract: The present invention provides probes and methods of use thereof in the diagnosis and/or prognosis of certain types of cancers, particularly human papillomavirus (HPV)-associated cancers. The probes are designed for hybridization with genomic material in a manner indicative of one or more aberrations in the genetic material present in the test sample. The identified aberrations are biomarkers of HPV-associated cancer. The methods of the invention comprise contacting a sample to one or more probes, allowing any genetic material in the sample to hybridize to the genomic regions provided in the probes, analyzing the hybridizations, and analyzing the hybridizations to identify detected aberrations as biomarkers indicative of HPV-associated cancer progression.

Abstract: The present invention provides a microarray useful as a tool in the diagnosis and/or prognosis of certain types of cancers, particularly urogenital cancers. The microarray can include a plurality of genomic regions represented thereon, the genomic regions corresponding to regions wherein alterations, such as copy number aberrations, at such locations correlate to specific, identifiable cancers, particularly prostate, renal, or bladder tumors. The invention further provides methods of diagnosing certain types of cancers, particularly urogenital cancers, more particularly renal cortical cancers. The methods can comprise analyzing genetic material from a human individual to determine the presence or presence of certain aberrations and using a decision tree to classify the subtype of renal cortical neoplasm present in the sample.

Abstract: The present invention provides a novel, highly sensitive and specific probe panel which detects the type of renal cortical neoplasm present in a biopsy sample. As such, the invention permits diagnosis of the predominant subtypes of renal cortical neoplasms without the use of invasive methods. The present invention further provides a molecular cytogenetic method for detecting and analyzing the type of renal cortical neoplasm present in a renal biopsy sample.

Abstract: The present invention provides a novel, highly sensitive and specific probe panel which detects the type of renal cortical neoplasm present in a biopsy sample. As such, the invention permits diagnosis of the predominant subtypes of renal cortical neoplasms without the use of invasive methods. The present invention further provides a molecular cytogenetic method for detecting and analyzing the type of renal cortical neoplasm present in a renal biopsy sample.

Abstract: The present invention provides a novel, highly sensitive and specific probe panel which detects the type of renal cortical neoplasm present in a biopsy sample. As such, the invention permits diagnosis of the predominant subtypes of renal cortical neoplasms without the use of invasive methods. The present invention further provides a molecular cytogenetic method for detecting and analyzing the type of renal cortical neoplasm present in a renal biopsy sample.

Abstract: The present invention provides a microarray useful as a tool in the diagnosis and/or prognosis of certain types of cancers, particularly mature B-cell neoplasms. The microarray can include a plurality of genomic regions represented thereon, the genomic regions corresponding to regions wherein alterations, such as copy number alterations, at such locations correlate to specific, identifiable cancers, particularly mature B-cell neoplasms. The invention further provides methods of diagnosing and providing prognosis certain types of cancer, particularly mature B-cell neoplasms. The methods can comprise contacting a sample to a microarray according to the invention, allowing any genetic material in the sample to hybridize to the genomic regions on the microarray, analyzing the hybridizations, and correlating the hybridizations to certain cancer types, particularly mature B-cell neoplasms.

Abstract: The present invention provides a microarray useful as a tool in the diagnosis and/or prognosis of certain types of cancers, particularly mature B-cell neoplasms. The microarray can include a plurality of genomic regions represented thereon, the genomic regions corresponding to regions wherein alterations, such as copy number alterations, at such locations correlate to specific, identifiable cancers, particularly mature B-cell neoplasms. The invention further provides methods of diagnosing and providing prognosis certain types of cancer, particularly mature B-cell neoplasms. The methods can comprise contacting a sample to a microarray according to the invention, allowing any genetic material in the sample to hybridize to the genomic regions on the microarray, analyzing the hybridizations, and correlating the hybridizations to certain cancer types, particularly mature B-cell neoplasms.

Abstract: The present invention provides a microarray useful as a tool in the diagnosis and/or prognosis of certain types of cancers, particularly mature B-cell neoplasms. The microarray can include a plurality of genomic regions represented thereon, the genomic regions corresponding to regions wherein alterations, such as copy number alterations, at such locations correlate to specific, identifiable cancers, particularly mature B-cell neoplasms. The invention further provides methods of diagnosing and providing prognosis certain types of cancer, particularly mature B-cell neoplasms. The methods can comprise contacting a sample to a microarray according to the invention, allowing any genetic material in the sample to hybridize to the genomic regions on the microarray, analyzing the hybridizations, and correlating the hybridizations to certain cancer types, particularly mature B-cell neoplasms.

Abstract: The present invention provides probes and methods of use thereof in the diagnosis and/or prognosis of certain types of cancers, particularly human papillomavirus (HPV)-associated cancers. The probes are designed for hybridization with genomic material in a manner indicative of one or more aberrations in the genetic material present in the test sample. The identified aberrations are biomarkers of HPV-associated cancer. The methods of the invention comprise contacting a sample to one or more probes, allowing any genetic material in the sample to hybridize to the genomic regions provided in the probes, analyzing the hybridizations, and analyzing the hybridizations to identify detected aberrations as biomarkers indicative of HPV-associated cancer progression.

Abstract: The present invention provides a microarray useful as a tool in the diagnosis and/or prognosis of certain types of cancers, particularly mature B-cell neoplasms. The microarray can include a plurality of genomic regions represented thereon, the genomic regions corresponding to regions wherein alterations, such as copy number alterations, at such locations correlate to specific, identifiable cancers, particularly mature B-cell neoplasms. The invention further provides methods of diagnosing and providing prognosis certain types of cancer, particularly mature B-cell neoplasms. The methods can comprise contacting a sample to a microarray according to the invention, allowing any genetic material in the sample to hybridize to the genomic regions on the microarray, analyzing the hybridizations, and correlating the hybridizations to certain cancer types, particularly mature B-cell neoplasms.

Abstract: The present invention provides probes and methods of use thereof in the diagnosis and/or prognosis of certain types of cancers, particularly human papillomavirus (HPV)-associated cancers. The probes are designed for hybridization with genomic material in a manner indicative of one or more aberrations in the genetic material present in the test sample. The identified aberrations are biomarkers of HPV-associated cancer. The methods of the invention comprise contacting a sample to one or more probes, allowing any genetic material in the sample to hybridize to the genomic regions provided in the probes, analyzing the hybridizations, and analyzing the hybridizations to identify detected aberrations as biomarkers indicative of HPV-associated cancer progression.

Abstract: The present invention provides a microarray useful as a tool in the diagnosis and/or prognosis of certain types of cancers, particularly mature B-cell neoplasms. The microarray can include a plurality of genomic regions represented thereon, the genomic regions corresponding to regions wherein alterations, such as copy number alterations, at such locations correlate to specific, identifiable cancers, particularly mature B-cell neoplasms. The invention further provides methods of diagnosing and providing prognosis certain types of cancer, particularly mature B-cell neoplasms. The methods can comprise contacting a sample to a microarray according to the invention, allowing any genetic material in the sample to hybridize to the genomic regions on the microarray, analyzing the hybridizations, and correlating the hybridizations to certain cancer types, particularly mature B-cell neoplasms.

Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.