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Prostate cancer gene profiles and methods of using the same

A technology of prostate cancer and gene expression profiling, applied in biochemical equipment and methods, microbial measurement/testing, instruments, etc.

Inactive Publication Date: 2017-05-31
THE HENRY M JACKSON FOUND FOR THE ADVANCEMENT OF MILITARY MEDICINE INC +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, apart from TMPRSS2 / ERG, little or no genetic basis is known about the CaP differences between AA and CA males [24]

Method used

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  • Prostate cancer gene profiles and methods of using the same
  • Prostate cancer gene profiles and methods of using the same
  • Prostate cancer gene profiles and methods of using the same

Examples

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Embodiment 1

[0151] Example 1. Comparative Genomic DNA Analysis

[0152] In a cohort of 7 AA and 7 CA CaP patients (28 samples), a comparative genome-wide analysis was performed using primary prostate tumors and corresponding normal tissues (blood). Cohorts were selected according to the following criteria: primary treatment radical prostatectomy, no neoadjuvant therapy, Gleason grades 3+3 and 3+4 (representing the majority of CaPs screened by PSA at diagnosis / primary treatment), having 80% Frozen tumor tissue with tumor cell content or higher, dissected tumor tissue with more than 2 μg of high molecular weight genomic DNA, availability of corresponding blood genomic DNA, and patient clinicopathological data.

[0153] 28 samples were sent to Illumina Inc. (UK) for sequencing. Sequences from tumor samples were mapped to a reference genome using Illumina's ELAND alignment algorithm. Sequencing reported good coverage (average 37). Apply the Strelka algorithm to simultaneously call variants...

Embodiment 2

[0156] Example 2. Comparative RNA Analysis

[0157] To complement the genomic DNA analysis, RNA-Seq analysis was performed in the same cohort of prostate tumor samples. RNA-Seq technology has the ability to interrogate multiple aspects of the transcriptome including gene fusions, gene and transcript expression. Peripheral normal tissues were collected from 4 of 14 patients. 2 of the normal tissue samples were from AA males and 2 from CA males.

[0158] RNA samples were shipped to Expression Analysis (Durham, NC) for transcriptome sequencing. The details of sequencing statistics are as follows: sequencing type: paired-end, average read length for each sample: 50 nt, average read quality: 37, number of reads: approximately 31 million per sample.

[0159] Raw reads for expression analysis of each sample were obtained in fastq format. These files contain all sequences that pass Illumina's purity filters and per-base quality scores defined by the Illumina phred metric. These r...

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Abstract

The present disclosure provides gene expression profiles that are associated with prostate cancer, including certain gene expression profiles that differentiate between subjects of African and Caucasian descent and other gene expression profiles that are common to subjects of both African and Caucasian descent. The gene expression profiles can be measured at the nucleic acid or protein level and used to stratify prostate cancer based on ethnicity or the severity or aggressiveness of prostate cancer. The gene expression profiles can also be used to identify a subject for prostate cancer treatment. Also provided are kits for diagnosing and prognosing prostate cancer and an array comprising probes for detecting the unique gene expression profiles associated with prostate cancer in subjects of African or Caucasian descent.

Description

[0001] Cross References to Related Applications [0002] This application claims the benefit of U.S. Provisional Patent Application No. 61 / 921,739, filed December 30, 2013, the entire contents of which are incorporated by reference into this application by virtue of its filing date. [0003] government interest [0004] This invention was made in part with Government support. The government has certain rights in this invention. [0005] sequence listing [0006] This application contains a Sequence Listing in ASCII format as electronically filed and is hereby incorporated by reference in its entirety. Said ASCII copy, created on December 29, 2014, is named HMJ-145-PCT_SL.txt and is 344,410 bytes in size. [0007] Background of the invention [0008] By 2013, an estimated 238,590 men will be diagnosed with prostate cancer (CaP), and an estimated 29,720 men will die from the disease [1]. This malignancy is the second leading cause of cancer-related death in American men. In...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N33/574
CPCA61P13/08A61P35/00C12Q1/6886C12Q2600/158G01N33/57434G01N2800/60C12Q2600/118
Inventor S.K.斯里瓦斯塔瓦A.多比G.佩特罗维奇T.维尔纳M.赛弗特M.谢尔夫
Owner THE HENRY M JACKSON FOUND FOR THE ADVANCEMENT OF MILITARY MEDICINE INC
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