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Transcriptome microarray technology and methods of using the same

A transcriptome and array technology, applied in the field of gene and RNA expression arrays, can solve problems such as difficult data association and general array difficulties, so as to improve safety, reduce the possibility of adverse drug reactions, and improve accuracy Effect

Inactive Publication Date: 2008-01-30
ALMAC DIAGNOSTICS LIMITED
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The main problem concerns the difficulty in comparing different configurations of the general array
That is, it is difficult to correlate data from a 20k sequence array with data from a 40k sequence array
The confusion is caused by contrasting annotations and different questions

Method used

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  • Transcriptome microarray technology and methods of using the same
  • Transcriptome microarray technology and methods of using the same

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0260] Example 1: Initial List of Colorectal Cancer Transcriptome Sequences

[0261] The following method was used to obtain initial colorectal cancer transcriptome array sequences, which are disclosed in European Patent Applications EP 04105479.2, EP 04105482.6, EP 04105483.4, EP 04105484.2, EP04105507.0 and EP04105485.9 and US Provisional Patent Applications 60 / 662,276 and 60 / 700,293 in.

[0262] Materials and methods

[0263] public data screening

[0264] All published expressed sequence tags (ESTs) from all downloaded databases were restored to FASTA format and all 921 databases were concatenated into a single sequence file containing 272,686 single ESTs. These ESTs were then screened using a combination of specific filters in the Paracel Filtering Package (PFP) (available at www.paracel.com) to ensure that no undesired sequence elements entered the pooling procedure. Select settings to mask low-complexity regions, vector sequences, and repetitive sequences. Sequen...

Embodiment 2

[0274] Example 2: Further Characterization of Colorectal Cancer Sequences

[0275] Additional colorectal sequence information was obtained through detection on microarrays containing publicly available information to identify additional transcripts expressed in colorectal tissue. These sequences complement the starting transcriptome array sequence information, providing a more complete array representative of the colorectal cancer transcriptome.

[0276] method

[0277]Forty RNAs from colorectal tissues (27 tumor and 13 normal) were labeled and hybridized to microarrays containing publicly available information. Transcript lists were obtained from these arrays for those targets present in at least one of the arrays and described in the Background Art (ie, identifying transcripts expressed in at least one colorectal sample).

[0278] Initial work on arrays using GI or probeset-associated numbering showed some discrepancies between the target sequence and the full sequence o...

Embodiment 3

[0284] Example 3: Antisense Sequences of Colorectal Cancer Transcriptome

[0285] With increasing scientific communication interest in the role of endogenous antisense RNA transcripts, colorectal cancer databases were checked for the presence of antisense transcripts.

[0286] method

[0287] After pooling, internal and public data contigs were BLASTed against the Genbank NT database for annotation purposes and to identify sequence orientation. In cases where contigs were identified as being in the opposite orientation compared to those listed in Genbank, the data were back-supplemented and both orientations were included in the final data set. Thus, combining the antisense and corresponding sense transcripts resulted in a gene sequence of 5,672 transcripts (Gene List H).

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PUM

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Abstract

Provided herein are arrays comprising transcriptomes of diseased tissues and methods of using the arrays for diagnosis, prognosis, screening, and identification of diseases. The genetic profile of a tissue sample for a disease state is analyzed using diseased tissue transcriptome arrays for disease diagnosis. The genetic profile is then correlated with the effectiveness of specific therapeutic agents. Correlation of therapeutic agent effects with expression profiles provides for further screening and selection of patients predicted to respond to these therapeutic agents, thus minimizing unnecessary exposure to ineffective treatments.

Description

[0001] Cross References to Priority and Related Applications [0002] This application claims priority from European Patent Application Nos. 04105479.2, 04105482.6, 04105483.4, 04105484.2, 04105507.0, 04105485.9, filed November 3, 2004, and U.S. Provisional Patent Application 60 / 662,276, filed March 14, 2005 , and US Provisional Patent Application 60 / 700,293, filed July 18, 2005. technical field [0003] This application relates to the field of gene and RNA expression array technology, and in particular to sequences containing transcripts expressed in diseased tissues and their use in diagnostic and therapeutic regimens. [0004] Index of files on CD-R submitted at the same time [0005] There are a total of 3 identical CD-R disks (labeled "Copy 1", "Copy 2" and "Copy 3") submitted here, each containing the following electronic text files. The CD-R disk was created on November 1, 2005, and the size notes for each file are listed below. All electronic files on CD-R disks are...

Claims

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Application Information

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IPC IPC(8): C12Q1/68
Inventor 保尔·哈金帕特里克·约翰斯顿卡尔·马利根奥斯汀·塔内
Owner ALMAC DIAGNOSTICS LIMITED
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