Composition for the detection of blood cell and immunological response gene expression

a technology of immunological response and immunological response, applied in the field of composition for the detection of blood cell and immunological response gene expression, can solve the problems of a variety of limitations and 10% mismatch in the current cdna-based array, and achieve the effect of minimizing secondary structure and improving hybridization

Inactive Publication Date: 2004-04-22
INCYTE
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  • Abstract
  • Description
  • Claims
  • Application Information

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Benefits of technology

0080] It is also advantageous to include quantitation controls within the sample to assure that amplification and labeling procedures do not change the true distribution of target polynucleotides in a sample. For this purpose, a sample is spiked with a known amount of a control target polynucleotide and the composition of polynucleotide probes includes reference polynucleotide probes which specifically hybridize with the control target polynucleotides. After hybridization and process...

Problems solved by technology

Current cDNA-based arrays suffer from a variety of l...

Method used

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  • Composition for the detection of blood cell and immunological response gene expression
  • Composition for the detection of blood cell and immunological response gene expression
  • Composition for the detection of blood cell and immunological response gene expression

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second embodiment

[0057] In either case, a transcript profile is obtained showing the genes that are differentially expressed in biological samples consisting of hematopoietic cells or tissues associated with an immunological response rather than with noninflamed and nonhematopoietic biological samples. In one embodiment, the top 100 most abundant transcripts, more preferably the top 40 most abundant transcripts, are selected to generate first polynucleotide probes. In a second embodiment all upregulated transcripts are selected. By upregulated is meant that the genes are not detectable in the subtraction transcript profile but are preferably at levels of at least about 2 copies per cell, more preferably at least about 3 copies per cell, in the target transcript profile.

[0058] A second selection protocol (II) can provide for second polynucleotide probes derived from genes abundantly expressed in an immunological response. A number of target cDNA libraries are prepared from second biological samples. ...

examples

[0108] I cDNA Library Construction

[0109] For purposes of example, the preparation and sequencing of the LNODNOT03 cDNA library, from which Incyte Clones 1573272, 1573553, 1574415, 1574617, 1574637, and 1576661 were isolated, is described in detail. Preparation and sequencing of cDNA libraries in the LifeSeq.RTM. database have varied over time, and the gradual changes involved use of kits, plasmids, and machinery available at the particular time the library was made and analyzed.

[0110] The LNODNOT03 cDNA library was constructed from microscopically normal lymph node tissue excised from a 67-year-old Caucasian male. This tissue was associated with tumorous lung tissue. The patient history included squamous cell carcinoma of the lower lobe, benign hypertension, arteriosclerotic vascular disease, and tobacco abuse. The patient was taking Doxycycline, a tetracycline, to treat an infection.

[0111] The frozen tissue was homogenized and lysed using a Brinkmann Homogenizer Polytron PT-3000 (B...

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Abstract

The present invention relates to a composition comprising a plurality of polynucleotide probes. The composition can be used as hybridizable array elements in a microarray. The present invention also relates to a method for selecting polynucleotide probes for the composition.

Description

[0001] This application is a continuation of U.S. application Ser. No. 09 / 023,655, filed Feb. 9, 1998, the entire contents of which is hereby incorporated by reference.[0002] The present invention relates to a composition comprising a plurality of polynucleotide probes for use in research and diagnostic applications.[0003] DNA-based arrays can provide a simple way to explore the expression of a single polymorphic gene or a large number of genes. When the expression of a single gene is explored, DNA-based arrays are employed to detect the expression of specific gene variants. For example, a p53 tumor suppressor gene array is used to determine whether individuals are carrying mutations that predispose them to cancer. The array has over 50,000 DNA probes to analyze more than 400 distinct mutations of p53. A cytochrome p450 gene array is useful to determine whether individuals have one of a number of specific mutations that could result in increased drug metabolism, drug resistance or d...

Claims

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Application Information

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IPC IPC(8): C12Q1/68
CPCC12Q2600/158C12Q1/6883
Inventor COCKS, BENJAMIN G.STUART, SUSAN G.SEILHAMER, JEFFREY J.
Owner INCYTE
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