Systems and Methods to Quantify and Amplify Both Signaling and Probes for CDNA Chips and Gene Expression Microarrays

Abstract

The invention provides a series of reagent compositions and methods for making and amplifying novel cDNA based probe sets from RNA samples to improve analysis with gene expression arrays. The methods globally produce probe sets with common universal linkers at one or both ends, called WRAP-Probes, wherein the linkers do not bind to the target sequences and they can efficiently bind added reporters to the probes. The universal linkers are also designed as primer binding sites for copying and amplifying the probes, either linearly with one linker, or exponentially with double linkers. The capacity to globally and exponentially amplify the probe set by PCR is a primary advantage. Adding reporters by terminal linkers also improves quantification since each probe gets equivalent signaling. The invention allows expression analysis of small research, clinical and forensic samples to enable improved diagnostics, drug discovery, therapeutic monitoring, and medical, agricultural and general research.

Description

CROSS-REFERENCE TO RELATED PATENT APPLICATION[0001]This application claims the benefit, pursuant to 35 U.S.C. §119(e), of applicant's provisional U.S. Patent Application Ser. No. 60 / 187,982, filed Mar. 9, 2000, entitled “Methods to Quantify and Amplify Both Signaling and Probes for DNA Chips and Gene Expression Microarrays”, which is hereby incorporate by reference herein for all purposes. This application further is a continuation-in-part of, and claims the benefit, pursuant to 35 U.S.C. §120, of, applicant's U.S. patent application Ser. No. 09 / 744,097 filed Jan. 16, 2001 entitled “Methods for Detecting and Mapping Genes, Mutations and Variant Polynucleotide Sequences,” which is hereby incorporated by reference herein for all purposes and which is a National Stage Application of International Patent Application Serial No. PCT / US99 / 16242 filed Jul. 16, 1999.BACKGROUND OF INVENTION[0002]1. Field of Invention[0003]The present invention relates generally to the field of detecting genes...

AI Technical Summary

Benefits of technology

[0015]The present invention provides methods and compositions of matter that allow quantitative, sensitive and rapid analysis of gene expression patterns in different cells and tissues as a means to detect functional changes associated with development and physiology, to diagnose abnormal variations related to disease, and to discover and assess pharmaceutical agents. The invention is designed for and particularly suited to multiple analyte formats such as cDNA chips and expression microarrays where the diagnostic value would be improved by increased signaling and by determining the true frequency of different mRNA transcripts in a sample and not just their approximate frequency—a standard poorly addressed by current methods. The invention is complementary to prior inventions of the applicant which provide a probe construction, known as WRAP probes, for detecting genes and nucleotide sequences, which employ generic reporters such as GeneTAGs or TinkerTAGs that are linked to terminal linkers of the probes, and which may employ multi-linker components to join multiple reporters to each probe.

[0016]The present invention employs novel primer, linker, adapter, extender and reporter compositions and molecular processing methods to globally transform a mixed pool of mRNAs into a pool of modified cDNA-based probes, called WRAP-Probes, that have common universal linkers at one or both ends for joining reporters, to thereby provide more defined signaling as well as greater signaling potential. The basic principle of these methods is to achieve signaling by affixing generic reporters to the ends of the probe, either directly or via terminal linkers, rather than by labeling the target specific segment which varies in size for each gene. This invention thus allows quantitative analysis of expression since the signaling element is effectively equalized for each transcript detected, and it improves sensitivity since reporters can be affixed that have greater signaling potential than a labeled probe. Alternate embodiments of the probes, the multi-linking units, and the generic reporters have been devised and these components can be used together in a modular manner to achieve different detection and signaling objectives.

[0017]When the set of WRAP-Probes is constructed with common universal linkers on both ends, this configuration creates an opportunity to use these linker sequences as global primers, thereby allowing the duplication of the entire pool of probes by exponential amplification procedures such as PCR. Alternate amplification methods were invented that produce either singular WRAP-Probes from each mRNA transcript or a fragment series of smaller WRAP-Probes from each transcript. These methods include novel compositions and procedures to create truncated probes and to affix double-linker / primer sites so that they can be reliably amplified by exponential methods. The probes are then globally amplified and labeled during PCR with a single primer set. These amplified probes can also achieve signaling quite simply and inexpensively with new compositions called ChipTAGs that are composed of one or more labeled polynucleotides which additionally serve both linker and primer functions. Thus effective methods were devised that transform a mRNA pool into a set of smaller probe subunits which are globally amplified and suitable for the analysis of gene expression with cDNA chips or microarrays. These methods and compositions improve the quantification of gene expression and allow highly improved detection of rare transcripts and or very small samples.

Problems solved by technology

While it would be possible to make individual WRAP-PROBEs from single genes in a pool of mRNA products in the same manner as RT-PCR is applied to individually copy and amplify a single mRNA gene product and determine its presence, such an approach would be costly, inefficient and would introduce bias.

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