Detection of STRP, such as fragile X syndrome

Abstract

Methods for detecting a short tandem repeat polymorphism (STRP), such as fragile X syndrome, wherein PCR is used to amplify nucleic acid along the chromosome in the genomic DNA which includes all of the STRs of interest plus a substantial contiguous segment of the nucleic acid adjacent to the STRs. Single-stranded product is then obtained, and colorimetric-labeled oligonucleotides which target for (i) STRs and (ii) the contiguous DNA segment are hybridized with this single-stranded product which is then bound to a solid phase and separated from the remainder of the target material. The labeled oligonucleotide target material is recovered by treatment with base and then hybridized to a microarray having a plurality of spots containing suitable oligonucleotide probes complementary thereto. Following hybridization, colorimetric intensities of the hybridized labeled target material present at specific spots on the microarray are measured to obtain individual values which are compared with results from known control samples to accurately quantify the number of STRs in the region of interest of the DNA being analyzed.

Description

field of invention [0001] The present invention relates generally to diagnostic tests for hereditary or sporadic genetic defects in adults, fetuses and embryos, and more particularly to the detection of diseases or defects caused by short tandem repeats (STRs), and more particularly to the detection of diseases or defects that cause Fragile X Detection of genetic defects in Fragile X syndrome. These STRP assays use polymerase chain reaction (PCR), which is then hybridized to a microarray and analyzed. Background of the invention [0002] Eukaryotic DNA has very short tandem repeats of simple sequences called short tandem repeat polymorphisms (STRPs). Repeat polymorphisms include dinucleotide, trinucleotide and tetranucleotide repeats. Trinucleotide and tetranucleotide repeats are repeats of 3 nucleotides and 4 nucleotides. An increasing number of diseases are known to be associated with expansion of trinucleotide STRs (Trottier, Y. et al., Current Biology 3:783-786 (1993)...

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Problems solved by technology

[0011] However, these methods are limited in their ability to determine the number of CGG repeats to provide an accurate diagnosis

The reason is usually the difficulty of PCR amplifying the CGG repeat region and not generating enough PCR product for accurate gel electrophoresis analysis (a large amount of PCR product is required for detection)

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