Microarray-based gene copy number analyses
AssigneeBoard of Trustees of Michigan State University
InventorsWenjiang Fu, Yalu Wen, Ming Li
Life of this patent
Estimating the term…
Abstract
This invention contemplates an accurate and efficient estimation of gene copy number using oligonucleotide microarrays. The method integrates gene copy number data obtained from perfect match and mismatch probe sequence structure intensities and probe binding affinities. In one embodiment, an accurate determination of single nucleotide polymorphisms (SNPs) sequences is obtained. In another embodiment, an accurate detection and determination of DNA copy number alteration is obtained. In another embodiment, an accurate estimation for RNA gene expression is obtained.
Claims11
A method, comprising:
- a) providing:
- i) a microarray comprising a first oligonucleotide and second oligonucleotide, said first oligonucleotide comprising a portion of a first allele, said second oligonucleotide comprising a portion of a second allele;
- ii) a labeled first probe having partial complementarity to a region of said first oligonucleotide;
- iii) a labeled second probe having complete complementarity to a region of said first oligonucleotide;
- iv) a labeled third probe having partial complementarity to a region of said second oligonucleotide;
- and
- v) a labeled fourth probe having complete complementarity of a region of said second oligonucleotide;
- b) exposing said first, second, third and fourth probes to said microarray under hybridization conditions to create bound probes;
- c) determining intensity measurements from said bound probes;
- and,
- d) determining a copy number for said first allele and said second allele using said intensity measurements of step c) and an algorithm, said algorithm utilizing an MA ratio.
Dependencies are inferred from the claim text.