title: Allele quantification using molecular inversion probes (MIP).
abstract: Detection of genomic copy number changes has been an important research area, especially in cancer. Several high-throughput technologies have been developed to detect these changes. Features that are important for the utility of technologies assessing copy number changes include the ability to interrogate regions of interest at the desired density as well as the ability to differentiate the two homologs. In addition, assessing formaldehyde fixed and paraffin embedded (FFPE) samples allows the utilization of the vast majority of cancer samples. To address these points we demonstrate the use of molecular inversion probe (MIP) technology to the study of copy number. MIP is a high-throughput genotyping technology capable of interrogating >20 000 single nucleotide polymorphisms in the same tube. We have shown the ability of MIP at this multiplex level to provide copy number measurements while obtaining the allele information. In addition we have demonstrated a proof of principle for copy number analysis in FFPE samples.
authors.affiliation: ParAllele BioScience, 7300 Shoreline Boulevard, South San Francisco, CA 94080, USA.
authors.forename: Yuker
authors.initials: Y
authors.lastname: Wang
authors.forename: Martin
authors.initials: M
authors.lastname: Moorhead
authors.forename: George
authors.initials: G
authors.lastname: Karlin-Neumann
authors.forename: Matthew
authors.initials: M
authors.lastname: Falkowski
authors.forename: Chunnuan
authors.initials: C
authors.lastname: Chen
authors.forename: Farooq
authors.initials: F
authors.lastname: Siddiqui
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Davis
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Willis
authors.forename: Malek
authors.initials: M
authors.lastname: Faham
mesh_terms: D000483:Alleles; D045744:Cell Line, Tumor; D002675:Child, Preschool; D019295:Computational Biology; D005404:Fixatives; D005557:Formaldehyde / Q000737:chemistry; D018628:Gene Dosage; D006801:Humans; D007223:Infant; D008297:Male; D015335:Molecular Probes / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D012015:Reference Standards
chemical_list: D005404:Fixatives; D015335:Molecular Probes; D005557:Formaldehyde