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Updated: May 19, 2026

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
Published on: August 14, 2018
Molecular inversion probes: a novel microarray technology and its application in cancer research
Yuker Wang1, MariEllen Cottman, Joshua D Schiffman
1Assay Development and Bioinformatics Department, Affymetrix, Inc., Santa Clara, CA, USA.
Molecular inversion probe (MIP) assay technology enables detection of various genetic variations, including somatic mutations, even in degraded DNA. This versatile genomic tool enhances cancer research and diagnosis using archived samples.
Area of Science:
- Genomics and Molecular Biology
- Cancer Research
- Biotechnology
Background:
- Molecular inversion probe (MIP) assay technology, initially for single nucleotide polymorphism (SNP) genotyping, has evolved to detect diverse genetic variations.
- The MIP assay demonstrates robust performance with limited and degraded DNA, including formalin-fixed paraffin-embedded (FFPE) samples, crucial for historical sample analysis.
- Padlock probes are central to MIP assays, enabling specific hybridization to DNA targets before polymerase chain reaction (PCR) amplification.
Purpose of the Study:
- To review the history, methodology, and applications of MIP assay technology in genetic variation detection.
- To highlight the utility of MIP assays in advancing cancer research and understanding disease subtypes.
- To explore the potential of MIP technology for improving cancer diagnosis, prognosis, and therapeutic strategies using FFPE samples.
Main Methods:
- Description of the MIP assay principle, involving padlock probes and PCR amplification for target DNA analysis.
- Discussion of MIP assay's adaptability for various genetic variations: SNPs, insertions/deletions, copy number alterations (CNAs), loss of heterozygosity (LOH), and somatic mutations.
- Review of current analysis techniques and recent publications utilizing MIP platforms.
Main Results:
- MIP assay requires minimal genomic DNA (75 ng) and performs well with highly degraded DNA from aged FFPE samples.
- The technology has facilitated significant discoveries in the molecular basis of cancer.
- MIP assays provide high specificity due to the hybridization mechanism of padlock probes.
Conclusions:
- MIP assay technology is a versatile and sensitive tool for detecting a wide spectrum of genetic variations.
- Application of MIPs to archived FFPE samples offers a powerful approach for retrospective cancer studies.
- This genomic technology holds promise for enhancing clinical cancer diagnosis, prognosis, and the development of novel therapeutics.
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