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Literature DB >> 15982637

Allelic dosage analysis with genotyping microarrays.

Shumpei Ishikawa¹, Daisuke Komura, Shingo Tsuji, Kunihiro Nishimura, Shogo Yamamoto, Binaya Panda, Jing Huang, Masashi Fukayama, Keith W Jones, Hiroyuki Aburatani.

Abstract

Genomic alternations, including dosage and allelic imbalance, constitute a major basis of neoplastic and other genetic disorders. Using oligonucleotide genotyping microarrays, here we report the development and usage of an algorithm, called genome imbalance map (GIM) algorithm, for allelic as well as total gene dosage analysis. Using the GIM algorithm, global genome imbalance status at over 100,000 loci was simultaneously analyzed with unprecedented accuracy and allelic discrimination.

Entities: Chemical Disease

Mesh：

Year: 2005 PMID： 15982637 DOI： 10.1016/j.bbrc.2005.06.040

Source DB: PubMed Journal: Biochem Biophys Res Commun ISSN： 0006-291X Impact factor: 3.575

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Cited

32 in total

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2. Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays.

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4. Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids.

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5. High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array.

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6. Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy.

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Allelic dosage analysis with genotyping microarrays.

1. Homozygously deleted gene DACH1 regulates tumor-initiating activity of glioma cells.

2. Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays.

3. Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny.

4. Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids.

5. High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array.

6. Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy.

7. Conditional random pattern model for copy number aberration detection.

8. Estimating genome-wide copy number using allele-specific mixture models.

9. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances.

10. Population-genetic nature of copy number variations in the human genome.