Allelic dosage analysis with genotyping microarrays

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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.

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Materials and methods

We used the whole genome sampling analysis (also called WGSA or sampling analysis) with allele-specific hybridization on arrays originally designed for SNP genotyping [8]. In this method, the genomic DNA is digested with restriction endonuclease XbaI or HindIII and subsequently adaptors are ligated and the fragments are amplified with adaptor-specific primers. This amplified product represents about 10% of the whole genome which is subsequently hybridized to 25mer oligonucleotide arrays (for

Results and discussion

To prove the principle that the noise from the arrays could be substantially reduced and the signal intensities from the probes on the array could change according to the original gene dosage, we examined the probe signal intensity ratio of a chr21 trisomy sample (Down syndrome) and compared that to the normal diploid reference sample. As expected, we observed increased signal intensity ratio for the trisomy sample at chromosome 21 loci (Fig. 1A) albeit with considerable noise fluctuations.

Acknowledgments

We gratefully acknowledge Hiroko Meguro and Kaori Shiina for technical assistance. This work was supported by Core Research for Evolutional Science and Technology (CREST) from Japan Science and Technology Agency, Grants-in-Aid for Scientific Research (S) 16101006 and (B) 13218019 from the Ministry of Education, Culture, Sports, Science and Technology, and Special Coordination Funds for Promoting Science and Technology from the Ministry of Education, Culture, Sports, Science and Technology of

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