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Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
Published on: August 5, 2008
Combining microarray-based genomic selection (MGS) with the Illumina Genome Analyzer platform to sequence diploid
David T Okou1, Adam E Locke, Karyn M Steinberg
1Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
Annals of Human Genetics
|July 4, 2009
Summary
Microarray-based genomic selection (MGS) combined with Illumina Genome Analyzer (IGA) sequencing provides high-quality data for human genetics research. This optimized method demonstrates accurate diploid genotype calling and reliable experimental variation analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Targeted sequencing methods for complex genomes are promising but lack validation for diploid genotype calling.
- Experimental variation and data accuracy are critical concerns for human genetics research using novel sequencing techniques.
Purpose of the Study:
- To optimize microarray-based genomic selection (MGS) for the Illumina Genome Analyzer (IGA).
- To evaluate the efficacy of MGS/IGA sequencing for diploid genotype calling and assessing experimental variation in human DNA samples.
Main Methods:
- Optimization of microarray-based genomic selection (MGS) for Illumina Genome Analyzer (IGA) sequencing.
- Targeted sequencing of a 1.7 Mb region on human chromosome X across ten HapMap samples.
- Analysis of sequence data quality, including base and site calling accuracy at various coverage thresholds (5X and 50X).
Main Results:
- High percentages of bases (93.9%) and segregating sites (94.9%) were called at 5X coverage.
- Data accuracy reached 98.9% at 5X and 99.6% at 50X coverage for known segregating sites.
- Accuracy at heterozygous sites exceeded 92% at 5X and nearly 97% at 50X coverage.
Conclusions:
- MGS/IGA sequencing generates high-quality data suitable for human genetics research.
- The optimized method demonstrates reliable diploid genotype calling and accuracy.
- This study provides critical validation for targeted sequencing approaches in complex genomes.
