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Download Array platforms for cytogenetic, expression and methylation analysis Stephen Wilcox
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Array platforms for cytogenetic, expression and methylation analysis Stephen Wilcox Australian Genome Research Facility June 2011 Arrays Arrays • Require genome information to construct oligos • Designed for model and non-model organisms • Catalogue arrays • Custom arrays • Wealth of array products for human studies Arrays • Oligo based technology • Targeted approach to generating results • Gene expression (RNA) • Genotyping (DNA) • Epigenetics (DNA) • (re)Sequencing (DNA) Arrays VARIATION METHYLATION COPY NUMBER Genomic DNA Gene TRANSCRIPTION mRNA miRNA TRANSLATION Protein sequence POST-TRANSLATIONAL MODIFICATIONS 3D Protein structure Arrays Genotyping arrays VARIATION COPY NUMBER METHYLATION Epigenetic arrays Genomic DNA Gene TRANSCRIPTION mRNA miRNA Gene expression arrays Array Types • Gene expression (RNA) • 3’ gene arrays • Exon arrays • Tiling arrays • miRNA arrays Array Types • Gene expression (RNA) • 3’ gene arrays • Exon arrays • Tiling arrays • miRNA arrays Monitoring expression levels for thousands of genes simultaneously. Also look at splicing and regional expression activity. Array Types • Genotyping arrays (DNA) • SNP arrays • CGH arrays (CNV) Array Types • Genotyping arrays (DNA) • SNP arrays • CGH arrays (CNV) Identifying polymorphism among alleles and number of copies within or between populations. Array Types • Epigenetic arrays (DNA) • Methylation arrays • Promoter arrays • CpG island arrays • Tiling arrays Array Types • Epigenetic arrays (DNA) • Methylation arrays • Promoter arrays • CpG island arrays • Tiling arrays Determining protein binding site occupancy throughout the genome or which regions of DNA are methylated. Array Platforms 3’ gene Exon miRNA CGH SNP Affymetrix 9 9 9 + 9 Agilent 9 9 9 9 + 9 illumina 9 + 9 9 Nimblegen 9 9 Meth Prom CpG 9 9 9 Tiling 9 9 Array Platforms • • • • Affymetrix Nimblegen Agilent illumina (25mer) (60mer) (60mer) (50mer)* Array Manufacture Types Affymetrix (mask photolithography) Array Manufacture Types Agilent (ink jet) G A A G T C C C T G G G A G A Array Manufacture Types illumina (beads) /\/\/\/ /\/\/\/ illumiCode #561 Array Manufacture Types Nimblgen (maskless photolithography) Current Array Status Gene Expression • Affymetrix • U133 Plus 2.0 • Exon 1.0ST • Gene 1.0ST • Agilent • 3’ gene array (8x60k, 4x44k) • Exon array (4x180k, 2x400k) • illumina • HT-12v4 • Nimblegen • 3’ gene array (12x135k, 4x72k, 1x385k) Current Array Status Cytogenetics • Affymetrix • Whole genome 2.7M • Cytoscan HD (Aug 2011) • Agilent • CGH arrays (8x60k, 4x180k, 2x400k, 1x1M) • CGH+SNP (4x180k, 2x400k) • illumina • CytoSNP-12 beadchip • Omni-1 Quad • Nimblegen • CGX cytogenetics (12x135k, 6x315k, 3x720k) Current Array Status Methylation • Affymetrix • Promoter 1.0R • Tiling 1.0R/2.0R • Agilent • Promoter (2x400k, 1x1M) • CpG (1x244k) • Methylation (1x244k) • illumina • Methylation 27k • Methylation 450k • Nimblegen • Promoter (3x720k, 2.1M) Application Options • Massive parallel sequencing • Low sample throughput (indexing) • All genetic information captured • High processing cost per sample • High bioinformatic and IT requirements • Arrays • High sample throughput • Limited to content on array • Lower processing cost • Bioinformatics focused
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