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Paola CASTAGNOLI Maria FOTI Microarrays. Applicazioni nella genomica funzionale e nel genotyping DIPARTIMENTO DI BIOTECNOLOGIE E BIOSCIENZE Microarrays: Applicazioni nella Genomica Funzionale e nel Genotyping ** *** SAGE Nylon membrane Illumina Bead Array Different Technologies GeneChip Affymetrix cDNA microarray Agilent: Long oligo Ink Jet CGH Affymetrix Gene Chips Whole genome expression Expression variability Whole genome genotyping Sequence variability Mapping 10k, 100k and 500k 10,000, 100,000 and 500,000k genotypes Analysis of Genomics, Microarrays gene expression and proteomics data contained in public databases can identify the gene involved in a particular human disease 2D gel Only one candidate gene Disease Gene Identified with mutations Computer Search Microarray Gene expression data Identification the candidate genes involved in human diseases More than one candidate gene NCBI National Center for biotechnology information SNPs Single Nucleotide Polymorphism Haplotype Blocks in Human Genome a) a) Each human chromosome is made up of regions called haplotype blocks 3 to 7 variants occuring at a frequency of 5% in the population. Each haplotype block has different colors b) Two individuals with differents haplotype carrying 30% of variation of the total haplotype diversity in the human population Haplotype block b) Individual 1 Individual 2 Applications of Microarray Technology • Gene expression profiling – – – – In different cells/tissues During the course of development Under different environmental or chemical stimuli In disease state versus healthy • Molecular diagnosis: – Molecular classification of diseases • Drug development – Identification of new targets • Pharmacogenomics – Individualized medicine Applications of microarrays • Cancer research: Molecular characterization (taxonomy) of tumors on a genomic scale more reliable diagnosis and effective treatment of cancer. • Immunology - bacterial infections: study of host / pathogen interactions in terms of their transcriptional response • Developmental biology: • Molecular biology: (conditional) gene knockout - find regulated genes • Response of cells / tissues to drugs / injury Improvements in Medicine • Diagnostics –Faster and more accurate diagnosis –Positive prognosis –Predictable symptoms –Ability to make arrangements before things happen Improvements in Medicine • Disease Control and Prevention –Increased knowledge about genetic diseases • Vaccines • Treatments • Education programs Poor signature Good signature Gene Expression “Signature” as a Predictor of Survival 70 reporter genes Molecular Classification and Outcome Prediction of Acute Leukemia in the Genomics Era: A Paradigm for Molecular Medicine Cancer Molecular Medicine Tailoring Therapy to the Disease and the Host Genomics Integration of Molecular, Genomic, and Ultimately Functional Biologic Approaches into Diagnosis Clinomics Assessment of Genetics, Gene Expression Profiles for New Molecular Classification Schemes and Identification of Diagnostic and Therapeutic Targets Assessment of Host Polymorphisms to Assess Disease Risk and Potential Therapeutic Efficacy or Toxicity Tailoring Therapy to Disease and Host Uses of DNA Microarrays • Transcriptome profiling: – Massive parallel analysis can reveal patterns of gene expression allowing researchers to predict gene associations and pathways – Microarrays have been used over the past five years for transcriptome analyses in organisms ranging from bacteria to fungi to humans to higher plants under hundreds of different conditions • Diagnostics: RNA or DNA samples hybridized to small arrays to detect expression of marker genes (stress/pathogens, developmental events) • Molecular genetics: Genomic DNA samples are hybridized to a limited number of probes to detect single nucleotide polymorphisms (SNPs) for mutational analyses (pedigrees, gene mapping) • Gene promoter analyses: ChIP to Chip assays – overlapping or ‘tiled’ DNA probes representing an entire genome are hybridized with labeled, putative trans-acting proteins to detect binding to cis elements in promoter regions