Paola CASTAGNOLI Maria FOTI Microarrays. Applicazioni nella genomica funzionale e nel genotyping DIPARTIMENTO DI BIOTECNOLOGIE E BIOSCIENZE

* * * * * GeneChip Affymetrix cDNA microarray Nylon membrane Agilent: Long oligo Ink Jet Illumina Bead Array CGH SAGE Different Technologies Microarrays: Applicazioni nella Genomica Funzionale e nel Genotyping

Affymetrix Gene Chips Sequencevariability Expressionvariability Whole genome genotyping Mapping 10k, 100k and 500k 10,000, 100,000 and 500,000k genotypes Whole genome expression

Analysis of Genomics, Microarrays gene expression and proteomics data contained in public databases can identify the gene involved in a particular human disease Only one candidate gene Computer Search 2D gel Microarray Gene expression data Disease Gene Identified with mutations

Identification the candidate genes involved in human diseases SNPs Single Nucleotide Polymorphism NCBI National Center for biotechnology information More than one candidate gene

Haplotype Blocks in Human Genome Individual 1 Individual 2 a) b) Haplotype block 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

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

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 Improvements in Medicine

Gene Expression “Signature” as a Predictor of Survival Good signature Poor signature 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  Integration of Molecular, Genomic, and Ultimately Functional Biologic Approaches into Diagnosis GenomicsClinomics  Assessment of Host Polymorphisms to Assess Disease Risk and Potential Therapeutic Efficacy or Toxicity   Tailoring Therapy to Disease and Host  Assessment of Genetics, Gene Expression Profiles for New Molecular Classification Schemes and Identification of Diagnostic and Therapeutic Targets

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