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Transcript
Genomic Analysis Chapter 19 Overview of topics to be discussed How to sequence genomic DNA (we will have to touch briefly on polymerase chain reaction—a topic from the upcoming “PCR” lab). cDNA Microarray Analysis The Human Genome Project How to use information from any genome sequence: Single Nucleotide Polymorphisms Predicting Function from Sequence cDNA: mRNA Reverse transcriptase cDNA can also be studiedwww.bio.davidson.edu/Courses/genomics/RTPCR/RT_PCR.html : SEQUENCING DNA Sanger-Dideoxymethod Dideoxy key point! Sanger Method dideoxynucleotides: lack a 3’ OH But have the 2’ and 3’ have hydrogen NO DNA EXTENSION DNA PCR amplification is performed prior to sequence analysis Autoradiogram Can you sequence without using radioactivity? Radioactive! Yes: Example of Labelled Probes ddGTP ddATP ddTTP ddCTP Orange Black Red Blue Microarray Analysis Microarray Protocol DNA or cDNA is added robotically to chip Chips exposed to labeled cDNA Label monitored by laser Example of: Microarrays from breast tumors cDNA from breast tumors from 2 groups of patients Metastatic Cancer Disease Free Microarrays of 70 genes (row is a patient; column a gene) Metastatic cancers Genomic DNA Transcriptome DATA BASE Proteome Human Genome Project June, 2002 Dr. Craig Venter President Clinton Dr. Francis Collins The initial draft of the Human Genome •3.4 billion base pairs •32,000 genes •Average gene 27,000 bases •Chromosome 17, 19, 22 high density •May encode 96,000 proteins Mouse: Mus musculus 2.6 billion bp 99% in common with human genome Genomic Projects: provide us information about: Expressed-sequence tags (ESTs) Need to understand cDNA Single-nucleotide polymorphisms (SNPs) & Haplotypes Variable Number Tandem Repeats (VNTRs) Haplotype: A set of SNPs and other variants on the same chromosome Variable number tandem repeats (VNTRs) in multiple loci Short stretches of DNA base pairs that are repeated at multiple loci in the chromosomes. GAGGAG GAGGAGGAG GAGGAGGAG GAGGAGGAGGAGGAG GAGGAGGAGGAG GAG GAGGAGGAG GAGGAGGAGGAG GAGGAGGAGGAGGAGGAG GAGGAGGAGGAGGAGGAG Predicting Function from Homology Search Computational method prediction Paralog Ortholog Paralogs: Homologous sequences in same species Orthologs Homologous Sequences in Different species
