Genomics and Bioinformatics Gabriel Cap Biomedical Engineering Survey Wednesday, March 1, 2006
Outline • Basic principles of molecular biology • Major types of data in genome projects • Practical applications and uses of genomic data • Understanding the major topics in the field of bioinformatics and DNA sequence analysis • Learn about key bioinformatics databases and web resources Chapter 13: Genomics and Bioinformatics
Introduction • Genomic Era • In April 2003 the human genome was sequenced • 3 billion nucleotides • Importance? • 1631 human genetic diseases are associated with known DNA sequences • Only 100 known before genome was sequenced Chapter 13: Genomics and Bioinformatics
Genomic Era • Human Genome not the only item to be sequences • The complete genomes were available for many items • 1557 viruses • 165 microbes • 26 eukaryotes • Yeast • Rice Chapter 13: Genomics and Bioinformatics
Genomes • Important so that genes can be compared in order to eliminate deadly threats • Advance in technologies are needed • Speed up pace • Reduce expense • Methods to interpret data • Applications to medicine Chapter 13: Genomics and Bioinformatics
DNA • Phosphate and Deoxyribose Backbone • Adenine binds with thyamine • Cytosine binds with guanine Chapter 13: Genomics and Bioinformatics
Ratios of Bases Chapter 13: Genomics and Bioinformatics
Arrangement • DNA is doubled and • twisted to form a • double helix Chapter 13: Genomics and Bioinformatics
Double Helix Chapter 13: Genomics and Bioinformatics
Background • DNA to RNA to Protein • 3 Steps • Storing Genetic Information • Processing Information • Transmitting Information from parent to offspring • Genetic Information Stored in DNA • Deoxyribose sugar • Genome size has some effect on organism complexity • Genes to Protein • Not a one to one ratio, one gene does not mean 1 protein • Single lines can produce multiple genes Chapter 13: Genomics and Bioinformatics
Genes to Proteins • Transcription of DNA • RNA Polymerase binds to gene • Creates RNA Molecule • This mRNA will serve as template for protein • Introns and Extrons help split up the sequence to isolate certain strands • Translation of RNA • Reads the mRNA template • Produces Protein Chapter 13: Genomics and Bioinformatics
DNA Replication Chapter 13: Genomics and Bioinformatics
Protein Translation • Nucleotides line up in protein • Group up in codons (3) • Ribosomes interact with tRNA to interpret codon • Each codon encodes one amino acid • 20 amino acids make up the protein Chapter 13: Genomics and Bioinformatics
Core Laboratory Technologies • Genome science driven by advances in order to allow for rapid and inexpensive data collection techniques • 3 Prominent Uses • Provide the starting point to understand the underpinnings of an organism • Facilitate studies of gene regulation • Understanding the variation between different species Chapter 13: Genomics and Bioinformatics
Gene Sequencing • The most widely used sequencing technique • Reporter attached to nucleotide and speed measured as it travels through a medium • DNA sequences have an orientation • 5’ left end • 3’ right end • Through a series of tests one can complete the target sequence Chapter 13: Genomics and Bioinformatics
Sanger Sequencing • Uses fluorescent dyes to mark nucleotides • Laser based systems read the sequences • Modern devices can read 800 nucleotides at a time • Graphs and statistical analysis produce results of which bases are at each position • Also give error probably for each site • A single DNA sequencer can produce 1,000,000 nucleotides per day Chapter 13: Genomics and Bioinformatics
Whole Genome Sequencing • Shotgun Sequencing for large regions of DNA • Copy genome • Randomly cut genome into fragments • Align the overlapping fragments • Read the complete genome sequence by following a gap free path Chapter 13: Genomics and Bioinformatics
Gene Expression • Uses to survey the abundance of the gene products • Microarray Experiment • Compare normal tissue and tumor tissue • Look for differences in genes in biological process • Time Course Experiment • The change in expression is measured against time • Groups are formed where they experience an increase or decrease in expression levels Chapter 13: Genomics and Bioinformatics
Mutations Chapter 13: Genomics and Bioinformatics
Diagnosis • If gene expression matches reference samples • Patient can be diagnosed • Microarray technology has greatly improved accuracy of diagnosis • Types of Gene Sequencing • cDNA microarrays • Creation of microarray slide • Oligonucleotide arrays Chapter 13: Genomics and Bioinformatics
Polymorphisms • Variations from individual to individual • SNP Consortium • Characterized 1.8 million polymorphisms in humans • Should help accelerate the process of the description of genetic diseases • Simple Sequence Repeats also used Chapter 13: Genomics and Bioinformatics
Core Bioinformatics Technologies • Bioinformatics-analysis of Genomic data • Database systems • Engineering • Mathematical Analysis • Computational Chapter 13: Genomics and Bioinformatics
Genomics Databases • Project data from scientific community available • National Center for Biotechnology Information • Contains Genbank of DNA and RNA sequences • Has BLAST database searching tools • Uses algorithms to find sequence alignments in Chapter 13: Genomics and Bioinformatics
Sequence Alignment • Most fundamental computational algorithm • Goals • Accept two or more sequences • Identify similar sequences • Output sequences with the similar positions aligned in columns Chapter 13: Genomics and Bioinformatics
Uses of Sequence Alignment • Uses • Determine whether sequences have similar functions • Shows patterns of similarity • Can infer history of species • Reconstruct sequences in ancestral organisms • Can pick which parts have been added or deleted Chapter 13: Genomics and Bioinformatics
Database Searching • Searching GenBank for sequences that are similar to a sequence of interest • Most common bioinformatics task • Can help narrow down what type of disease or what similar types of viruses are formed from strand Chapter 13: Genomics and Bioinformatics
Hidden Markov Models • HMMs are a class of mathematic tools • Identify important regions • Genes • Binding sites • Come in the form of relatively short contiguous blocks of DNA • Proved to be an excellent tool for identifying genes in newly sequenced genomes • Can determine which nucleotides are in each region Chapter 13: Genomics and Bioinformatics
Gene Prediction • Purpose • Take a long sequence of DNA • Identify the locations of genes • Identify start and stop codons • Problems • Could lead to a high false positive rate • HMMs also very suited for gene finding • Gene finding algorithms Chapter 13: Genomics and Bioinformatics
Functional Annotation • Once genome is sequenced • The biological function of the genes is determined • Two approaches for function are used • Comparative Genomics • HMMs • Database comparisons are used to determine other genes with similar functions • Genes compared to proteins in the PFAM database Chapter 13: Genomics and Bioinformatics
Identifying Differentially Expressed Genes • Two different “treatments” used to compare two types of tissue • Technologies • Microarray • Oligonucleotide • Genes leave spots on microarray so they can provide measurements of gene expressions • These results are graphed an analyzed Chapter 13: Genomics and Bioinformatics
Clustering Genes • Used to identify sets of genes that respond to two or more treatments • Used in time course study • Expression levels are measured at specific intervals • Plots produced and compared Chapter 13: Genomics and Bioinformatics
Conclusion • Genomic Science opened the door for new technology • Started the wave of using computers for analysis • Diagnostic Procedures are changing due to genomics • More medicines will develop from our studies in genomics • Gene therapies are the next step to allow for repair of genetic defects Chapter 13: Genomics and Bioinformatics
The End • Questions? • Comments? • Arguments? • Rebuttal? • Discourses? • Problems? • Issues • Queries? Chapter 13: Genomics and Bioinformatics
