Genomics

1. Genomics Prof. Arnaldo Ferreira

2. 15.1 Genomic Sequencing is an Extension of Genetic Mapping • Mutant genes are the basis of genetic disorders • Mapping helps identify genes that cause disease • The first step in developing diagnostic tests and treatments for these disorders

3. Mapping Genes by Linkage • Linkage • Two or more genes located on the same chromosome that do not show independent assortment and tend to be inherited together • When the degree of recombination (crossing-over) between linked genes is measured, the distance between them can be determined

4. Recombination Frequencies are Used to Make Genetic Maps • A genetic map is made in two steps • Finding linkage between two genes • Measuring how frequently crossing-over takes place between them • Centimorgan (cM) • Unit of distance between genes on chromosomes • One centimorgan equals a value of 1% crossing-over between two genes

5. Linked Genes on the Same Chromosome • Crossover frequencies are used to construct genetic maps, giving the order and distance between genes on the chromosome

6. Linkage and Recombination Can be Measured by Lod Scores • Lod method • A probability technique used to determine whether two genes are linked • Lod score • The ratio of probabilities that two genes are linked to the probability that they are not linked, expressed as a log10 • Scores of 3 or more establish linkage

7. Recombinant DNA Technology Changes Gene-Mapping • Positional cloning • A recombinant DNA-based method of mapping and cloning genes with no prior information about the gene product or its function • Inheritance of molecular markers is used to follow the inheritance of genetic disorders in pedigrees

8. 15.2 Origins of the Human Genome Project • Instead of finding and mapping markers and disease genes one by one, scientists organized the Human Genome Project (HGP) to sequence all the DNA in the human genome, identify and map the thousands of genes to the 24 human chromosomes, and assign a function to all the genes in the human genome

9. Keep In Mind • The Human Genome Project grew out of methods originally developed for basic research: recombinant DNA technology and DNA sequencing

10. 15.3 Genome Projects Have Created New Scientific Fields • The size of the human genome required development of new technologies, including automated methods of DNA sequencing and advances in software to collect, analyze, and store the information derived from genome sequencing

11. New Scientific Fields • Genomics • The study of the organization, function, and evolution of genomes • Bioinformatics • The use of software, computational tools, and databases to acquire, store, analyze, and visualize the information from genomics

12. Methods of Sequencing DNA • To sequence a small amount of DNA, DNA bases (A, T, C, G) are tagged with a radioisotope and combined with DNA fragments, which are then separated by size onto a gel with four lanes • To sequence an entire genome, the process is automated; each base is labeled with a different fluorescent dye which can be read in a single lane by a scanner linked to a computer

13. Bioinformatics: Storing and Accessing Genetic Information • Genomes are stored in databases; the human genome contains over 3 billion nucleotides

14. Some Fields of Genomics • Comparative genomics • Compares genomes of different species for clues to the evolutionary history of genes or a species • Structural genomics • Derives three-dimensional structures for proteins • Pharmacogenomics • Analyzes genes and proteins to identify targets for therapeutic drugs

15. 15.4 Genomics: Sequencing, Identifying, and Mapping Genes • Geneticists developed two strategies for genome sequencing • The government’s genome project used the clone-by-clone method • The privately-funded Celera genome project used the shotgun method

16. The Clone-by-Clone Method • Clone-by-clone method • A method of genome sequencing that begins with genetic and physical maps • Uses clones from a genomic library that have been arranged to cover an entire chromosome • After the order of clones is known, they are sequenced

17. Shotgun Cloning • Shotgun sequencing • A method of genome sequencing that selects clones at random from a genomic library • After the clones are sequenced, assembly software organizes them into the genomic sequence

18. Completing the Genome • The bacterium Haemophilus influenzae was the first organism to have its genome sequenced • Drafts of the human genome were published in 2001and 2003; neither project sequenced the 15% of the genome in heterochromatic regions

19. Keep In Mind • Genomics relies on interconnected databases and software to analyze sequenced genomes and identify genes

20. Annotation is Used to Find Where Genes Are • Annotation • Analysis of genomic nucleotide sequence data to identify protein-coding genes, non-protein-coding genes, their regulatory sequences and functions • Only 5% of human DNA encodes genes

21. How are Genes Identified in a DNA Sequence? • If a DNA sequence encodes a protein, its nucleotide sequence is an open reading frame • Open reading frame (ORF) • Codons in a gene that encode the amino acids of the gene product • Control sequences (CAAT, CCAAT) at the beginning of genes; splice sites between exons and introns; poly-A tail at the end

22. Genetic Sequence from Hemoglobin • Splice junctions between introns and exons (blue); site where transcription begins (green)

23. Geneticists Discover Gene Functions and Products • After a gene has been identified by annotation, its amino acid sequence is derived and compared with sequences already in protein databases • So far, functions have been assigned to about 60% of known genes

24. Amino Acid Sequence From Hemoglobin • Derived from the DNA sequence

25. 15.5 What Have We Learned So Far About the Human Genome? • Only about 5% of our 3 billion nucleotides of DNA encode genetic information • Genes are distributed unequally on chromosomes • Clusters are separated by gene-poor bands • Humans have 20,000 to 25,000 genes • Far fewer than the predicted 80,000 to 100,000

26. What Have We Learned So Far about the Human Genome? • There are more proteins in the body than genes • mRNAs are processed in many ways so 20,000 to 25,000 genes can produce 300,000 proteins • Genomes of humans and other higher organisms are similar • We share half our genes with the fruit fly and more than 90% with mice

27. Keep In Mind • The human genome has a surprisingly small number of genes and produces a surprisingly large number of proteins using a number of different mechanisms

28. 15.6 Using Genomics and Bioinformatics to Study a Human Genetic Disorder • Where is the gene located? • What is the normal function of the protein encoded by this gene? • How does the mutant gene or protein produce the disease phenotype?

29. Mapping Genes and Gene Function • The cystic fibrosis gene was easy to map, convert to amino-acid sequence, and determine its function, but more than half of identified genes have no known function

30. Friedreich Ataxia • Determining the mechanisms of Friedreich ataxia is more difficult • Friedreich ataxia • A progressive and fatal neurodegenerative disorder inherited as an autosomal recessive trait • Symptoms appear between puberty and age 25

31. Studying Friedreich Ataxia • Using positional cloning, the FRDA gene was mapped to chromosome 9, then isolated, cloned and sequenced • Parts of the frataxin protein matched sequences found in bacteria related to mitochondria • Researchers found frataxin in mitochondria and determined its structure, but its specific function is still unknown

32. 15.7 Proteomics is an Extension of Genomics • Proteomics is the study of the structure and function of proteins, which is important in development of new diagnostic tests and drugs • Proteomics • Study of expressed proteins in a cell at a specific time under a particular set of circumstances

33. Role of Proteomics • Understanding gene function and its changing role in development and aging • Identifying proteins that are biomarkers for diseases; used to develop diagnostic tests • Finding proteins for development of drugs to treat diseases and genetic disorders

34. Proteins Expressed in a Cell • Separated by size and electric charge and displayed on a gel

35. 15.8 Ethical Concerns about Human Genomics • To deal with the impact of genomic information on society, the HGP set up the ELSI (Ethical, Legal, and Social Implications) program to ensure that genetic information would be safeguarded, not used in discriminatory ways • ELSI works to develop policy guidelines for the use of genomic information

36. 15.9 Looking Beyond the Genome Project: What the Future Holds • In 2003, scientists of the Human Genome Project published a paper describing the impact of genomics, organized around 3 major themes: Research in biology, health care, and society • Each theme poses challenges

37. The Future of Genomics Research • Six fields were targeted for development as genomic and genetic information grows • Resources: Genome sequences and libraries • Technology such as new sequencing methods • Software for computational biology • Training professionals in interdisciplinary skills • Ethical, legal, and social implications • Education of health professionals and public

38. Genetics in Society:Who Owns Your Genome? • When John Moore had his spleen removed due to a rare form of cancer, his doctor patented a cell line and products derived from the spleen • When Moore sued to share in the profits, the court ruled that patients had no property rights over tissues removed from their bodies

39. Keep In Mind • Genomics is affecting basic research in biology and generating new methods of diagnosis and treatment of disease

40. New Methods of DNA Sequencing • With current methods, it costs about $5 million to sequence a human genome • A prize of $10 million has been offered for development of a method to reduce the cost and increase the speed of genome sequencing