1. Human Genome Project Chapter 9

2. Central Points (1)  Large, international project analyzing human genome  Information from sequencing and mapping all human genes  Gene mapping to locate human genes  Number of surprises as human genome analyzed

3. Central Points (2)  Scientists apply information from Human Genome Project (HGP) to medical diagnosis and treatment  Physicians use genome to give better medical care  Gene therapy is a future application of the HGP  Ethical and legal aspects of the HGP discussed

4. 9.1 Goals of HGP (1) 1. Create maps of the human and other creatures’ genomes 2. Find location of all genes 3. Compile lists of expressed genes and nonexpressed sequences 4. Discover function of all genes

5. 9.1 Goals of HGP (2) 5. ID proteins encoded by genes and their functions 6. Compare genes and proteins between species 7. Analyze DNA differences between genomes 8. Set up and manage databases based on genomes discovered

6. DNA Sequence

7. HGP Timeline

9. Chromosome Maps  Map shows where all the genes are located on each chromosome

10. Methods  Began in 1990, human genome ~3.2 billion nucleotides  Required development of automated methods  Bioinformatics created software, web-based databases, and research tools to collect, analyze, and store information  Genomics: study of genomes

11. HGP Now  Portion that carries genes was sequenced in 2003  Function of remaining 15% unknown and currently being sequenced  Sequenced portion studied to ID genes and assign functions  Proteomics: study of protein structure and function

12. 9.2 Gene Mapping  Genes close together on same chromosome tend to be inherited together and show linkage  In 1936, hemophilia and color blindness found to be linked, both on X chromosome  Difficult to map genes on autosomes, requires very large families with two specific genetic traits

13. X-Linked Genes

14. Autosomal Linkage  ABO blood group and nail-patella syndrome

15. Linked Genes Separate by Crossing Over  Separation of the two alleles is result of crossing over between two genes  Occurs randomly in meiosis  Frequency of crossing over related to distance between two genes  Linkage map of a chromosome can be constructed

16. Crossing Over

17. Linkage or Genetic Map  Order of genes on a chromosome and distance between them  Expressed as percentage of crossing-over events  10% = 10 map units or centimorgans (cM) apart  From this pedigree, frequency of crossing over: 2/16 = 12.5%. or 12.5 cM (actual value ~10cM)

18. Autosomal Linkage  ABO blood group and nail-patella syndrome

19. Human Linkage Map

20. Positional Cloning  Markers identified that show differences in: Restriction enzyme cutting sites Number of repeated DNA sequences (i.e., STRs)  Markers assigned to chromosomes  Used to follow genetic disorder in pedigrees  Map one gene at a time, and by late 1980s, more than 3,500 genes and markers

21. Genes Mapped by Positional Cloning

22. DNA Sequencing Today  Can rapidly sequence DNA with computer programs  Sequence entire DNA sequence in genome  Uses high-speed sequencers and computers  Allowed HGP to succeed

23. 9.3 Whole Genome Sequencing  Construct a genomic library that contains all sequences in a genome  Fragments of DNA placed in a DNA sequencer  Generates nucleotide sequence (As, Cs, Gs, and Ts)  Assemblers (specialized software) produce sequence of genome

24. Finding Genes from Sequence  Software programs scan sequences, searching for promoter sequence  Sequences that follow promoter are genes  AA sequence determined by matching the nucleotide triplets to corresponding AA  ID protein encoded by this gene

25. A DNA Sequence

26. Animation: Gene Sequencing

27. 9.4 What Have We Learned?  > 3 billion nucleotides of DNA  ~5% genes code for proteins  Many remnants of genome’s evolutionary history  > Half the genome is repetitive DNA

28. Types Repetitive DNA  45%: transposons New copies can move (or transpose) Most not functional Do not replicate and move around  17%: LINE 1 sequence  10%: Alu sequences  Others including short tandem repeats (STRs)

29. Importance of Alu Sequences  Appeared in primate genomes ~65 million years ago (MYA), important in evolution of our genome  Many associated with genetic diseases  2.8 MYA, Alu sequence moved, may be associated with increased brain size

30. Other Surprises from HGP  20,000–25,000 genes but > 500,000 known proteins (possibly exceed 2 million)  Possible mechanisms During processing mRNA, the coding segments can be rearranged Proteins modified after synthesis  Human Proteome Project (HUPO): ID proteins, functions, and interactions

31. 9.5 How Can Information Be Used? 1.ID location of gene 2.Function of the protein encoded by this gene 3.How the mutated gene or its protein product results in a disorder  Allow development of treatments and medications

32. Cystic Fibrosis (CF) Gene  Positional cloning ID gene, long arm of chromosome 7  Isolated nucleotide sequence, ID AA sequence of CF protein  Compared to databases of other organisms, protein in plasma membrane  Now developing medications

33. 9.6 Future of Genome Sequencing  New technologies to reduce cost and time  Make sequencing routine in medical care  Possible for doctors to monitor your health  Provide: Information to reduce risks for certain diseases Early diagnosis of conditions

34. 9.7 Gene Therapy  Recombinant DNA technology to treat genetic disorders  Transfer copies of normal genes into cells (or people) with defective copies of these genes  Normal genes directs synthesis of the normal protein

35. How Are Genes Transferred?  Cells removed from the body  Normal copies inserted using virus, or vector  Cells grown in the laboratory  Checked that normal gene actively making protein  Cells transferred back into the body

36. First Gene Therapy Patient (1990)  Ashanti DeSilva had severe combined immunodeficiency disorder (SCID)  No functional immune system, die from infection  Inserted gene for adenosine deaminase (ADA) into her white blood cells  Treated cells injected into her, allowed her to develop an immune system

37. Problems with Gene Therapy  In many cases, gene therapy has not worked  Few patients developed leukemia  At least two people died  Scientists working to correct problems  Need to develop new approaches to use genes to treatment genetic diseases

38. Spotlight on Law: Moore v. Regents of the University of California (1)  John Moore treated at UC Hospital for hairy cell leukemia  Spleen removed and over years blood, sperm, serum, bone marrow removed as “part of his treatment”  Signed consent form for doctors to do research on cells and expenses paid for by UCLA

39. Spotlight on Law: Moore v. Regents of the University of California (2)  Moore’s doctors received patent on cell line and sold cell line for stock options and $330,000 Issues:  Informed Consent: Moore did not receive enough information to make an informed consent  Doctor/patient relationship: Moore treated fraudulently, experienced emotional distress