THE HUMAN GENOME PROJECT

1. THE HUMAN GENOME PROJECT Presented by : Asma Mohammad Riaz ShahzadIqbal MadihaLiaquat SagarZulfiqar Aisha Ijaz-ul-Haque Rozinarazzaq Qamar-un-Nisa Presented to : Sir Faiz-ul-Ameen

2. GENOME The genome is the entirety of an organism's hereditary information. It is encoded either in DNA or RNA.

3. Human genome • 23 pairs of chromosomes • Haploid human genome occupied 3 billion DNA base pairs. • 23,000 protein coding genes ------- only 1.5% of the total genome

4. Human Genome Project • The Human Genome Project, comprised of the U.S. Department of Energy and NIH Human Genome Programs, is the national coordinated effort to characterize all human genetic material by determining the complete sequence of DNA in the human genome.

5. HISTORY OF HGP • In October 1990---------- James D.Watson at NIH. • Working draft was released in 2000 and a complete one in 2003. • HGP was cosponsered by two institutes; • DOE • NIH • The Director of the Human Genome Project, Francis Collins.

8. MCDB involvement in Human Genome Project:  • Dr. Kenneth Krauter, a member of the MCDB faculty…………….. high resolution physical mapping and assembly of contigs………. human chromosome 12. • currently working on a similar project for human chromosome 18.

11. Objectives of human project (1) Complete a human genetic linkage map with about 2 Mb resolution (Mb = million base pairs). (2) Complete a physical map of the human genome with 0.1 Mb resolution (3) Acquire a complete set of overlapping clones covering the entire genome (4) Determine the complete sequence of the human genome (5) Identify all of the genes in the human genome

12. Human linkage groups • Measurement of genetic linkage in humans • Types of polymorphic markers • Alleles of protein-coding genes • DNA markers (RFLP, VNTR, STRP). • Human linkage maps.

13. Physical mapping of human genome • Deletion mapping • Hybrid cells containing small numbers of human chromosomes • Fluorescent in situ hybridization (FISH) • Sequence-tagged sites (STS) • Expressed sequence tags (EST)

14. Assembly of collections of cloned sequences • Bottom-up approach • Top-down approach • Assembly of contigs

15. IDENTIFICATION OF HUMAN DISEASE GENES

16. Marfan syndrome:  • An autosomal dominant condition that causes alterations in connective tissue. Effects: skeleton lungs eyes blood vessels Heart

17. Approaches in (marfan syndrome) • Fibrillin was identified as a likely candidate. Identification of a gene that is mutated in marfan syndrome Identification of genes coding for proteins known to function in various types of connective tissue.

18. Fibrillin

19. Neurofibromatosis Is a genetically-inherited disorder in which the nerve tissue grows tumors (i.e., neurofibromas) Types NF2 NF1

20. Type 1 neurofibromatosis • Is an autosomal dominant condition associated with a wide range of nervous system defects, including benign tumors and learning disabilities.

21. FBN1 gene has been cloned and mapped on chromosome 15. RFLP studies verified a linkage between the inheritance of Marfan syndrome and markers on chromosome 15. Cloning of the fibrillin gene from individuals with Marfan syndrome then verified the substitution of a proline for arginine at position 239 in the protein

22. Approaches in (NF) • The overall process that led to the discovery of the NF1 gene is callled positional cloning. • The wild-type gene appears to function • In intracellular signal transduction, • More specifically in down-regulating cellular reproduction. Gene was localized sequencing studies that showed mutations in individuals afflicted with the disease. chromosome walking was undertaken until a candidate gene was encountered. Verification, involved in disease or not

23. HUNTINGTON’S DISEASE: An autosomal dominant progressive neuro-degenerative genetic disorder

24. pedigree of the family covered seven generations, with the disease apparently traced back to a settler of European origin The G8 probe identifies a complex RFLP pattern in DNA cut with Hind III

25. G8 PROBE • The actual polymorphisms involve 1- a 15.0 kb fragment vs. a 17.5 kb fragment 2- a 4.9 kb fragment vs. fragments of 1.2 and 3.7 kb • In the Venezuelan family, HD was strongly associated with the C haplotype (possessing both polymorphic cut sites).

26. CHROMOSOMAL LOCALIZATION OF HD GENE • G8 probe was associated with chromosome 4 • HD gene near one of the ends of chromosome 4 • a region of about 500 kb on chromosome 4 IDENTIFICATION OF HD GENE EXON TRAPPING

27. TRIPLE REPEATS • a large protein (3,144 amino acids) that did not closely resemble any known proteins---HUNTINGTON— -----short arm of chromosome 4 at 4p16.3 -----a sequence of three DNA bases—cytosine-adenine-guanine (CAG)— repeated multiple times (i.e. ... CAGCAGCAG ...), known as a trinucleotide repeat. -----CAG is the genetic code for the amino acid glutamine, -----a polyglutamine tract (or polyQ tract), and the repeated part of the gene, the PolyQ region.

28. HD is one of several trinucleotide repeat disorders which are caused by the length of a repeated section of a gene exceeding a normal range. • When the same gene was isolated from known HD patients, the number of CAG repeats was found to be greatly expanded, ranging from 42 to about 100 in initial studies

29. Cystic fibrosis • Cystic fibrosis is a complex disease • Thickened mucuos leads to respiratory problems and pneumonia • Numerous problems including digestive difficulties and abnormal composition of sweat • It was located on the long arm of chromosome 7 • Active genes have CCGG sequences in which second gene is not methylated • While inactive gene have methylated site

30. Brute force sequencing • It is a problem solving technique where a series of possible answers are worked out and each possibility is tested for accuracy • 1.5 megabase • 250kb yeilded a gene that proved to be altered in CF patients • Gene codes for membrane –spanning chloride transport channels whose malfunctioning explains the diverse phenotypic properties • Molecular defect is loss of for genetIC function of key part of protein that binds ATP to provide energy • The defect in gene provides a basis for genetic screening

31. Deletion analysis • Females do not exhibit the disease • Rare female cases results from inheritance • Karyotypic analysis of female patients revealed small deletion in one of their x- chr • Analysis of genetic region in which deletions occurred led to identification of DMD gene

32. Hereditary breast cancer • HBC involved a varietyof competing laboratories • Gene was found on chr 17 and localized within about 600 kb • The gene BRCA1 was found to be mutated in familial breast cancer cells • BRCA1 codes for protein of 1863 A.A that has DNA binding property and an acidic C-terminal domain that appear to act as a transcription control factor

33. Abnormal localization of brca1 protein • In breast cancer cells, BRCA1 protein is abnormally found in the cytoplasm rather than in the nucleus where it act as a transcription factor • Interactions or BRCA1 with other proteins are needed for normal function of BRCA1 protein

34. Duchenne muscular dystrophy • It is a sex linked disease causes skeletal muscles to be very fragile • This disease does not menifest itself until 3-5 years of age • There is unusual high rate of mutations to generate new cases of DMD

35. Genes and genomes (mining thegenomes) Computationalanalysis of genomes Comparativegenomics

36. APPLICATIONS OF HGP • The mammalian genome and Human Health • Understanding Gene sequences • Understanding Human genetic diseases • Gene Therapy • Genetic engineering of bacteria, animals and plants • Development of Bioinformatics

38. GENOMIC MAPPING THE LINKAGE MAP THE PHYSICAL MAPPING STS and ESTs

39. X-Ray Hybrid mapping • X-ray hybrids are made by irradiating a human cell line with 3000 rad of X-rays, fusion to hamster cells, and isolation of hybrid cell lines in culture

41. Clone contigs • A clone contig is a series of cloned DNA segments that overlap each other, assembled in the correct order along the genome .

42. SEQUENCING

46. DEVELOPEMENTOF BIOINFORMATICS • Essential to the overall success of the Human Genome Project is what is known as bioinformatics – the establishment of facilities for collecting, storing organizing, interpreting, analyzing and communicating the data from the project, which can be widely shared by the scientific community at large.

47. WEBSITES FOR ACCESSING THE HUMAN GENOME PROJECT DATA • U. S. Department of Energy Human Genome Project. • The Science Behind the Human Genome Project. • Genethon in France  • Online Mendelian Inheritance in Man.( OMIM ) This is the definitive site to visit for information of specific human genetic loci and human genetic diseases.

48. ETHICAL LEGAL AND SOCIAL ISSUES : • Fairness in the use of genetic information. • Privacy and confidentiality. • Psychological impact and stigmatization. • Genetic testing. • Reproductive issues. • Education, standards, and quality control. • Commercialization. • Conceptual and philosophical implications.

49. BENEFITS OF HUMAN GENOME PROJECT

50. Many new medicines will be available new medicines