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THE HUMAN GENOME PROJECT. Presented by : Asma Mohammad Riaz Shahzad Iqbal Madiha Liaquat SagarZulfiqar Aisha Ijaz-ul-Haque Rozina razzaq Qamar -un- Nisa. Presented to : Sir Faiz-ul-Ameen. GENOME.

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The human genome project

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


Genome
GENOME

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


Human genome
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


Human genome project
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.


History of hgp
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.


  • Mcdb involvement in human genome project
    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.


    Objectives of human project
    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


    Human linkage groups
    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.


    Physical mapping of human genome
    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)


    Assembly of collections of cloned sequences
    Assembly of collections of cloned sequences

    • Bottom-up approach

    • Top-down approach

    • Assembly of contigs



    Marfan syndrome
    Marfan syndrome: 

    • An autosomal dominant condition that causes alterations in connective tissue.

      Effects:

    skeleton

    lungs

    eyes

    blood vessels

    Heart


    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.



    Neurofibromatosis
    Neurofibromatosis

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

    Types

    NF2

    NF1


    • Type 1 neurofibromatosis

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


    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


    Approaches in nf
    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


    Huntington s disease
    HUNTINGTON’S DISEASE:

    An autosomal dominant progressive neuro-degenerative genetic disorder


    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


    G8 probe
    G8 PROBE disease apparently traced back to a settler of European origin

    • 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).


    Chromosomal localization of hd gene
    CHROMOSOMAL LOCALIZATION OF HD GENE disease apparently traced back to a settler of European origin

    • 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


    Triple repeats
    TRIPLE REPEATS disease apparently traced back to a settler of European origin

    • 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.


    • 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


    Cystic fibrosis
    Cystic fibrosis are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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


    Brute force sequencing
    Brute force sequencing are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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


    Deletion analysis
    Deletion analysis are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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


    Hereditary breast cancer
    Hereditary breast cancer are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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


    Abnormal localization of brca1 protein
    Abnormal localization of brca1 protein are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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


    Duchenne muscular dystrophy
    Duchenne are caused by the length of a repeated section of a gene exceeding a normal range. 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


    Genes and are caused by the length of a repeated section of a gene exceeding a normal range.genomes (mining thegenomes)

    Computationalanalysis of genomes

    Comparativegenomics


    Applications of hgp
    APPLICATIONS OF HGP are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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


    GENOMIC MAPPING are caused by the length of a repeated section of a gene exceeding a normal range.

    THE LINKAGE MAP

    THE PHYSICAL

    MAPPING

    STS and ESTs


    X ray hybrid mapping
    X-Ray Hybrid mapping are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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


    Clone contigs
    Clone are caused by the length of a repeated section of a gene exceeding a normal range.contigs

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


    Sequencing
    SEQUENCING are caused by the length of a repeated section of a gene exceeding a normal range.


    Developementof bioinformatics
    DEVELOPEMENTOF BIOINFORMATICS are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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.


    Websites for accessing the human genome project data
    WEBSITES FOR ACCESSING THE HUMAN GENOME PROJECT DATA are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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.


    Ethical legal and social issues
    ETHICAL LEGAL AND SOCIAL ISSUES : are caused by the length of a repeated section of a gene exceeding a normal range.

    • 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.


    Benefits of human genome project
    BENEFITS OF HUMAN GENOME PROJECT are caused by the length of a repeated section of a gene exceeding a normal range.


    Many new medicines will be available
    Many new medicines will be available are caused by the length of a repeated section of a gene exceeding a normal range.

    new medicines


    Medicines will be safer due to genome scans
    Medicines will be safer due to genome scans. are caused by the length of a repeated section of a gene exceeding a normal range.

    • Side effects

    • Gene chip

      complete sequence information

      mutations can be noted

      Example:

      Albuterol for asthma


    Longer and healthier life
    Longer and healthier life are caused by the length of a repeated section of a gene exceeding a normal range.

    • Pre-embryonic gene therapy

    • Anti-oxidant enzymes

    • Gene for longer life

    • Average lifespan


    Designing the generation
    Designing the generation are caused by the length of a repeated section of a gene exceeding a normal range.

    • Genetic disorder

    • Manipulating human traits

    • Improved phenotype & genotype generation


    In nature’s infinite book of secrecy are caused by the length of a repeated section of a gene exceeding a normal range.

    A little I can read


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