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    Celera Genomics Public Consortium

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    api-19481102
    The document discusses sequencing the human genome and identifying all genes. It notes the goal was to sequence the 3 billion base pairs of human DNA. It outlines the process of sequencing DNA reads and increasing throughput over time. The timeline and increasing capacity of sequencing centers is shown. Standard techniques like agarose gels are compared to newer robotic systems and capillary array electrophoresis machines. Assembly of the whole genome sequence is discussed, comparing BAC-by-BAC and shotgun approaches. The future of sequencing more genomes is mentioned. The document also discusses using sequencing to find all human mutations, establish gene function and disease mechanisms, and enable diagnostics. Epigenetics and its role in genomic variation between cell types is briefly outlined.

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    Celera Genomics Public Consortium

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    api-19481102
    94 views24 pages
    The document discusses sequencing the human genome and identifying all genes. It notes the goal was to sequence the 3 billion base pairs of human DNA. It outlines the process of sequencing DNA reads and increasing throughput over time. The timeline and increasing capacity of sequencing centers is shown. Standard techniques like agarose gels are compared to newer robotic systems and capillary array electrophoresis machines. Assembly of the whole genome sequence is discussed, comparing BAC-by-BAC and shotgun approaches. The future of sequencing more genomes is mentioned. The document also discusses using sequencing to find all human mutations, establish gene function and disease mechanisms, and enable diagnostics. Epigenetics and its role in genomic variation between cell types is briefly outlined.

    Original Title

    What-is-the-Human-Genome-Project

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    The document discusses sequencing the human genome and identifying all genes. It notes the goal was to sequence the 3 billion base pairs of human DNA. It outlines the process of sequencing DNA reads and increasing throughput over time. The timeline and increasing capacity of sequencing centers is shown. Standard techniques like agarose gels are compared to newer robotic systems and capillary array electrophoresis machines. Assembly of the whole genome sequence is discussed, comparing BAC-by-BAC and shotgun approaches. The future of sequencing more genomes is mentioned. The document also discusses using sequencing to find all human mutations, establish gene function and disease mechanisms, and enable diagnostics. Epigenetics and its role in genomic variation between cell types is briefly outlined.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    94 views24 pages

    Celera Genomics Public Consortium

    Uploaded by

    api-19481102
    The document discusses sequencing the human genome and identifying all genes. It notes the goal was to sequence the 3 billion base pairs of human DNA. It outlines the process of sequencing DNA reads and increasing throughput over time. The timeline and increasing capacity of sequencing centers is shown. Standard techniques like agarose gels are compared to newer robotic systems and capillary array electrophoresis machines. Assembly of the whole genome sequence is discussed, comparing BAC-by-BAC and shotgun approaches. The future of sequencing more genomes is mentioned. The document also discusses using sequencing to find all human mutations, establish gene function and disease mechanisms, and enable diagnostics. Epigenetics and its role in genomic variation between cell types is briefly outlined.

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    Public Consortium Celera Genomics

    Sequence Genetic Mapping,


    Genomes
    Find Genes Mutation Detection

    Establish
    Function and Diagnostics/
    Disease Mechanism Prognostics

    Drug
    Candidates Cure Gene Therapy
    “Sequence the 3 billion (+) base pairs of human DNA
    and identify all genes contained in the human genome”

    DNA Sequence
    ‘Reads’ -
    Need
    60,000,000
    of them!!
    Time Line of the Human Genome Project
    BCM-HGSC: Sequencing Throughput
    2,000,000

    1,800,000 Today 1.9 M reads


    1,600,000

    1,400,000

    1,200,000

    1,000,000

    800,000

    600,000

    400,000

    200,000

    0
    Jan-00 May-00 Sep-00 Jan-01 May-01 Sep-01 Jan-02 May-02
    Standard Molecular Biology techniques – running agarose gels.
    CS-Packard DNA Production Robotic Systems (x 3)
    Multiplexed (104) Capillary Array for Electrophoresis
    State of the Art - ABI 3700 “Prism” DNA Sequencer
    US $300,000 Each!

    A room full of 3700 Sequencers – total price tag of US $22.5 Million


    “State of the Art”: Assembly
    Whole Genome
    BAC by BAC
    Shotgun (WGS)
    Versus

    -Front end loaded,


    - Tractable Assembly -Efficient front end,
    Problem - Huge Assembly Problem
    BCM-
    HGSC
    Linux Farm
    Very small changes in technology
    have had a huge impact on the HGP…..

    Imagine what a large change


    in technology would do…
    The Future: More Genomes!!
    Rat, Mouse, Rabbit, Dog, Chimp, Rhesus, Zebrafish,
    Fugu, Hamster, Cow, Sheep, Pig, Chicken, Honey Bee,
    Silk Worm, Shark, Dolphin, Whale, Frog, Sea Urchin,
    Sea Squirt, Sea Turtle, Salmon, Hydra, Wallaby,
    Platypus, Rice, Wheat, Maize, Sorgum, Soy,
    Banana, Poplar, Potato, Corn, Sea Turtle, Wheat,
    Pine ……….
    COMPLETE (HETEROZYGOUS)
    MUTATION DETECTION

    ABI 370:
    Universal
    Primer
    Tag PCR

    exon
    13,000
    OMIM - 10,000 Entries

    BCM-
    HGSC
    Dextrocardia and Situs Inversus

    Disorders of laterality
    occur in
    2 – 3 per 10,000 live births
    Pulmonary valve
    stenosis mutations

    BCM-
    HGSC
    SCREENING 160 SPORADIC PATIENTS IN
    NODAL SIGNALING PATHWAY
    RECEPTORS NODAL + LEFTYA competing for receptor
    TYPE 1 (ALK2 “ACVR1”
    ALK4 “ACVR1B”; ALK7
    components
    (mouse)
    TYPE 2 (ActRIIA “ACVR2”;
    ActRIIB “ACVR2b”) EGF-CFC
    Co-Factor Proteins
    Cripto and Cryptic
    Interacts with ALK4 receptor

    INTRACELLULAR MEDIATORS, SMAD2, SMAD3, SMAD4

    SMADS INTERACTS w/ SMADS INTERACTS w/


    TGIF to repress pathway FAST1 to activate gene

    Human mutations in
    Target Genes: PITX2 + NODAL +
    all loci marked in read LEFTYB
    Epigenetics/Methylation

    Epigenix web site

    Genomic DNA can be different in


    Different cells of the same person…..
    BCM-HGSC ~ 230 Personnel

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