Read about the human genome project at httpwww.ornl. govsci by yyc62487

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									Human genome project
Read about the human genome project
at
http://www.ornl.gov/sci/techresources/
Human_Genome/home.shtml
  Genomes that have already
  been sequenced
Phage ΦX174 1977        Drosophila 2000
Mycoplasma genitalium   Caenorhabditis elegans
1995                    1998
Haemophilus             Arabidopsis thaliana
                        2001
influenzae 1995
                        Rice 2002
Yeast 1996
                        Anopheles gambiae
E. coli 1997            2002
                        Human genome 2003
What is the human genome
project
 International 13 year effort (began
 October 1990)
 30,000 genes
 3 billion DNA base pairs
 Coding regions only 2% of the genome
   Early reactions

“It endangers all of    The idea of trudging
 us, especially the     through the genome
young researchers”     sequence by sequence
   David Botstein        does not command
   Science, 1986        wide and enthusiastic
                         support in the UK.
                       Sydney Brenner, 1986
Support builds
   The sequence of the human
  genome would perhaps be the
most powerful tool ever developed
to explore the mysteries of human
     development and disease
        Leroy Hood, 1987
The project starts!

    It is essentially immoral
    not to get it [the human
    genome sequence] done
       as fast as possible.
      James Watson 1990
Goals of The Human Genome
Project
 Identify all the approx. 30,000 genes
 Determine the sequences of the 3
 billion bps public databases
 Develop faster more efficient
 sequencing technologies
 Tools for data analysis
 Address ethical, legal, and social issues
 (ELSI)
Who is the U.S. Human
Genome Project?
 National Center for Human Genome
 Research
  Department of Energy Ari Patrinos

  National Institutes of Health Francis
  Collins
Where
 DOE Joint Genome Institute
   3 DOE national labs
 Baylor College of Medicine
 Sanger Centre
 Washington University Genome
 Sequencing Center
 Whitehead Institute/MIT Center for
 Genome Research
Where locally?
 University of Washington Genome
 Center

 University of Washington
 Multimegabase Sequencing Center
Whose?
 A reference sequence - not an exact
 match for any one person
 Blood (female) or sperm (male)
 samples taken from a large number of
 donors.
 Ethnically diverse
 Few samples processed
 Names protected
Patents?
 1987 Walter Gilbert announces plans to
 start Genome Corp. with goal of
 sequencing and copyrighting the human
 genome and selling data for profit
 Patents

          I am
         horrified


James Watson 1991
An Independent Genome
Project? 1998

Celera Genomics Corporation CEO
Craig Venter

Proposes to sequence human genome
in 3 years for $3 million

Invented new sequencing technologies
  A Truce
Sequencing Progress
Draft Sequence:
Completed June 26,
2000

Joint announcement
by Venter and
Collins
    Current Status of HGP
AREA           GOAL                 ACHIEVED           DATE ACHIEVED

Genetic Map    2- to 5-cM           1-cM resolution    September 1994
               resolution map       map (3,000
               (600 – 1,500         markers)
               markers)


Physical Map   30,000 STSs          53,000 STSs        October 1998

DNA Sequence   95% of gene-         99% of gene-       April 2003
               containing part of   containing part of
               human sequence       human sequence
               finished to          finished to
               99.99% accuracy      99.99% accuracy
AREA             GOAL                      ACHIEVED               AREA

Human            100,000 mapped            3.7 million mapped     February 2003
Sequence         human SNPs                human SNPs
Variation




Gene             Full-length human         15,000 full-length     March 2003
Identification   cDNAs                     human cDNAs


Model            Complete genome           Finished genome        April 2003
Organisms        sequences of              sequences of E. coli,
                 E. coli, S. cerevisiae,   S. cerevisiae,
                 C. elegans,               C. elegans,
                 D. melanogaster           D. melanogaster, plus
                                           whole-genome drafts
                                           of several others,
                                           including C. briggsae,
                                           D. pseudoobscura,
                                           mouse and rat
Functional Genomics
ELSI
 Research informed public policy

 40 states in the US have passed genetic
 non discrimination bills

 3000 judges went through 20
 workshops on fundamentals of genetics
Beyond the human genome
project?
 Genomics
 Proteomics
 Genomics-based medicine
   Hereditary factors in heart disease
   Cancer
   Diabetes
   Schizophrenia
 Individualized medicine
Recent events in HGP
The DNA sequence and analysis of human
chromosome 13
A Dunham et al.
Nature 428, 522-528 (2004)
Chromosome 13 is the largest acrocentric
human chromosome.
Lowest gene density of all chromosomes
Medically interesting genes on
chromosome 13

   BRCA2               RB1



 DAOA locus associated with bipolar
    disorder and schizophrenia.
         Disease                                  localisation    Sequence     OMIM
Gene                                                              containing   reference
                                                                  gene
ATP7B    Wilsons Disease                          13q14.3-q21.1   AL162377     606882
                                                                  AL138821

BMIQ2    Quantitative trait for body mass index   13q14           Not cloned   606643


BRCA2    Breast cancer 2,early onset              13q12.3         AL442512     600185
                                                                  AL137247

BRCA3    Breast cancer 3                          13q21           Not cloned   605365


CLN5     Ceroid-lipofuscinosis, Neuronal-5        13q21.1-        AL355879     608102
                                                  q32

BRCD1    Breast cancer, ductal                    13              Not cloned   211410


D13S25   B-cell chronic lymphocytic leukaemia     13q14           Not cloned   109543


DDX26    Non small cell lung cancer               13q14.12-       AL137780     604331
                                                  q14.2           AL354820

EDNRB    Hirschsprung Disease                     13q22           AL139002     131244


ENUR1    Nocturnal Enuresis                       13q13-q14.3     Not cloned   600631


ERCC5    Xeroderma pigmentosum                    13q33           AL157769     133530


F10      Factor X deficiency                      13q34           AL137002     227600
F7       Factor VII deficiency                           13q34       AL137002     227500


FGF14    Fibroblast growth factor 14                     13q34       AL160153     601515


FLT3     Decreased survival in Acute myeloid leukaemia   13q12       AL356575     136351
                                                                     AL445262
                                                                     AL356915



FOXO1A   Alveolar                                        13q14.1     AL133318     136533
         rhabdomyosarcoma                                            AL355132



DAOA     Schizophrenia                                   13q34       AL359751     607408


GER      Gastroesophageal reflux                         13q14       Not cloned   109350


GJA3     Cataract, zonular                               13q11       AL138688     121015
         pulverulent-3

GJB2     Deafness, autosomal                             13q11       AL138688     121011
         recessive-1

GJB6     Deafness, autosomal                             13q12       AL355984     604418
         dominant-3

HTR2A    Psycotic illness                                13q14-q21   AL136958     182135
                                                                     AL160397



ING1     Squamous cell carcinoma,                        13q34       AL157820     601566
         head and neck

IPF1     Pancreatic aqenesis,                            13q12.1     AL353195     600733
         maturity-onset diabetes
IRS2    Noninsulin-dependent             13q34         AL162497                         600797
        diabetes mellitus

ITM2B   Dementia                         13q14         AL139322                         603904


LDLR    Cholesterol lowering factor      13q           Not cloned                       604595


LIG4    LIG4 syndrome                    13q22-q34     AL157762                         601837


MBS1    Moebius syndrome                 13q12.2-q13   Not cloned                       157900


MCOR    Congenital microcoria            13q31-32      Not cloned                       156600


PAPA2   Postaxial polydactyl,            13q21-q32     Not cloned                       602085
        TypeA2

PCCA    Propioninacidemia                13q32         AL356575                         232000
                                                       AL355338
                                                       AL136526
                                                       AL353697
PHF11   Asthma,atopic hypersensitivity   13q14.1       AL139321                         607796


RB1     Retinoblastoma                   13q14.1-      AL136960                         180200
                                         q14.2         AL392048

RFXAP   Bare lymphocyte syndrome         13q14         AL159973                         601861


RHOK    Oguchi disease-2                 13q34         Partialy Contained in BX537316   180381


RIEG2   Rieger syndrome                  13q14         Not cloned                       601499
Chromosome 19
 April 2004

 Most Gene rich of all
How do you sequence a whole
genome?
 Vectors for large scale
 genome projects
YACS Yeast Artificial Chromosomes
   Megabase!


BACS Bacterial Artificial Chromosomes
   Vector 6.9 kbps
  Insert average 150 kb
YACS
BACS
How do you sequence a whole
genome?
 Clone by Clone
   requires a map



 Shotgun sequencing Figure 24.7
Maps
 Genetic map
   determined from recombination
   frequencies


 Physical map
   based on physical distances
   the physical location of a particular
   cloned sequence of DNA
Genetic markers - landmarks
on the map
 Morphological markers
   scorable phenotypes e.g. hemophilia,
   wrinkled pea


 Physical markers
   RFLPs, CAPS, VNTR, STS
Critical to the success of the HGP clone
   by clone sequencing strategy was
 development of a physical map of the
   human genome placing molecular
           markers on this map.
  STS = sequence tagged sites were
             particularly used.
One of a kind
markers not
duplicated
anywhere else in
the genome
    Current Status of HGP
AREA           GOAL                 ACHIEVED           DATE ACHIEVED

Genetic Map    2- to 5-cM           1-cM resolution    September 1994
               resolution map       map (3,000
               (600 – 1,500         markers)
               markers)


Physical Map   30,000 STSs          53,000 STSs        October 1998

DNA Sequence   95% of gene-         99% of gene-       April 2003
               containing part of   containing part of
               human sequence       human sequence
               finished to          finished to
               99.99% accuracy      99.99% accuracy
       Physically mapping whole
       chromosomes

Large scale mapping        cytogenetics


                              FISH

                      Somatic cell hybrid mapping




                       STS mapping figure 24.6
   Fine mapping
 Mapping a whole genome
Recognizing
chromosomes
Somatic Cell hybrid mapping

  Locate DNA fragment to particular
  chromosome
Locate markers to
chromosomes


                    A is on 1

                    B is on 7

                    C is on 5
 Radiation hybrid map

•Map based on the co-occurrence of
markers in a panel of radiation hybrid
cell lines, resulting in an ordering of
    markers along a chromosome
               backbone.
      Radiation hybrids
      Irradiate with X rays before fusion
Chromosome 10               C 1 2 3 4 5 M




        1 2 3 4 5
Fine structure mapping
 STS mapping
 Used to order BAC clones
 Generate contigs
 Principle:
   If the same STS marker can be PCR
   amplified from two clones the clones
   overlap
CLONE      STS
        A B C D E
  1     + + + - -
  2     + - + - +
  3     + + - + -
  4     - + - + -

                    2   E   C   A
                    1               B

                    4                   D

                    3

								
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