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TRANSCRIPT
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HistoryandBackgroundofHuman
Genome
ProjectHaroldRiethman,Ph.D.
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I. Background&OverviewofTheHuman
GenomeProject
II.ChromosomeStructureReview
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PhysicalBasisFor
GeneticInformation
Replication
Finite
Watsonand
Crick,
Nature
1953
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Image from NHGRI Web Site
Human male karyotype
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MendelsLawsofInheritance Mendel,1866
Genetic
Linkage
Maps Sturtevant,
1913
PhysicalMaps(Cytogenetic) Painter,1933
Structureof
DNA Watson
&
Crick,
1953
MolecularCloning CohenandBoyer,1972
DNASequencing Sanger,
Maxam,
and
Gilbert,Midseventies
HumanRFLPMapping Botsteinetal.,1980
GenomicsPre1982:
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Genomics 19821988:
Pulsedfield gel electrophoresis Schwartz and Cantor, 1983
Polymerase Chain Reaction Mullis 1983
Multipoint Linkage Mapping Lathrop et al., 1984.
Global Physical Clone Maps Olson et al., 1985
Sulston et al., 1985
First proposals to sequence DeLisi, DOE, mid80s
human genome
Yeast Artificial Chromosome (YAC) Burke et al., 1987
Automated DNA Sequencers Hood, midlate 80s
Mapping and Sequencing the National Research Council, 1988
Human Genome
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1. PulsedfieldGel
Electrophoresis
2. Maplarge
chromosomeregions
3. 2.Largeinsert
Cloning
FromRiethmanetal.,GenomeAnalysisVol 1,1997
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PolymeraseChainReaction
Invitro
synthesis
of
DNA
Markerstorageanddistribution
bycomputer
Sensitivescreeningand
detection
FromFanningandGibbs,GenomeAnalysisVol 1,1997
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MappingandSequencingtheHumanGenome
NationalResearch
Council,
1988
Aspecialeffortshouldbeorganizedandfundedtomap,sequence,andincreaseunderstandingofthe
HumanGenome.
Technologydevelopmentessentialforeveryphaseoftheproject.
Earlygoalsshouldbeahighresolutiongeneticmap,acollectionoforderedclones,andaseriesof
complementaryphysicalmapsofincreasingresolution.Thenucleotidesequence,theultimategoal,will
requiremajoradvancesinDNAhandlingandsequencingtechnologies.
Acomparativegeneticapproachisessentialforinterpretingtheinformationinthehumangenome.
Competing,peerreviewedprogramsemphasizingtechnologydevelopment.
Componentsubprojectsshouldhavethepotentialtoimproveby5to10foldincrementsthescaleor
efficiencyofmapping,sequencing,analyzing,orinterpretingtheinformationinthehumangenome.
Establishcentralizedfacilitiesforstoringanddistributingclones,andadatacenterforthecomputer
basedcollectionanddistributionoflargeamountsofDNAsequenceinformation.
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Maps
Landmarks Fragment Ends
DNA probes Restriction Enzyme
STS Meiosis
RadiationClone ends
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SequenceTaggedSite(STS)1989
ReplacesclonedDNAprobemappinglandmarkswithPCRassays.
EachSTSisuniquelydescribedbyapairofoligonucleotides,aproductsize,and
PCRreactionconditions. Canbestoredanddistributedelectronically.
Enables mergingofmappingdataobtainedfrommanylabsusingmanydifferentmethods
intoasingleconsensusmapoflandmarksalongachromosome.
Eliminatestheneedforhugecollectionsofclonedprobesegmentsuponwhich
priormaps
depended.
UniversalLandmark
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MeioticBreaks GeneticLinkageMaps
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RadiationinducedBreaks RadiationHybrid(RH)Maps
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Cloneends
Clonebased
PhysicalMap
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Thefirst5yearplan(19911995)
GeneticMap:
fullyconnected,2to5centimorgan resolution,eachmarkeridentifiedbyanSTS
PhysicalMap:
100kbresolutionSTSmap
2Mbcontigs formostofgenome
Sequencing:
Improve/developtechnologytoreducecostto0.50/base
Generatetotalof10Mbofhumansequenceinlargestretchesduringtechnologydevelopment
ModelOrganisms:
Geneticmap
of
mouse
Generatetotalof20Mbofsequencefrommodelorganisms,focusoncontiguousstretchesof1Mb,during
technologydevelopment
Informatics:
Developsoftware
and
database
designs
to
support
large
scale
mapping
&
sequencing
Createdatabasetoolsthatprovideeasyaccessandpermitcomparisonsofuptodatedatasets
Developalgorithmsandanalyticaltoolstointerpretinformation
ELSI Ethical,Legal,andSocialImplications
Training
TechnologyDevelopment
Support
innovative
&
high
risk
projects
TechnologyTransfer toindustryandthemedicalcommunity
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2nd 5yrplan
19931998
HGP
FrancisCollinsandDavidGalas
OriginallypublishedinScience
262:4346(1993)
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Figure 2 Worldwide human genome sequencing progress is shown (measured as base pairs
of fin ished sequence deposited with GenBank).
F S Coll ins et al. Science 1998;282:682-689
Published by AAAS HGP3rd 5yrplan19982003
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CapillarySequencers,Automation,19971998
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Green,1997 WeberandMeyers,1997
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InternationalHumanGenomeSequencingConsortium
DraftHuman
Genome
Sequence:
Nature
Feb.15,
2001
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CeleraGenomicsDraftHumanGenomeSequence
ScienceFeb.16,
2001
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InternationalHumanGenomeSequencingConsortium
FinishedHumanGenomeSequence:Oct.21,2004
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AVisionfortheFutureofGenomicsResearch, Nature,April24,
2003.Collins,Green,Guttmacher &Guyer,NHGRI
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Genomics
to
Biology
Comprehensivelyidentifythestructuralandfunctionalcomponents
encodedinthehumangenome.Encode.
Elucidatetheorganizationofgeneticnetworksandproteinpathwaysand
establishhowtheycontributetocellularandorganismalphenotypes.
Develop
a
detailed
understanding
of
the
heritable
variation
in
the
human
genome.HapMap
Understandevolutionaryvariationacrossspeciesandthemechanisms
underlying
it.
Developpolicyoptionsthatfacilitatethewidespreaduseofgenome
informationinbothresearchandclinicalsettings
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Technologydevelopment
DNAsequencing
Geneticvariation
Thegenome
'parts
list
Proteomics
Pathwaysandnetworks
Geneticcontributionstohealth,diseaseanddrugresponse
Molecularprobesforexploringbasicbiologyanddisease
Computationalresourcesforstorage,analysis,andintegrationof
hugedatasets
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Theabilitytodetermineagenotypeatverylowcost,allowinganassociation
studyinwhich2,000individualscouldbescreenedwithabout400,000genetic
markersfor$10,000orless.
Theability
to
sequence
DNA
at
costs
that
are
lower
by
four
to
five
orders
of
magnitudethanthecurrentcost,allowingahumangenometobesequenced
for$1,000orless.
The
ability
to
synthesize
long
DNA
molecules
at
high
accuracy
for
$0.01
per
base,allowingthesynthesisofgenesizedpiecesofDNAofanysequencefor
between$10and$10,000.
TheabilitytodeterminethemethylationstatusofalltheDNAinasinglecell.
Theabilitytomonitorthestateofallproteinsinasinglecellinasingle
experiment.
QuantumLeaps
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ChromosomeStructure
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Imagefrom
NHGRI
Web
Site
Humanmalekaryotype
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Gene
GeneticConcept Functionalpieceof achromosome
PhysicalConcept Stringofnucleotidesthatencodea
discretefunction
Proteinencodinggene
NoncodingRNAs
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Heterochromatin
Highly condensed chromosome regions
Large heterochromatic tracts are usually repetitive
sequence
Can be very difficult to clone and assemble sequences
Often gene-poor, low transcription levels
Enriched near centromeres and telomeres
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Heterochromatic Centromere Satellites
Heterochromatin
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Euchromatin
Less condensed chromosome regions
Very wide range of DNA sequence types andorganization
Contains most genes, but very unevenly distributed
Mostly accessible to cloning and assembly
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Euchromatic Region
FromUCSC
Web
Browser
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SegmentalDuplicatons
LargesegmentsofrecentlyduplicatedDNA
>1kb,
>90
%
Highlyenrichedinpericentromeresandsubtelomeres
Associated
with
large
polymorphisms
and
diseaseassociateddeletions
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Hillieretal.
Nature2003
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ChromosomeFunction
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Replication
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DNAReplication
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Centromeresand
Telomeres
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Centromeres
ensure
proper
segregation
of
chromosomes
Sequence Organization of Human Centromere and Pericentromere
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SequenceOrganizationofHumanCentromereandPericentromere
She et al. Nature 2004
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Telomeresarerequiredforchromosomereplicationandstability
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http://www.biologyreference.com/
Telomerase
replicates
telomeres
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Subtelomeres Rapidlyevolving
Highlyvariable
Duplicatedsequences
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Pryde etal,1997.
Curr Opin GenetDev
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Cell
cycle,
Meiosis,
Mitosis
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I=interphase
M=mitosis
S=DNAsynthesis
CellCycle
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MarstonAL,
Amon
A.
2004.
Nat
Rev
Mol
Cell
Biol.
MitosisandMeiosis