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Transcript of genomic medicine
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Genomic Medicine:
Basic Molecular Biology
Childrens Hospital Informatics Program
Childrens Hospital BostonHarvard Medical School
Massachusetts Institute of Technology
www.chip.org
Basic Biology
functions over a lifetime
specific protein
Organisms need to produce proteins for a variety of
Enzymes to catalyze reactions
Structural support
Hormone to signal other parts of the organism
Problem one: how to encode the instructions for making a
Step one: nucleotides
Atul Butte, MD
arvard-MIT Division of Health Sciences and TechnologyST.512: Genomic Medicine
rof. Atul Butte
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Basic Biology
Naturally form double helixes
Redundant information in each strand
Complementary nucleotides form base pairs
Base pairs are put together in chains (strands)
Chromosomes
chromosome
We do not know exactly how strands of DNA wind up to make a
Each chromosome has a single double-strand of DNA
22 human chromosomes are paired
In human females, there are two X chromosomes
In males, one X and one Y
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What does a gene look like?
regulatory elements
There is a code for the start and end of the proteincoding portion
sequence syntax alone
Each gene encodes instructions to make a single protein
DNA before a gene is called upstream, and can contain
Introns may be within the code for the protein
Theoretically, the biological system can determinepromoter regions and intron-exon boundaries using the
Area between genes
is repeated sequences
between individuals
The human genome contains 3 billion base pairs (3000 Mb)but only 35 thousand genes
The coding region is 90 Mb (only 3% of the genome)
Over 50% of the genome
Long interspersednuclear elements
Short interspersednuclear elements
Long terminal repeats
Microsatellites
Many repeatedsequences are different
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Genome size
largest genome, right?
3000 Mb
Wheat has 17000 Mb
Were the smartest, so we must have the
Not quite
Our genome contains
(~750 megabytes)
E. coli has 4 Mb
Yeast has 12 Mb
Pea has 4800 MbMaize has 5000 Mb
Genomes of other organisms
Plasmodium falciparum chromosome 2
Please see Figure 1 of Science. 1998 Nov 6; 282(5391):1126-32.
Chromosome 2 sequence of the human malaria parasite
Plasmodium falciparum. Gardner MJ, et al.
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mRNA is made from DNA
proteins
The design of a proteinneeds to be duplicable
from DNA within thenucleus
cytoplasm, where theprotein is formed
Genes encodeinstructions to make
mRNA is transcribed
mRNA moves to the
Digitizing amino acid codes Proteins are made of 20
(21) amino acids
only be one of 4nucleotides
3 nucleotides to encodea single amino acid
made from mRNA
Yet each position can
Nature evolved into using
A chain of amino acids is
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Genetic Code
Lander ES, et al.
Please see figure 34 of Nature. 2001 Feb 15; 409(6822): 860-921.
Initial sequencing and analysis of the human genome.
Molecular Biology
Nucleotides
Double helix tRNA
mRNA
Signal Sequence
Prefixed by
Amino Acid
Protein
Chromosome
Gene/DNA
Genome
Are in
Are in
Holds
Held in
Ribosome
Joined by
Operates on Are in
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Central Dogma
Nucleotides
Double helix tRNA
mRNA
Signal Sequence
Prefixed by
Amino Acid
Protein
Chromosome
Gene/DNA
Genome
Are in
Are in
Holds
Held in
Ribosome
Joined by
Operates on Are in
Protein targeting
Works in conjunction with other cellular machinery to
The first few amino acids may serve as a signal peptide
direct protein to the right place
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Transcriptional Regulation
transcription factors
Amount of protein is roughly governed by RNA level
Transcription into RNA can be activated or repressed by
What starts the process?
Transcriptional programscan start from
Hormone action on receptors
Shock or stress to the cell
New source of, or lack ofnutrients
Internal derangement of cellor genome
Many, many other internaland external stimuli
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Temporal Programs Segmentation versus Homeosis: same two houses at
Please see Figure 1 of Cell. 2000 Jan 7; 100(1):27-40.
Development: the natural history of genes. Scott MP.
different times
mRNA
nucleotides per minute
transcribe
mRNA can be transcribed at up to several hundred
Some eukaryotic genes can take many hours to
Dystrophin takes 20 hours to transcribe
Most mRNA ends with poly-A, so it is easy to pick out
Can look for the presence of specific mRNA using thecomplementary sequence
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Periodic Table for Biology Knowing all the genes
knowing the periodictable of the elements
our periodic table
is the equivalent of
Instead of a table,
may read like a tree
More Information
Molecular Genetics
imer/primer.pdf
Sons, 1999.
Department of Energy Primer on
http://www.ornl.gov/hgmis/publicat/pr
T. A. Brown, Genomes, John Wiley and
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Gene Measurement TechniquesDNA
Sequencing
Polymorphisms
RNA
Serialanalysisofgeneexpression DNAMicroarrays
Wafers
Protein
2D-PAGE
Massspectrometry
Proteinarrays
Please refer to Annu Rev Biomed Eng.
1999; 1: 649-78.
Instrumentation for the genome project.
Jaklevic JM, Garner HR, Miller GA.
Please see Figure 1 of J Biotechnol.
2000 Jan 7;76(1): 1-31.
Sequence analysis of genes and
genomes.
Sterky F, Lundeberg J.
Sequencing Reactions
Sanger Chain Termination
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Please see Buetow KH, et al.
Nature Genetics 21:323 (1999).
Sequencing Reactions
perday
PHRAP:assemblessequencedatausingbase-qualityscoresinto
sequencecontigs
Assembly-qualityscores
Mostofthegenomewas
sequencedover12months
Highestthroughputcenterat
Whitehead:100,000sequencing
reactionsper12hours
Robotspick100,000colonies,sequence60millionnucleotides
Sequencing Reactions
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Assembly Contaminationfromnon-humansequencesremoved
Clonesoverlaidonphysicalmap
High-qualitysemiautomaticsequencingfrombothendsofverylargenumbersofnumbersofhumangenomefragments
Overlapstakememory:Drosophila600GBRAM
Human104-processor4GBand16-processor64GB,10KCPUhrs
Genome Browsers Genomebrowsers:UniversityofCaliforniaatSantaCruzand
EnsEMBL
Overlapsequence,cytogenetic,SNP,geneticmaps
Overlapannotations,diseasegenes
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Single Nucleotide
Polymorphisms
Threestepapproach
First,findthegenesyouareinterestedin
Second,catalogallthepolymorphismsina
gene(bysequencing)
Third,measurethose
polymorphismsina
largerpopulation
Clinical use of SNPs
NewpublicationwithassociationofSNPwithdiseaseisalmostadailyoccurrence
Please see Gao, X. et al.
Effect of a
single amino acid change in MHC
class I molecules on the rate ofprogression to
AIDS. N EnglJMed344,
1668-75 (2001).
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SNPs and pharmacogenomics
side-effects
Please see Sesti F. PNAS 97:10613, 2000.
Geneswillhelpusdeterminewhichdrugstouseinparticulardiseasesubtypes
Geneswillhelpuspredictthosewhoget
Please refer to Madden, S. L., Wang,C.J. &
Landes, G.Serial analysisof gene expression:
from gene discoveryto target identification.
Drug Discov Today 5, 415-425 (2000).
Serial Analysis of Gene
Expression
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RNA expression detection chips
Tissueor
Tissueunderinfluence
RNA cDNATagged
withfluorcopy
cDNAspottedonglassslideor
oligonucleotidesbuiltonslide
Quantitative,absoluteorrelative
GeneschosenarbitrarilySchenaM,etal.PNAS93:10614(1996).
NeedsfunctionaltissueNatureGenetics,21:supplement(Jan1999).
Please see Lockhart, DJ. Winzeler,
EA. Nature 405, 827-36 (2000).
roarray of genes aka
gene chips
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Experiment Design
QuantitatespecificRNA
expressionbeforeandafter
anintervention
Compareexpression
betweentwotissuetypes
Compareexpressionbetweendifferentstrainsorconstructedorganisms
Compareexpression
betweenneighboringcells
Please see Luo L, et al. Nature Medicine;
5: 117(1999).
Validation
Insituhybridization
Real-timePolymeraseChainReaction
Microarrays in DiagnosisPlease see Figure 3b of Science. 1999 Oct 15; 286(5439):
531-7. Molecular classification of cancer: class discovery andclass prediction by geneexpression monitoring.
Difficulty
Golub TR, Slonim DK, Tamayo P, Huard C,
distinguishing
Gaasenbeek M, Mesirov JP, Coller H, Loh ML,
betweenleukemias
Downing JR, Caligiuri MA, Bloomfield CD,
Microarrayscanfind
Lander ES
genesthathelpmake
thediagnosiseasier
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Microarrays in Prognosis
Pleasesee Nature. 2000 Feb 3; 403 (6769):503-11. Distinct
types of diffuselarge B-cell lymphoma identified by gene
expression profilling.Alizadeh AA, et al.
PatientswithseeminglythesameB-cell
lymphoma
Lookingatpatternofactivatedgenes
helpeddiscovertwosubsetsof
lymphoma
Bigdifferencesinsurvival
After microarrays comes wafers Chromosome21has21millionbase-pairs
Each5inchsquarewafers(Perlegen)hold60millionprobes
Cansequenceanentirechromosomeinoneexperiment
Eachscantakesuparound10terabytes
CansequenceallSNPswithinahumanin10days
Please see Patil N. Science 2001, 294:1719.
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2D-PAGE
Twoaxis=two
propertiesofproteins:
pHversusmass
Globalviewof
proteins Patternscanbe
scanned,savedand
searched
Spotsneedtobe
pickedfor
identification
Unfortunately,not
veryquantitative
Please see Gygi, S. P., Rochon, Y., Franza,
B. R. & Aebersold, R. Correlation between
protein and mRNA abundance in yeast.
Mol Cell Biol
19, 1720-30 (1999).
Please see Gygi, S. P. & Aebersold,
R.Proteomics: A Trends Guide. (2000)
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Please see Gygi, S. P. & Aebersold, R. Mass
spectrometry and proteomics.
Curr
Opin
Chem
Biol
4, 489-94 (2000).
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Clinical uses for
proteomics
Petricoin,etal.,usedthistechnique
onserum
Findingmarkersdistinguishingovariancancerversusnon-neoplasia
Questforbiomarkers
Please see Petricoin, E. F. et al. Use of
proteomic patterns in serum to
identify ovarian
cancer. Lancet
359, 572-7. (2002).
Quantitative proteomics
Theexamplessofardemonstrateidentification,not
quantification
Onecantakeadvantageoftheextremesensitivityof
detectionofmassspectrometry
Addtotheproteinsaknownamountoflabel
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Protein chips
Function
Please see Williams, D. M. & Cole, P. A.Kinasechips hit the proteomics era.
Trends BiochemSci26, 271-3 (2001).
Detectionvs.
Kinasechips
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Protein
Detection
Specificantibodies
Antibodiesneedtobeavailable
Gene Measurement TechniquesDNA
Sequencing
Polymorphisms
RNA
Serialanalysisofgeneexpression
DNAMicroarrays
Wafers
Protein
2D-PAGE Massspectrometry
Proteinarrays