1

• The instructions for assembling every organism
• on the planet--slugs and sequoias, peacocks and
• parasites, whales and wasps--are all specified in
  DNA
• sequences that can be translated into digital
• information and stored in a computer for
  analysis. As
• a consequence of this revolution, biology in the
  21st
• century is rapidly becoming an information
  science...

...hypotheses will arise as often in silico as in
vitro.
Eric Lander, Science 287 (5459), 1777-1782
2
BioinformaticsFunctional Genomics
...TGTTATTGCCAATGCATCATGATCGTAGAGATGTAGGCTAAAGAAAC
TTTTTTAAAGTGTGATTTTACACAGCAGCTGGTGGTTACTGCTTAGCCAT
AAAATTATGTGTTGATATTGACATAAGTGGAATGTCGAAAACATGTTTAT
TCATACACGTATATTGTTGAAAGAAGTGTTAAACACATCATACGTTTAAA
GTAGACAAATCTAGAAATATATAACAAAAGAGAATTTGTTTGTACATTTA
AAAAGCCTTAGCTCTTTTTGAGCAAAATATGTAATATTATAATTTCAACA
CTTTTGAGTGTGTTTACTAAAACTAACAACCTTTATGAAGCAATTGGGAT
GGGTTTGTGTGATCTAAAATTGAGGTAGGATCGTGGGACCAGGAGAACAT
GAGATGCATCGAAGGCAAAGTCCAAAGACACTACGTCACTTTGAGTGGAT
TGTGTACGTGAGGTTGTACGAACCATCATTTCACGTTACATATGTTGCAA
CGCTGCGTAATCTGTCCCCACCATCCAACTTATTTCTAATTCTTTTTCAT
AATTATATTTGTATCTAAACTAAGTAGAATACCTACATATTGAAAAGAAA
TATTACTTGCTAGGGCCTAGGGATAAACGTTAAAGAGAAATATTACTATA
GAGAAAAACCCTTTAGTTTTGAACACAATTTCTATGTGTAAACATGCGTG
ATTGTTATGTAGGCAGATGTGCACTAAGCACTTAAACAGAAAAAGAGACA
AGTTTTGAACATGAGTTATGAGTAAAACATATAATTATAAAGTTTTGAAC
ATGAGTTATGAGTAAAAACATATCATTATAAAGTTTTGAGAGCATCTATG
AGTAAAAACAGACTAAATTAAATAGAACATATATATGGACAATATAGCAA
GTAAAATCTCTCGGACTGACGAAATAGATGTAACTATACTACCAATGCTT
GCGATTCAAACCGTCAAAAGTGAAAAATACTGTGAAATAACAAGTCAACT
TCTATAAATGAAAATTAATATATATTGTAGACGGTTTATATATACGTTTG
GATCATATCGATTCACTAATAAAAAAGTAACAAGTGTTATTCCACAAGTT
GCATTTTTCATTTGTCTATAAGAACTTTATTGATCTTAAATAACGTTTAT
GCTTTTTCTTACACATATATGGAACCGAATTCAACAAAAACTTTCAAATA
GATTTGTTTTATATGAACACAATTATGTATATTGATTGTCCATTTATGAA
GAAAAGAATAATCTTATGCTTCACACCGTTGACAAAAAAAGATAAACGTA
TGTCATTAACCCTCTCTTTTTCTGGTACATGTCAGAGCAAAGAAAATTTA
CTAAAAGGTTATTTTGTTTTTCCTTGTTTGTCTATAAATCTACTGAAAGC
TTTAAATGCAATTTTATTATTTTCAAGAATCGGTCTTTTTACACTTCCGC
GATACTAGCTAAAGGAATGTACACGTGTCAGGATATTATTGTAGCATCTG
ATTTTTACCATTGATGGTAACTAAAGTTAGTAACAGAACCATCAGGTCCA
TCACCGTAAAATATGACTAGCACAGTAGCACCTTTACCAGAAAATAACGC
CGTTAGCTGTTTTCATCAAGTCAACAACAACCATTTTAACGGCAGTTTAG
ATATATTTTAATTTTTTTTAACCATATATCATTGGAAGTAAAAAGTTGTC
ATACTAAAATATATATCTTTTAAGATCTCAAGGTAATTAAAAAAATAATC
AAAGACGCTTAAAATCTGAAATTTTCAATAAAGTAATCATAAATTATTTT
ATGATTTAAATTTAGGTTTATCATAATAATCTTGAAAGAAATTAAATAAT
ATAATAGTTTTAAGGAAATCTATTTATTTGTTTTTTGATAAATTACATAT
CTATAGTAAATTAATGATATTGAATGGTGTAGTTGGTTTCTCATAGGTAG
AATTAAGACTTTCTCTTTTGTATTAATAAAATTTTATTTGACAACAAACA
GAAGAAACCTTTTAATAAATTGAGAGAGATATACTATAGGACATGATATG
ACAAAACTGTCCTACTCAGTGAACTTCACTAACAGAGCTCAAATTTGAAA
TCTCAATGAATTAATATTTAATGACATAACAAGTCAAAGTGATGATATTA
AATCTTTCCTCCTTGACAAGACGATAATACTTCAATTAACAAAAAAAAAA
AAAAAAAGAGATGATAATTTTTCCAGAATAAAATATTTTCGACTTGGACT
GGGAATAAAAAAAATGGGGTGACCTAAACCGACGTCGCATAGTTACGAGA
GGCATATAAATAGAGAGCCACCAAATAGCCTAACGTAGTCCACCTTCACT
TGCTCTCTTTTTTCCGAAGAATCTGGTTCGTTTCTCTTTGAATTATCTCT
TTCTCTGTTCTTCTTCTTTTTCTAAAGTCTCGAATATATCTTCATTATCA
TTACTTTATTTGCTTCGTTCTTCCGCAGTTTTGTGCAAAGTTTTAACGAT
TTTTTGGTTTTGAACGAAGGCACAGAGAGAAGATGGCGAGTGGCCTCGAG
GATATCGTGAACGAGAATGTTGATTTGGTATGGATTTCTTCTTTTTACTC
TGTATATATTTTTTTGTTTCGTTTGTTTAACTTGTTTAATGAATATACGA
GAGGAAAGTTTAGTTTGGTTTTGTTTTTTACTTAACGATTCGATCAAATT
AGGGTTGTACACAAATCTCGTTACATCATCGTTGAACTATTGACTTCATG
TTTTAGCATGAGATTTTTATTGTTTGATTTCGATGAGAAAAGAATCCATG
AAAAAGTGTTAATATTATCATAATTATTTCAGTTTTTCTGCTTTTTTTTC
AAAATTACTTTTTCTTTATTTATTTTTTTATTAGATTTTGCAACTGCACT
AATTTAAAACAATTTGCAGTCACCAGAAATTTAGTTACAATTATGTAAAA
GTTGTTTCCAAATAAAGCAAAAGTAATTACATTAGTAGTACTCTCTACTT
TCACATGATCTATCTTAATGAGTATACTTTGAGATTTCTTAGAGAAGTTT
TAGTCAATTCTGTTTTCAATTACTACGTTTTTGGATTTTTCATACTCATG
GAATATCGCCTTATCAATCGGTTAATCACTTCCCTAGATAAAACTAAACT
TCAATCTTCACCTGATTTTCTGGACTCAATTTAAGATACCATGTTATATA
GACAGATTTGCCCCTATCAATACATCTTCCGTTACAATGGGCCTTATTGG
GCCTTTAGGCTTATTATATAAGCGAATTAAAGTACAAGGCCTTGTGGTCC
CACCTTAGATTCTCTGACATCGACAGCTACAGAACATTCCATAATTTTGG
TCATCTAATATTTTTATGCTTTGATAAATAATTATAATCTTGATTATCTA
TTAATTTGCATGCTTATATTTTTTTCTTTTTTTTTGCTTTTTTTAGTACT
GTAAAAGGTTAACATTTGTATCTGTAAAAAAGATGTACTACAGATAAAAA
CATACTTGGTTGTTTATTGGTGTAGGAGATACATAATTATTGAACACCAT
TTGAATTAGTCTAACATCGTGTTCATATTATATTGCAGGAGAAAATACCT
ATTGAGGAAGTGTTCCAGCAGTTGAAATGCAGCAGAGAAGGTTTATCTGG
AGCAGAAGGAGAAAACAGACTCCAGATCTTTGGCCCCAACAAACTCGAGG
AGAAGAAGGTATAGTTTGGTTTTAACCATTATCAAAGTCATCATACATGA
GCTAAGTCACTAACTATGTAATGGTGGTTTCAATAAATAGGAAAGCAAGT
TACTCAAGTTCTTGGGTTTTATGTGGAACCCTCTCTCTTGGGTCATGGAA
GCAGCTGCAATCATGGCTATTGCCTTGGCTAATGGCGGTGGAAAGCCACC
GGATTGGCAAGATTTTGTCGGTATCGTTTGTCTTTTGGTTATCAATTCAA
CTATCAGTTTTGTCGAAGAAAACAATGCTGGAAATGCTGCTGCTGCTCTT
ATGGCTGGTCTTGCTCCCAAAACTAAGGTCCCTCTTTATAAACTCCCTTC
AAATACTCCTCTTTGCATTAGCATTTACGTGTATGTTTACTGTATACTTG
GCATACGAATTACGCGAGTTTAACTATGTTACATAATTAGATTCTTAGCA
CCTAGTAGTTGTCTAACTTGAAAATGTTTGGCATAAGTAATTGGTTTACA
TATAATTTCATTACAAGCTTTTAATAATATTTGTTTTGTTATGACCAGGT
TCTAAGAGATGGCAAATGGTCAGAGCAAGAAGCTTCTATTCTTGTTCCTG
GAGATATTGTGAGCATCAAGCTTGGTGACATCATTCCTGCTGATGCACGT
CTTCTTGAAGGTGATCCTTTAAAAGTCGACCAATCTGCTTTGACCGGAGA
ATCTCTTCCCGCAACGAAAGGTCCAGGGGAAGAAGTTTTCTCCGGTTCTA
CCTGCAAGCAAGGTGAGATTGAAGCGGTTGTGATAGCCACTGGAGTCCAT
ACTTTCTTCGGTAAAGCGGCTCATCTAGTCGACAGCACAAACCAAGTTGG
ACATTTCCAGAAAGTTCTTACGGCGATTGGAAACTTCTGCATATGTTCCA
TAGCTGTTGGTATTGCGATTGAGATCGTTGTCATGTATCCGATCCAGCGC
AGACACTACAGAGACGGAATCGACAATCTTCTTGTTCTTTTGATTGGTGG
TATCCCCATTGCAATGCCTACTGTCTTGTCTGTCACAATGGCTATTGGAT
CTCACAAGTTGTCTCAACAAGGAGCTATCACAAAACGAATGACCGCCATT
GAAGAAATGGCTGGTATGGATGTTCTGTGCAGCGATAAAACCGGGACTCT
CACGCTAAACAAGCTTAGTGTTGACAAGAATCTTATTGAGGTTTATTGTA
AAGGCGTTGAGAAAGATGAAGTTTTGCTTTTTGCTGCTAGAGCTTCAAGA
GTTGAGAACCAAGATGCTATTGATGCTGCTATGGTTGGAATGCTCGCTGA
TCCAAAAGAGGTAATATATATAACTCTGTTTTTTCCTCTGTTTTAAAATT
CTGTTTTTTCCTCTGTTTTGTTTCTTGAAGAAAATGTTCTGTTCTGTTTC
TCATTGTTTGTTTCTTTCAGGCAAGAGCTGGAATCAGAGAGATTCACTTC
CTACCATTCAATCCAGTTGATAAGCGAACCGCTTTGACGTTTATCGACAG
CAACGGAAACTGGCACCGAGTAAGCAAAGGAGCTCCCGAGCAGGTAACTA
AAACTGATTTTGGTTCTTAAGCTAAGTTAAGTGTTGTGACTTCTTAAAAA
AACTGATTCTTTGATGATTTCAGATTCTTGATCTCTGTAACGCGAGAGCT
GATCTGAGGAAGAGAGTCCACTCTACAATCGATAAGTACGCTGAGCGTGG
ACTTAGGTCATTAGCTGTTTCAAGACAGGTGAGAAGAAATCTTACATTTT
GTAACAAGTTATAGGAAGAAGGAAAAAGAGAGAGAGAGTTTAATGTAAAT
TTTGTGTGTCTATGTTTCAGACTGTACCAGAGAAAACAAAAGAAAGCTCT
GGTAGTCCATGGGAATTTGTTGGTGTGTTGCCTCTGTTTGATCCTCCAAG
ACATGATAGTGCCGAAACCATTAGAAGAGCTCTAGACCTCGGTGTCAATG
TCAAGATGATTACTGGTTTATATCTAAACATTACTCTTCGCTATAGCGAA
AACACCGAATTTCTTACTAATGTTTCCAATGGTTTTATAGGTGATCAACT
TGCTATTGCGAAAGAGACAGGACGTAGACTTGGAATGGGATCAAACATGT
ACCCATCCTCTTCTTTACTCGGTAAACACAAAGACGAAGCCATGGCTCAC
ATTCCTGTTGAGGATTTGATTGAGAAAGCTGATGGCTTTGCTGGAGTCTT
CCCAGGTTTGTTTAAGAGCCATTTTTGTTTCCACAAACACAAACTTGCTC
TTCTCTCTGTAACATTTGGTCTCTTTTTTTTCTTTACCAAATTCATTCAG
AGCACAAATACGAAATTGTGAAGAAGTTGCAAGAAAGGAAGCATATCTGT
GGTATGACTGGAGATGGAGTGAATGACGCTCCAGCATTGAAGAAAGCGGA
TATAGGTATCGCTGTGGCGGATGCAACTGACGCTGCACGAGGTGCTTCTG
ATATTGTCCTCACCGAGCCAGGTCTCAGTGTGATCATCAGCGCGGTTCTA
ACCAGTAGAGCCATCTTCCAGAGAATGAAGAACTACACAGTGAGTGTTCT
CTTAATCTTAAACCATAACCTTTTTAGAATCTTTACACCATGATAACTTG
TTCTCATGGTGTTTTTAAATGTTCCTTTAAACAGATATATGCAGTCTCAA
TTACCATTCGTATAGTGGTAAGTAATCAATCTTGTATGTATTCTTGAATA
TCATCAAATAATCTCTTTTTCTATATGATTTCTCACTTTGTGCCTTTTCA
CAGTTTGGGTTTATGCTCATTGCTCTAATATGGAAGTTCGACTTTTCACC
ATTCATGGTTTTGATCATTGCTATATTAAACGATGGTGAGTTTTTTTCTT
CTCTTTAAAAGCTCTCTCTAAATTTTGGCTCTAATCGACTAACACATCAT
TAACTTACGCAACAGGAACCATCATGACTATCTCAAAGGACAGAGTCAAG
CCTTCTCCAACACCAGATAGCTGGAAACTCAAAGAAATCTTCGCAACCGG
CGTTGTTCTTGGAGGCTACATGGCTATAATGACTGTTGTTTTCTTCTGGG
CCGCATACAAAACCGATTTCTTCCCGGTATGTAACATATAAACAACCTCT
CTTTAGATTCCTTGTCACACAAGCATTAACTTTGTTTGTTTCCTATAGAG
AACATTCCACGTGAGAGACTTGAGAGGCAGTGAACATGAGATGATGTCTG
CTTTATACTTACAAGTCAGTATTGTGAGCCAAGCTCTTATATTCGTCACT
CGATCTAGAAGCTGGTCTTTTACAGAACGACCTGGATATTTCTTGCTAAT
TGCTTTCTGGGTAGCACAATTGGTAAGCATTGTATCTTCTTGATTGATTA
TAAACTCTCTTGAATGATTGATTCATAAACTTTGACCTTGTAGATTGCAA
CGGCTATTGCGGTTTACGGTAATTGGGAATTTGCAAGAATCAAAGGAATA
GGATGGGGATGGGCTGGAGTAATCTGGCTTTACAGTATTGTCTTCTACTT
TCCATTAGACATAATGAAATTCGCAATCCGTTACATACTAGCCGGAACAG
CCTGGAAGAATATCATTGACAACAGGGTACGTTTTGCTTTCTTCTTAGTT
CTTCTTCTGAAATGTGATTTTAAGACTTAAACAAAATCTCTCTGTGTCTT
TGAAAAAACAGACTGCGTTTACCACTAAGCAAAACTATGGAATAGAGGAG
AGGGAAGCACAATGGGCTCATGCACAAAGGACTTTACACGGTCTTCAGAA
CACTGAAACAGCCAACGTTGTCCCGGAGAGAGGTGGTTACAGAGAACTGT
CTGAGATTGCAAATCAAGCCAAGAGACGAGCTGAGATCGCAAGGTAAATG
ATTTGTAAAAAGTAATTTCGGTTTCTTGTGAGAGAAGTTAACGTTAGGGT
TTTTGTTTACAGGCTTAGGGAACTTCATACGCTTAAAGGACATGTAGAGT
CAGTGGTGAAGCTAAAGGGACTAGACATTGAGACAGCTGGTCACTACACC
GTTTAATAAAGATTTAACAAGAAGATGATTAAGGAAGAAGAAGATCCTTT
TGTTTAAGAGATGATAATGATGATGATTTTATAACAAGAGAATAAGGTTT
TTTTTCTGTGTATGTTAAGTTCCTCTAAACTCCTGGGGTTTTTCTTCCTT
CCTTATTCATGGTTTTAGACTTTAATTATAACCATGTGTTTTTGTTTCCC
CTCTCTTGAATAAAAAAGAGAAGATACTAATATCATAGGTTTAATACGTT
TATGTTTTATAAAAGTTCAATAGATATTGTTTTTGGATATTATGTGAACA
TAACAATATTTATAAATTCACCTTTCAATTTTCTTATGAGATGATATCAT
CTTTACTACTTAAAATATCTTCTAATTAAACCAAAAGCAGATTTAGGTCC
GGTTAGATGAATAACCGGTTCGATTAATTTCGTCAGACCGATTTGATCCG
TGGATATCATTAATCCGTGGAATACATGTGTGTTCTTGAGTAGGCCACTA
GTTATAATCCACGTGGCAAGCATTTTATCACAAACCCAGAGCTACAAAAA
CAAAACCAAGAAGACGAGAAGGATCTTTAACAGAGAAAAAAGAGCTTTAG
ACCAAATCACCAGAAACAAAACAAAAATGTATTTCGCCGCCATAGCTTCT
TCACGACAAAGCTTTTTGTCAAACAATTTCAGTTTCCAACACAGTTTTAA
ACCCAAATCCAATGTTAACCTCACTCGTCCTAATTCAATCTGTTGTAAAT
CTTCACACCACGACGACGAAACTGATTCTTCTCGGTAATTTTTATTTACC
TTTAGAAAATTTTTTTCCGATTCTAAACTCGGGTTTGGTCTTATTCAATC
TTTTATTTATCTATTGATTAGGAAAAATGAAAATCAGCTGGCGAAGTTGG
CAATCGCGACGCTAGCGGTTGGCGTTTTGGCTTATTAAGGAAGAAGAAGA
TCCTTTTGTTTAAGAGATGATAATGATGATGATTTTATAACAAGAGAATA
AGGTTTTTTTTCTGTGTATGTTAAGTTCCTCTAAACTCCTGGGGTTTTTC
TTCCTTCCTTATTCATGGTTTTAGACTTTAATTATAACCATGTGTTTTTG
TTTCCCCTCTCTTGAATAAAAAAGAGAAGATACTAATATCATAGGTTTAA
TACGTTTATGTTTTATAAAAGTTCAATAGATATTGTTTTTGGATATTATG
TGAACATAACAATATTTATAAATTCACCTTTCAATTTTCTTATGAGATGA
TATCATCTTTACTACTTAAAATATCTTCTAATTAAACCAAAAGCAGATTT
AGGTCCGGTTAGATGAATAACCGGTTCGATTAATTTCGTCAGACCGATTT
GATCCGTGGATATCATTAATCCGTGGAATACATGTGTGTTCTTGAGTAGG
CCACTAGTTATAATCCACGTGGCAAGCATTTTATCACAAACCCAGAGCTA
CAAAAACAAAACCAAGAAGACGAGAAGGATCTTTAACAGAGAAAAAAGAG
CTTTAGACCAAATCACCAGAAACAAAACAAAAATGTATTTCGCCGCCATA
GCTTCTTCACGACAAAGCTTTTTGTCAAACAATTTCAGTTTCCAACACAG
TTTTAAACCCAAATCCAATGTTAACCTCACTCGTCCTAATTCAATCTGTT
GTAAATCTTCACACCACGACGACGAAACTGATTCTTCTCGGTAATTTTTA
TTTACCTTTAGAAAATTTTTTTCCGATTCTAAACTCGGGTTTGGTCTTAT
TCAATCTTTTATTTATCTATTGATTAGGAAAAATGAAAATCAGCTGGCGA
AGTTGGCAATCGCGACGCTAGCGGTTGGCGTTTTGGCTTTGGGAAGTGTT
GGGGATGCGTTTGCGGCCAAAAGCGGTGGAAGAATCGGCGGTCAAGCGTT
TCGGTCTTCAGCTCCTCGTCCTCCTCCCAGAATTAACAATCGATCAAGGT
AAAATTTTTTACTTGAAGCTCTAATCTCGATTTTAATTATTTAATATGTA
TATGATTAAAATACTGGCGAAAAAAGTATATATTTAAATTAAGACCTTAA
TTGAGATTTCTTACAAGAGACTCCATGTATGGGCTTTTAGCAGCCTCATA
TCCACATTAAAGCCCATTAGTAAACTTTAAGCCTCTTATAATTTTCTATT
ACACTTTATATTTTGAACCCCATAATTACAATTCGAATCCAAGATACCCC
AACGACCAACACTAATAACTTGATTCAATGCATTAGGCTTTTCTGTTTGC
ATTATATAATCACGACTTTAGTCTTAGTAGTTAGTACCTTTGCATTCTAA
ACGCAGCTTTGTTTTCGCAGGACCAACATCTACGTGAATCCTCAGGTTGC
ACCACCTTTGATCGGTGGCTATGGATATGGTTACGGAGGTTACGGATGGT
CACCGTTTTCCTTTTTTGCCCCTGGTCCTGCGGTGGCAGTAGGTGTTGGC
GGTGGCTTTGACCTCCTACTTCTCTTCATGTTTTTTGGAGCCGCTTCAGC
CGTCGCTAGAAACTTTTTCCGATCAAGAAATGATGAAGATGACGAAGACG
ACTATTAGAGGAGAAAACGGAGAGAGGCTTATGTAACAATAGTCATACAT
ACGATTTTGTGTAAAAAAATATGATGGAAGAAGACGGATATATGTGGAAA
TCTTGAAATAAGTAACTAAAGACCCATCTTAAAGTTAATAGAGGCAATTT
GAAAACACCTCCAAATACTAAATTTATATACAAATTTTCTCTGTTTTTCC
TTCATTCTTTATATTTTAGGTTCTAGTGTATGACCTCATTGGTCTCCGAA
AGCAAGTGAAAATAAATTCTTTAAGCAACCAAATATAAAGAAAACATTGG
TATATTTTGTCAATGGTTTATCAGTGTTAACGAAGAAGAATAATTAGACC
TAGCTAAAAGTGAAATCAGTAAATCTCGTAAATAATAATAACGATAAATC
AGATACAAAAAGAAAATAAAAAAATCAAGAAGAAGACGAAGAAGAAAAAA
GAAAGAGTCAGTGAATTAACAAAAATCAAGAAGAGGTTCGGTTAATACTA
AGTCCTTGAAAGAGCCAATGAGGTCTCTTCTTCTCTCGATCCAACGACGT
CGTACTTGAGCTGCTCATAGGCGTGTTTGGTCCGCTACTTTCTTGGTTAT
TATTGCTGTTATTATATAGATTATTATTGCTCTGATTATTACAATTATCC
GATGATGAT...

• The analysis of the DNA sequence of genes and
  genomic regions reveals evolutionary
  relationships, and can be used to (amongst a
  gazillion other things), to...
• assign function to DNA that codes for peptides,
• at the physiological level (i.e medical in
  Humans),
• at the protein structure level.

3
(No Transcript)
4
The Problem(s)
Big Problem Cardiovascular Disease 40.1 of
deaths in 1999 (USA)
Genomic Challenges besides working with a huge
genome

• recognizing genes in the genome,
• Exons/Introns,
• Alternative Splicing/Termination,
• Alternate transcription start/stop sites,
• Tandem Repeats, Psuedogenes, etc.
• We dont really understand all there is to know
  about gene structure,
• etc.

• determining the function of the gene,
• no known homologies,
• gene families,
• etc.

quantitative loci
5
Cardiovascular Disease
Nature 407, pp. 234
6
Lipidsmajor players in heart disease.

• Triglycerides,
• most common fat in the body, energy storage
  molecule,
• found in fat cells, blood plasma, and cell
  membranes,
• derived from eaten fats or made from other energy
  sources.

• Cholesterol,
• a steroid alcohol (sterol) used to insulate
  nerves, produce human sex hormones and as a
  component in cell membranes,
• produced by the body and supplied by diet.

7
Lipoproteinsand classes.
8
Chromosome 11 (H.s.)

• Several apolipoproteins map to a region of
  chromosome 11, including two APOA genes,
• There is a polymorphism that is linked with high
  serum triglyceride levels that maps to the same
  region.

9
Hypertriglyceridemia Why bad?

• high levels have been linked with coronary
  artery disease,

• American Health Association Recommendation
• Changes in lifestyle habits are the main therapy
  for hypertriglyceridemia
• If you're overweight, cut down on calories to
  reach your ideal body weight.
• Reduce the saturated fat and cholesterol content
  of your diet. 
• Reduce your intake of alcohol considerably.
• Be physically active for at least 30 minutes on
  most days each week. 
• Substitute monounsaturated and polyunsaturated
  fats  
• Substitute fish high in omega-3 fatty acids
  instead of meats that are high in saturated fat.

10
A Solutionto finding genes.

• Mouse Genome
• 2.75 Gb,
• 19 autosomes X and Y chromosomes,
• 99 per cent of the mouse genes have a sequence
  match in the human genome,
• 96 lie within 'syntenic' regions of mouse and
  human chromosomes.

Nature 420, 515 - 516
11
Conserved Synteny
Description of DNA segments in which gene order
is identical between species.
12
The SolutionComparative Genomics
High homology, no annotation.
How did they know the region was expressed? - not
including the Northerns.
13
New Gene Structure?
Mouse 1107 Open Reading Frame (ORF), 368
AA, Human similar structure, 366 AA,

• Most similar to each other (71 identity, 78
  similarity),
• Next most similar to APOAIV (27, 48)

14
The Solutionto determining function (I, II).
movie

• I. Transgenic Mice
• - DNA is integrated in a random fashion
• by injecting it into the pronucleus of a
• fertilized ovum,

• II. Knock-Out Mice
• - DNA is introduced first into embryonic
• stem (ES) cells. ES cells that have
• undergone homologous recombination are
• identified and injected into a 4 day old mouse
• embryo - a blastocyst.

15
Pronucleus either of the 2 haploid gamete nuclei
just prior to their fusion in the fertilized
ovum.
Transgenic Mice Pronuclear Injection
16
Fig. 2
H.s. APOAV probe
17
APOAV Transgenic Miceoverexpressors

• n48 (transgenics), n46 (controls), P lt 0.0001

18
Typical KO vectorand homologous recombination.
tkthymidine kinase gancyclovir lethal
19
KO Mice w/ Embryonic Stem Cells
20
Transformed ES cells are injected into blastocysts
21
Chimeric mouse
Black/White Chimeric Example
Cross and look for offspring with germ-line
transfection.
22
(No Transcript)
23
Ref. 25
Fig. 2
24
APOAV KO Miceunderexpressors
n13 (wt), n22 (hets), n 10 (homozygous mut.)
P lt 0.001
Fig. 3
25
Murine Models are Goodbut what about us?

• Identified 4 SNPs in and near the human APOAV
  locus (each occurs at gt8),

• Surveyed 500 Caucasians for numerous lipid
  parameters before and after high- and low-fat
  diets,

Fig. 1A
26
1,1 homozygous for major allele
1,2 heterozygous for major allele

• Individuals heterozygous for the minor alleles at
  SNPs 1-3 had significantly higher triglyceride
  levels and VLDL mass.
• SNP4 does not show a significant difference in
  triglyceride levels or VLDL mass.

27
Linkage disequilibrium When the observed
frequencies of haplotypes in a population does
not agree with haplotype frequencies predicted by
multiplying together the frequency of individual
genetic markers in each haplotype, English
Translation The co-occurrence of genetic markers
more often than would be expected.
SNP1, SNP2, SNP3 have significant
disequilibrium with each other while SNP4 is not
in linkage disequilibrium with any other
SNP, English Translation this genetic region
containing SNP1-3 segregates as a unit.
28
Independent Association Study

• Data from an independent set of individuals
  demonstrating that subjects with minor alleles at
  SNP3 are significantly more likely to have high
  triglyceride levels than low.

29
Summary

• SNP data shows that APOAV plays a significant
  role in plasma triglyceride and VLDL homeostasis.
• Polymorphisms of APOAV could be used as
  prognostic indicators for hypertriglyceridemia.
• Modulation of APOAV is a potential strategy for
  reducing risk of cardiovascular disease.

• Comparative Genomics uncovered a new gene in the
  human genome.
• Mouse transgenic and KO experiments suggest that
  the protein contributes to triglyceride and VLDL
  levels.

30
APOAV Update
APOAV
31
Weds.

• Genome scale KO experiment.