What is DNA?
A
G
C
T
type of molecule
every cell of every living thing
polymer
nbc, gwryieodr ltame h,hr s, nerof tahgnaiodr
ptnenfnnntdphe leesunF tet ccna
bed orda ahrieatrtospoooaataa
ccietsonuuel iaotnshveo t eyrn
tcr q ieuodore ivt stdneuio aL .e i,
Four score and seven years ago our
fathers brought forth, upon this continent, a new
nation, conceived in Liberty, and
dedicated to the proposition that all
men are created equal.
ACCCTCTTCAGAGCTGCACTAGACATTCACAGGGAATTGAGGTTCCCTATGCAGAAAGGTTTTCAGACAGAGGACCCAGCCCATTTTCTCTCTCCAAATCCTCCTCCCTCCCTCTTTTGTGGTTGCAGCTATAAAATAATGATTCAACAATCAAAGAGCCTCTCATGAGATGGGAGAAGGAAGGGAACGAAAGGGGAAGAGGTGCCCTGGGCTGAAAACCTGTAGATTTTTTCTAAGTGACAAAGGGCAAGGGTCCTTTTTTGAAATTAGGAGAGAGACAGCTGTTTCCTCAATCGAAACTTCGCACATTACAACCAGCCTTGGGAAAAGCCAACACCACCAGGGAGGAAGTGCTATGGGGTTTTGAAGCCAGACACTGATTTCTGGCTGTAATACTTTCCAGCCGTGTCTCTAAGCCTCGGCTTCTGCCTCCATCTGTAGAGTGGGCTTAATAATTTTGACCATCTCACAGAGTTGATGTGAAAATTAAAATAACCCGAACAGAACAGGCGATATATACAGGAATTAATGAAAGATTCCTGACATAATGCTTATAAGTTCATGATGCTTAGGAAGATAAAATTCATTGTAGAGATGCCGAACGGGGGTCTAGAGCTTGCCTTTTCGGGGTCTCTCCCGTCCTTCTCCATCCTCCTTATCTCCTGGGCTGCCCCCTCTCCCCCCGCGCCCCGCTCTCCCTGGCTCGCCCGGGCCTAGGGCGCCGCCTGCAGTTGCGCGCGGCCGCCTCTAGATGGAACTTTCTCACCAACGCAAGGCCCGGCCGGAGCAGCTACCCGGGAGCTGGGCGGCGAGGGGCTACTTTCTCTCATTCCGGCGGGTGCAGGATCGGGGGGCCTGGGCAGTAACTAGTGGGGAGGAGCGCTGGACTGTGCACGTCGAGCCCGGCAGGTTTCCGCATGCGGCATGCGAAGGGAATCCCGAGGTTTCCCTGCAGAACCCGAGCACGGCTCCCCCGGAGTTTCCTGCCCCGCGTCTGCGGCTCCTTGAATCATCTCAATAAAATGACCGTCCCGGTAGCCACCCATGCCCCTTCCTGCGCAGTGCCCGCAGCGGACCGCGCTGTGTGGTACCTCGAGCCCTGGGGACTCTGTTGCACGCGTCCCTCAGACCCTCGGGGGCGGGGAGTGGGGAGACAATCGCCAGAGCCGCGGGGCGGGACAAATGGCGGAACCGCCGCGCGGCGCCAGGCAAACTTTGCAAGGGAACCGCGCGGCTTGCCGGCTCTACTTTAAGCATTCCCGAAAAGAAAGCATGTGGCGGGACACTTGTCATCTACCATGTGTTATTCTCGGTGACGCTTTCTGGAGCTGTGTTCACCGGGGACCCGGGCTCGCGGGTGCTGCCCGCTGTGCTCGGGCGGGCGTCGCGCCTCCCCGCGCCGGTCCCGGGCTCGCCAGGCAGCCGGAGCCGCTGGGCTCCTCCACAACCATATTCCTTCTTCTACCGCTCCCGCTTCTTCCCACCCTCTCACTCTGTAGTTGGGTCCTCCCCTTTTTCTTGGGGGCGGGGAAGGGGGGATGATTTTTAAAAATCAGAACTATTGACATTTCTGGTCTCCTCGTCGCTTCAGGCTGAAGAGCGGAGGGGGATCCGCGGGCCGAGGGTCCCCCTCCCTGCCCGCGCCAGGGCCGCTGGGTGACACCGAAATCCAGAGGCTCCCGCCCCTCGGGGGTTCCTCCTCCCGCTTCCCGAGGTGACTGGTTGGCGCGAAGCGATTGGCGATCCCGGGCGCGATCCTGGCCGCGGCTCCCCGCGCCGCGCCGGGTGAATGGCCGCGGGCGGAGGATCGGGAGGGCCCGGGCGCAGACCAATCGCGGCCGCCGGTGGGAGTATTTGTTATTCACATGGAAGAGACTTGGCGCCTGCTAGGCCAGCTCAGCCCCCTCAGCCCAGAGATCAGCCACAAGTGCGGCCGCTGTGCTCGCCTCACGCGGCGGCGGCGGCGGCGGCGGCGGCGCTGACATGGAGCTGCGGGCCCCCGGCGGGCTTCCTCACCGCGCCCTCTGCGGGGAGCAGGGTAAGACTCGCCGCCCGGCAGCAGAAAGCGGCTCCGAGGAAAGCAAGTGCCGAACCACGGGACAAAAAGCCCCTGGCCCCCAAACTTCCCCAAAACGCCCTGCTTGTTGGAAAAGGAGAATCCCCCCGTTTTATTCCCCTTTCCGTTTTCTTCTCTAAAACCTTTCAGCGGACAGCCAGGTGCACCATTCCTTCTCATATCACTCTAGTGATTTGTTTTTCCTGAGCACAAGTAGATGGCCCTGCATGTCCGTAGTCTGTGAGAGAAATAGCGGGCGGAGGTGACGGGAATGGGGGGAGAAGGAGAGTGGGCACCAGGGGGCGAGGGGCTGGCCGGGCATTGGAGCTTGATTGGGTGTCTGTTGATTTTACGTTGCAAAGAACAAGGCAGCCACCCCTCTTGTCTGCCCATGATTACATTACAGTAAAGAGGTTCAGAAAAGAGGGAGACTTTACCCGGAACTCCCAAGGCTTGGAGATGTGATCCCCCAAAAGTTTAGTCGGCGAATGGGAGACTGAAGGGTGACGGGAAGGGGGCAGGCGCGCTCGGCGCTCTGACTGGGCGTGCGGCGGCAGGATTTTAAAGCGCTCTGCCTCGGATCGTCTGCCCTGGGTGACCTCCCGGACCTGCCCTGGTGGAATCCGGACTTG
ACCCTCTTCAGAGCTGCACTAGACATTCACAGGGAATTGAGGTTCCCTATGCAGAAAGGTTTTCAGACAGAGGACCCAGCCCATTTTCTCTCTCCAAATCCTCCTCCCTCCCTCTTTTGTGGTTGCAGCTATAAAATAATGATTCAACAATCAAAGAGCCTCTCATGAGATGGGAGAAGGAAGGGAACGAAAGGGGAAGAGGTGCCCTGGGCTGAAAACCTGTAGATTTTTTCTAAGTGACAAAGGGCAAGGGTCCTTTTTTGAAATTAGGAGAGAGACAGCTGTTTCCTCAATCGAAACTTCGCACATTACAACCAGCCTTGGGAAAAGCCAACACCACCAGGGAGGAAGTGCTATGGGGTTTTGAAGCCAGACACTGATTTCTGGCTGTAATACTTTCCAGCCGTGTCTCTAAGCCTCGGCTTCTGCCTCCATCTGTAGAGTGGGCTTAATAATTTTGACCATCTCACAGAGTTGATGTGAAAATTAAAATAACCCGAACAGAACAGGCGATATATACAGGAATTAATGAAAGATTCCTGACATAATGCTTATAAGTTCATGATGCTTAGGAAGATAAAATTCATTGTAGAGATGCCGAACGGGGGTCTAGAGCTTGCCTTTTCGGGGTCTCTCCCGTCCTTCTCCATCCTCCTTATCTCCTGGGCTGCCCCCTCTCCCCCCGCGCCCCGCTCTCCCTGGCTCGCCCGGGCCTAGGGCGCCGCCTGCAGTTGCGCGCGGCCGCCTCTAGATGGAACTTTCTCACCAACGCAAGGCCCGGCCGGAGCAGCTACCCGGGAGCTGGGCGGCGAGGGGCTACTTTCTCTCATTCCGGCGGGTGCAGGATCGGGGGGCCTGGGCAGTAACTAGTGGGGAGGAGCGCTGGACTGTGCACGTCGAGCCCGGCAGGTTTCCGCATGCGGCATGCGAAGGGAATCCCGAGGTTTCCCTGCAGAACCCGAGCACGGCTCCCCCGGAGTTTCCTGCCCCGCGTCTGCGGCTCCTTGAATCATCTCAATAAAATGACCGTCCCGGTAGCCACCCATGCCCCTTCCTGCGCAGTGCCCGCAGCGGACCGCGCTGTGTGGTACCTCGAGCCCTGGGGACTCTGTTGCACGCGTCCCTCAGACCCTCGGGGGCGGGGAGTGGGGAGACAATCGCCAGAGCCGCGGGGCGGGACAAATGGCGGAACCGCCGCGCGGCGCCAGGCAAACTTTGCAAGGGAACCGCGCGGCTTGCCGGCTCTACTTTAAGCATTCCCGAAAAGAAAGCATGTGGCGGGACACTTGTCATCTACCATGTGTTATTCTCGGTGACGCTTTCTGGAGCTGTGTTCACCGGGGACCCGGGCTCGCGGGTGCTGCCCGCTGTGCTCGGGCGGGCGTCGCGCCTCCCCGCGCCGGTCCCGGGCTCGCCAGGCAGCCGGAGCCGCTGGGCTCCTCCACAACCATATTCCTTCTTCTACCGCTCCCGCTTCTTCCCACCCTCTCACTCTGTAGTTGGGTCCTCCCCTTTTTCTTGGGGGCGGGGAAGGGGGGATGATTTTTAAAAATCAGAACTATTGACATTTCTGGTCTCCTCGTCGCTTCAGGCTGAAGAGCGGAGGGGGATCCGCGGGCCGAGGGTCCCCCTCCCTGCCCGCGCCAGGGCCGCTGGGTGACACCGAAATCCAGAGGCTCCCGCCCCTCGGGGGTTCCTCCTCCCGCTTCCCGAGGTGACTGGTTGGCGCGAAGCGATTGGCGATCCCGGGCGCGATCCTGGCCGCGGCTCCCCGCGCCGCGCCGGGTGAATGGCCGCGGGCGGAGGATCGGGAGGGCCCGGGCGCAGACCAATCGCGGCCGCCGGTGGGAGTATTTGTTATTCACATGGAAGAGACTTGGCGCCTGCTAGGCCAGCTCAGCCCCCTCAGCCCAGAGATCAGCCACAAGTGCGGCCGCTGTGCTCGCCTCACGCGGCGGCGGCGGCGGCGGCGGCGGCGCTGACATGGAGCTGCGGGCCCCCGGCGGGCTTCCTCACCGCGCCCTCTGCGGGGAGCAGGGTAAGACTCGCCGCCCGGCAGCAGAAAGCGGCTCCGAGGAAAGCAAGTGCCGAACCACGGGACAAAAAGCCCCTGGCCCCCAAACTTCCCCAAAACGCCCTGCTTGTTGGAAAAGGAGAATCCCCCCGTTTTATTCCCCTTTCCGTTTTCTTCTCTAAAACCTTTCAGCGGACAGCCAGGTGCACCATTCCTTCTCATATCACTCTAGTGATTTGTTTTTCCTGAGCACAAGTAGATGGCCCTGCATGTCCGTAGTCTGTGAGAGAAATAGCGGGCGGAGGTGACGGGAATGGGGGGAGAAGGAGAGTGGGCAC
How big is a genome?
Poliovirus 7 thousandHIV virus 10 thousand
E. coli 5 millionM. tuberculosis 4 million
Rice 400 millionMosquito 300 million
Chicken 1 billionMouse 3 billionHuman 3 billion
Opposum 4 billionToad 7 billion
How do we sequence genomes?
(1) Break the DNA in to manageable chunks
(2) Convert A, G, C & T 4 colorsand sequence one chunks at a time
3’-…GACTAGATACGAGCGTGA…-5’ [template]5’-…CTGAT [primer]
…CTGATC…CTGATCT…CTGATCTA…CTGATCTAT…CTGATCTATG…CTGATCTATGC…CTGATCTATGCT…CTGATCTATGCTC…CTGATCTATGCTCG
polymerasedNTPslabeled ddNTPs
3’-…GACTAGATACGAGCGTGA…-5’ [template]5’-…CTGAT [primer]
…CTGATC…CTGATCT…CTGATCTA…CTGATCTAT…CTGATCTATG…CTGATCTATGC…CTGATCTATGCT…CTGATCTATGCTC…CTGATCTATGCTCG
polymerasedNTPslabeled ddNTPs
(3) Assemble the chunks into a genome sequence
DNA sequencing technology
1996 1998 2001
100's 1,000's 1,000,000's
nucleotides sequenced per day
Year
H. influenzae(bacteria)
1995
S. cerevisiae (yeast)
19961998
C. elegans(worm)
D. melanogaster(fruit fly)
2000
M. musculus(mouse)
2001
H. sapiens(human)
2002
P. troglodytes (chimp)
2005
questions?
ACCCTCTTCAGAGCTGCACTAGACATTCACAGGGAATTGAGGTTCCCTATGCAGAAAGGTTTTCAGACAGAGGACCCAGCCCATTTTCTCTCTCCAAATCCTCCTCCCTCCCTCTTTTGTGGTTGCAGCTATAAAATAATGATTCAACAATCAAAGAGCCTCTCATGAGATGGGAGAAGGAAGGGAACGAAAGGGGAAGAGGTGCCCTGGGCTGAAAACCTGTAGATTTTTTCTAAGTGACAAAGGGCAAGGGTCCTTTTTTGAAATTAGGAGAGAGACAGCTGTTTCCTCAATCGAAACTTCGCACATTACAACCAGCCTTGGGAAAAGCCAACACCACCAGGGAGGAAGTGCTATGGGGTTTTGAAGCCAGACACTGATTTCTGGCTGTAATACTTTCCAGCCGTGTCTCTAAGCCTCGGCTTCTGCCTCCATCTGTAGAGTGGGCTTAATAATTTTGACCATCTCACAGAGTTGATGTGAAAATTAAAATAACCCGAACAGAACAGGCGATATATACAGGAATTAATGAAAGATTCCTGACATAATGCTTATAAGTTCATGATGCTTAGGAAGATAAAATTCATTGTAGAGATGCCGAACGGGGGTCTAGAGCTTGCCTTTTCGGGGTCTCTCCCGTCCTTCTCCATCCTCCTTATCTCCTGGGCTGCCCCCTCTCCCCCCGCGCCCCGCTCTCCCTGGCTCGCCCGGGCCTAGGGCGCCGCCTGCAGTTGCGCGCGGCCGCCTCTAGATGGAACTTTCTCACCAACGCAAGGCCCGGCCGGAGCAGCTACCCGGGAGCTGGGCGGCGAGGGGCTACTTTCTCTCATTCCGGCGGGTGCAGGATCGGGGGGCCTGGGCAGTAACTAGTGGGGAGGAGCGCTGGACTGTGCACGTCGAGCCCGGCAGGTTTCCGCATGCGGCATGCGAAGGGAATCCCGAGGTTTCCCTGCAGAACCCGAGCACGGCTCCCCCGGAGTTTCCTGCCCCGCGTCTGCGGCTCCTTGAATCATCTCAATAAAATGACCGTCCCGGTAGCCACCCATGCCCCTTCCTGCGCAGTGCCCGCAGCGGACCGCGCTGTGTGGTACCTCGAGCCCTGGGGACTCTGTTGCACGCGTCCCTCAGACCCTCGGGGGCGGGGAGTGGGGAGACAATCGCCAGAGCCGCGGGGCGGGACAAATGGCGGAACCGCCGCGCGGCGCCAGGCAAACTTTGCAAGGGAACCGCGCGGCTTGCCGGCTCTACTTTAAGCATTCCCGAAAAGAAAGCATGTGGCGGGACACTTGTCATCTACCATGTGTTATTCTCGGTGACGCTTTCTGGAGCTGTGTTCACCGGGGACCCGGGCTCGCGGGTGCTGCCCGCTGTGCTCGGGCGGGCGTCGCGCCTCCCCGCGCCGGTCCCGGGCTCGCCAGGCAGCCGGAGCCGCTGGGCTCCTCCACAACCATATTCCTTCTTCTACCGCTCCCGCTTCTTCCCACCCTCTCACTCTGTAGTTGGGTCCTCCCCTTTTTCTTGGGGGCGGGGAAGGGGGGATGATTTTTAAAAATCAGAACTATTGACATTTCTGGTCTCCTCGTCGCTTCAGGCTGAAGAGCGGAGGGGGATCCGCGGGCCGAGGGTCCCCCTCCCTGCCCGCGCCAGGGCCGCTGGGTGACACCGAAATCCAGAGGCTCCCGCCCCTCGGGGGTTCCTCCTCCCGCTTCCCGAGGTGACTGGTTGGCGCGAAGCGATTGGCGATCCCGGGCGCGATCCTGGCCGCGGCTCCCCGCGCCGCGCCGGGTGAATGGCCGCGGGCGGAGGATCGGGAGGCGCCGGGCGCAGACCAATCGCGGCCGCCGGTGGGAGTATTTGTTATTCACATGGAAGAGACTTGGCGCCTGCTAGGCCAGCTCAGCCCCCTCAGCCCAGAGATCAGCCACAAGTGCGGCCGCTGTGCTCGCCTCACGCGGCGGCGGCGGCGGCGGCGGCGGCGCTGACATGGAGCTGCGGGCCCCCGGCGGGCTTCCTCACCGCGCCCTCTGCGGGGAGCAGGGTAAGACTCGCCGCCCGGCAGCAGAAAGCGGCTCCGAGGAAAGCAAGTGCCGAACCACGGGACAAAAAGCCCCTGGCCCCCAAACTTCCCCAAAACGCCCTGCTTGTTGGAAAAGGAGAATCCCCCCGTTTTATTCCCCTTTCCGTTTTCTTCTCTAAAACCTTTCAGCGGACAGCCAGGTGCACCATTCCTTCTCATATCACTCTAGTGATTTGTTTTTCCTGAGCACAAGTAGATGGCCCTGCATGTCCGTAGTCTGTGAGAGAAATAGCGGGCGGAGGTGACGGGAATGGGGGGAGAAGGAGAGTGGGCACCAGGGGGCGAGGGGCTGGCCGGGCATTGGAGCTTGATTGGGTGTCTGTTGATTTTACGTTGCAAAGAACAAGGCAGCCACCCCTCTTGTCTGCCCATGATTACATTACAGTAAAGAGGTTCAGAAAAGAGGGAGACTTTACCCGGAACTCCCAAGGCTTGGAGATGTGATCCCCCAAAAGTTTAGTCGGCGAATGGGAGACTGAAGGGTGACGGGAAGGGGGCAGGCGCGCTCGGCGCTCTGACTGGGCGTGCGGCGGCAGGATTTTAAAGCGCTCTGCCTCGGATCGTCTGCCCTGGGTGACCTCCCGGACCTGCCCTGGTGGAATCCGGACTTG
ACCCTCTTCAGAGCTGCACTAGACATTCACAGGGAATTGAGGTTCCCTATGCAGAAAGGTTTTCAGACAGAGGACCCAGCCCATTTTCTCTCTCCAAATCCTCCTCCCTCCCTCTTTTGTGGTTGCAGCTATAAAATAATGATTCAACAATCAAAGAGCCTCTCATGAGATGGGAGAAGGAAGGGAACGAAAGGGGAAGAGGTGCCCTGGGCTGAAAACCTGTAGATTTTTTCTAAGTGACAAAGGGCAAGGGTCCTTTTTTGAAATTAGGAGAGAGACAGCTGTTTCCTCAATCGAAACTTCGCACATTACAACCAGCCTTGGGAAAAGCCAACACCACCAGGGAGGAAGTGCTATGGGGTTTTGAAGCCAGACACTGATTTCTGGCTGTAATACTTTCCAGCCGTGTCTCTAAGCCTCGGCTTCTGCCTCCATCTGTAGAGTGGGCTTAATAATTTTGACCATCTCACAGAGTTGATGTGAAAATTAAAATAACCCGAACAGAACAGGCGATATATACAGGAATTAATGAAAGATTCCTGACATAATGCTTATAAGTTCATGATGCTTAGGAAGATAAAATTCATTGTAGAGATGCCGAACGGGGGTCTAGAGCTTGCCTTTTCGGGGTCTCTCCCGTCCTTCTCCATCCTCCTTATCTCCTGGGCTGCCCCCTCTCCCCCCGCGCCCCGCTCTCCCTGGCTCGCCCGGGCCTAGGGCGCCGCCTGCAGTTGCGCGCGGCCGCCTCTAGATGGAACTTTCTCACCAACGCAAGGCCCGGCCGGAGCAGCTACCCGGGAGCTGGGCGGCGAGGGGCTACTTTCTCTCATTCCGGCGGGTGCAGGATCGGGGGGCCTGGGCAGTAACTAGTGGGGAGGAGCGCTGGACTGTGCACGTCGAGCCCGGCAGGTTTCCGCATGCGGCATGCGAAGGGAATCCCGAGGTTTCCCCGCAGAACCCGAGCACGGCTCCCCCGGAGTTTCCTGCCCCGCGTCTGCGGCTCCTTGAATCATCTCAATAAAATGACCGTCCCGGTAGCCACCCATGCCCCTTCCTGCGCAGTGCCCGCAGCGGACCGCGCTGTGTGGTACCTCGAGCCCTGGGGACTCTGTTGCACGCGTCCCTCAGACCCTCGGGGGCGGGGAGTGGGGAGACAATCGCCAGAGCCGCGGGGCGGGACAAATGGCGGAACCGCCGCGCGGCGCCAGGCAAACTTTGCAAGGGAACCGCGCGGCTTGCCGGCTCTACTTTAAGCATTCCCGAAAAGAAAGCATGTGGCGGGACACTTGTCATCTACCATGTGTTATTCTCGGTGACGCTTTCTGGAGCTGTGTTCACCGGGGACCCGGGCTCGCGGGTGCTGCCCGCTGTGCTCGGGCGGGCGTCGCGCCTCCCCGCGCCGGTCCCGGGCTCGCCAGGCAGCCGGAGCCGCTGGGCTCCTCCACAACCATATTCCTTCTTCTACCGCTCCCGCTTCTTCCCACCCTCTCACTCTGTAGTTGGGTCCTCCCCTTTTTCTTGGGGGCGGGGAAGGGGGGATGATTTTTAAAAATCAGAACTATTGACATTTCTGGTCTCCTCGTCGCTTCAGGCTGAAGAGCGGAGGGGGATCCGCGGGCCGAGGGTCCCCCTCCCTGCCCGCGCCAGGGCCGCTGGGTGACACCGAAATCCAGAGGCTCCCGCCCCTCGGGGGTTCCTCCTCCCGCTTCCCGAGGTGACTGGTTGGCGCGAAGCGATTGGCGATCCCGGGCGCGATCCTGGCCGCGGCTCCCCGCGCCGCGCCGGGTGAATGGCCGCGGGCGGAGGATCGGGAGACGCCGGGCGCAGACCAATCGCGGCCGCCGGTGGGAGTATTTGTTATTCACATGGAAGAGACTTGGCGCCTGCTAGGCCAGCTCAGCCCCCTCAGCCCAGAGATCAGCCACAAGTGCGGCCGCTGTGCTCGCCTCACGCGGCGGCGGCGGCGGCGGCGGCGGCGCTGACATGGAGCTGCGGGCCCCCGGCGGGCTTCCTCACCGCGCCCTCTGCGGGGAGCAGGGTAAGACTCGCCGCCCGGCAGCAGAAAGCGGCTCCGAGGAAAGCAAGTGCCGAACCACGGGACAAAAAGCCCCTGGCCCCCAAACTTCCCCAAAACGCCCTGCTTGTTGGAAAAGGAGAATCCCCCCGTTTTATTCCCCTTTCCGTTTTCTTCTCTAAAACCTTTCAGCGGACAGCCAGGTGCACCATTCCTTCTCATATCACTCTAGTGATTTGTTTTTCCTGAGCACAAGTAGATGGCCCTGCATGTCCGTAGTCTGTGAGAGAAATAGCGGGCGGAGGTGACGGGAATGGGGGGAGAAGGAGAGTGGGCACCAGGGGGCGAGGGGCTGGCCGGGCATTGGAGCTTGATTGGGTGTCTGTTGATTTTACGTTGCAAAGAACAAGGCAGCCACCCCTCTTGTCTGCCCATGATTACATTACAGTAAAGAGGTTCAGAAAAGAGGGAGACTTTACCCGGAACTCCCAAGGCTTGGAGATGTGATCCCCCAAAAGTTTAGTCGGCGAATGGGAGACTGAAGGGTGACGGGAAGGGGGCAGGCGCGCTCGGCGCTCTGACTGGGCGTGCGGCGGCAGGATTTTAAAGCGCTCTGCCTCGGATCGTCTGCCCTGGGTGACCTCCCGGACCTGCCCTGGTGGAATCCGGACTTG
“Personal” genomes
James D. Watson (5/31/2007)
J. Craig Venter (8/4/2007) New York Times,
3/4/08
questions?
DNA sequencing technology
1996 1998 2001 2007
100's 1,000's 1,000,000's 1,000,000,000's
nucleotides sequenced per day
Year
Personal Genomes for Health Care
U.S. Health Care = $5,000 / person / year
$1,000 genome / 73 years = $13 / year
Can “personal genomes”:
(1) reduce health care costs?
(2) improve health care outcomes?
Case Study 1: Phenylketonuria (PKU) gene
“recessive”: 2 defective copies of gene disease
1 in 15,000 babies
Untreated MR, seizures
Treated normal development
Case Study 2: the BRCA1 gene
Early onset breast cancer
“dominant”: 1 copy affected
Increases risk to 75%
Treatment ? yearly mammograms ? ? radical mastectomy ?
MC King1990
Case Study 3: the APO-E gene
I don’t want to know!
0 copy low risk1 copies normal risk2 copies high risk
“E4” variant associated with Alzheimer’s disease
No goodtreatments!
PKU, BRCA1, APO-E, …
ABCG8, ABI2, ADAMTS9, ADARB1, AIM1, ANGPTL3, ANGPTL3, DOCK7, ATG4C, ASIP, ATG16L1, B3GALT4, BANK1, BCL11A, BCL7B, TBL2, MLXIPL, BFZB, BMP6, BRDG1, BRUNOL4, BSN, MST1, BTBD9, C12orf30, C8orf13, BLK, CACNA1C, CCDC60, CCL4L2, CCR6, CD226,
CDC123,CAMK1D, CDC91L1, CDH4, CDK6, CDKAL1, CDKN2A, CDKN2B, CDKN2A,CDKN2B, CDKN2B, CELSR2, CELSR2,PSRC1,
CELSR2,PSRC1,SORT1, CERKL, CFH, CHI3L1, CHRNA3, CHRNA3,CHRNA5, CHRNB4, CHRNA3,CHRNA5,CHRNB4, CILP2,
PBX4, CNTN5, COG6, COL1A2, COLIA1, CRP, CSF2RA, CST9L, CST9, CST3, CTBP2, CTDSPL, CTNNA3, CYP2C8, DBC1, DCAMKL1, DGKH,
DLG2, DNAH5, DPP6, DPT, DQ515897, DRB1, ECHDC1,RNF146, EHBP1, EIF3H, ELMO1, ERBB3, ESR1, EXOC2, EYA1, FAM55B, FCER1A,OR10J3, FGFR2, FLJ22536, FLJ44180, FLJ32831, FTO, G6PC2, G6PC2,ABCB11, GAB2, GALNT2, GCKR, GDAP1, GDF5, GGT1, GLUT9, GNA12, GPR126, GPR98, HACE1, HAPLN1, HBB, HCP5, HERC2, HHEX, HHIP, HISTH1D, HLA-C, HMGA2, HNF1A,
HOMER1, HTRA1, IGF2BP2, IGFBP2, IL12A, SCHIP1, IL12B, IL18, IL1RAP, IL1RL1,IL18R1,IL18RAP, SLC9A4, IL21, IL23R, IL2RA, IL6R, IL7RA, IMPA2, IRF4, IRGM, ITGAM, ITGAM, ITGAX, ITPR2, JAZF1, KIA1109,TENR,IL2,, KIAA0350, KIAA1542, KIAA1598, KITLG, KLK3,
LCORL, LEPR, LMTK2, LOXL1, LPA, LPP, LRP5, LRRC18, LSP1, MAP2K5, LBXCOR1, MAP3K1, MATP, MC4R, MCF2L, AB116074,
AK092739, AB0023600, F7, CR603372, F10, PROZ, MEF2C, MEIS1, MHC, C6orf10, MLXIPL, MSMB, MST1, MTHFD1L, MVK,MMAB,
MYR1P, NCAN,CILP2, NEGR1, NEIL3, NKX2-3, NOLA1, NOS1AP, NRG1, NRG3, NUBPL, NUDT10, NUDT11, LOC340602, GSPT2,
MAGED1, NUMB, OBFC1, OPG, OR10J1, ORF DQ515897, PALB2,NDUFAB1,DCTN5, PARD3B, PDE3D, PDE4D, PDGFRA,
PITX2,ENPEP, PKHD1, POLG, PREX1, , PTGS2, PLA2G4A, PTPN1, PTPN2, PVT1, PXK, RAB5B, SUOX, IKZF4, ERBB3, CDK2, RANKL,
RAPGEF5, RGS1, RNF212, RPL21, RPL5, RYR2, RYR2,CHRM3,ZP4, SEC5L1,IRF4, SEMA5A, SH2B3,LNK,TRAFD1,, SLC22A3, SLC24A4,
SLC24A5, SLC2A9, SLC45A2, SLCO3A1, SLIT2, SMAD7, SNRPN, SPACA1, SPATA2, STAT3, SUSD1, TAGAP, TCF2, THADA, TMEFF2, TNCR9,LOC6,43714, TNFAIP3, OLIG3, TNFRSF11B, TNRC9, TPCN2,
TRAF1-C5, TRIB1, TRIP11,ATXN3, TSPAN8,LGR5, TYR, TYRP1, ZBTB38, ZBTB40, ZFP64, ZMAT4, ZNF536,
Osteonecrosis of the jaw, Crohn's disease, Juvenile idiopathic arthritis, Fasting plasma glucose, Warfarin maintenance dose, Fasting plasma blood glucose, Smoking cessation, Response to iloperidone treatment (PANSS-T score), Response to iloperidone treatment (QT prolongation), Melanoma, Blond vs. brown hair, Blue vs. green eyes, Burning and freckling, Freckles, Red vs. non-red hair, Skin sensitivity to sun, Black vs. blond hair color, Black vs. red hair color, Neuroblastoma, Protein quantitative trait loci, Knee osteoarthritis, Waist circumference and related phenotypes, Body mass index, Alzheimer's disease, Bone mineral density, Bone mineral density (hip), Bone mineral density (spine), C-reactive protein, YKL-40 levels, Height, Psoriasis, Lung cancer, Nicotine dependence, lung cancer and peripheral arterial disease, Colorectal cancer, Type 2 diabetes, Environmental confusion in the home, Breast cancer, Schizophrenia, Serum urate, Obesity, Bipolar disorder 1, Celiac disease, Methamphetamine dependence, Prostate cancer, Prostate cancer (aggressive), LDL cholesterol, Fetal hemoglobin levels, Recombination rate (females), Recombination rate (males), Iris color, General cognitive ability, Systemic lupus erythematosus in women, Systemic lupus erythematosus, Type 1 diabetes, Response to interferon beta therapy, HDL cholesterol, Triglycerides, Early onset extreme obesity, Amyotrophic lateral sclerosis, Coronary spasm in women, Rheumatoid arthritis, Skin pigmentation by reflectance spectroscopy, Lupus, Select biomarker traits, BMI, Waist circumference traits, Sleep duration, Sleepiness, Cystatin C, Thyroid stimulating hormone, Urinary albumin excretion, Blood lipid traits, Hip geometry, Atrial fibrillation, Heart failure, Major CVD, Blood pressure, Tonometry, Aging traits, Morbidity-free survival traits (free of CVD, cancer & dementia), Diabetes related insulin traits, Incident diabetes, Electrocardiographic traits, Heart rate variability traits, Coronary artery calcification, Other subclinical atherosclerosis traits, Cognitive test performance, Volumetric brain MRI, Echocardiographic traits, Endothelial function traits, Exercise treadmill test traits, Mean forced vital capacity from 2 exams, Other pulmonary function traits, Factor VII, Hemostatic factors and hematological phenotypes, Type 2 diabetes and 6 quantitative traits, F-cell distribution, Exfoliation glaucoma, Irritable bowel syndrome, Diabetic nephropathy, Neuroticism, Multiple sclerosis, Childhood asthma, ORMDL3 expression, Obesity-related traits:, (body mass index, hip circumference, body weight), HIV1 viral setpoint, Restless legs syndrome, Coronary disease, Gallstones, Atrial fibrillation/atrial flutter, APOE*e4 carriers with late onset Alzheimer's disease, Bipolar disorder, Hypertension, Response to ximelagatran treatment, Stroke, Myocardial infarction, Episodic memory, Nicotine dependence, Late onset Alzheimer's disease, End-stage renal disease, Progressive supranuclear palsy, Addiction, Inflammatory bowel disease, Memory performance, Wet age-related macular degeneration, Parkinson's disease, QT interval prolongation, Age-related macular degeneration,
Genome Wide Association Studies
Thousands of cases & thousands of controls
Hundreds of thousands of single nucleotide polymorphisms
Compare allele frequencies in cases & controls
evolution?
Charles Darwin
The Origin of Species (1859)
Why do we resemble our parents?
Variation is hereditary
… but mutations happen
Survival of the fittest
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