genome mapping genome sequencing next gen sequencing
TRANSCRIPT
Genome mapping
Genome sequencing
Next Gen sequencing
Genomics = resourcesgenome maps
genome sequences
genome clones
DNA microarrays
whole gene collections
functional genomics!
1980- 1998
1977- 2003
DNA mapping
Genomics
=
In the beginning…….
~ 1980 - 1998
http://home.comcast.net/~dmgt350/cytogenetics/images/ktype.gif
ATGAAGCTACTGTCTTCTATCGAACAAGCATGCGATATTTGCCGACTTAAAAAGCTCAAGTGCTCCAAAGAAAAACCGAAGTGCGCCAAGTGTCTGAAGAACAACTGGGAGTGTCGCTACTCTCCCAAAACCAAAAGGTCTCCGCTGACTAGGGCACATCTGACAGAAGTGGAATCAAGGCTAGAAAGACTGGAACAGCTATTTCTACTGATTTTTCCTCGAGAAGACCTTGACATGATTTTGAAAATGGATTCTTTACAGGATATAAAAGCATTGTTAACAGGATTATTTGTACAAGATAATGTGAATAAAGATGCCGTCACAGATAGATTGGCTTCAGTGGAGACTGATATGCCTCTAACATTGAGACAGCATAGAATAAGTGCGACATCATCATCGGAAGAGAGTAGTAACAAAGGTCAAAGACAGTTGACTGTATCGATTGACTCGGCAGCTCATCATGATAACTCCACAATTCCGTTGGATTTTATGCCCAGGGATGCTCTTCATGGATTTGATTGGTCTGAAGAGGATGACATGTCGGATGGCTTGCCCTTCCTGAAAACGGACCCCAACAATAATGGGTTCTTTGGCGACGGTTCTCTCTTATGTATTCTTCGATCTATTGGCTTTAAACCGGAAAATTACACGAACTCTAACGTTAACAGGCTCCCGACCATGATTACGGATAGATACACGTTGGCTTCTAGATCCACAACATCCCGTTTACTTCAAAGTTATCTCAATAATTTTCACCCCTACTGCCCTATCGTGCACTCACCGACGCTAATGATGTTGTATAATAACCAGATTGAAATCGCGTCGAAGGATCAATGGCAAATCCTTTTTAACTGCATATTAGCCATTGGAGCCTGGTGTATAGAGGGGGAATCTACTGATATAGATGTTTTTTACTATCAAAATGCTAAATCTCATTTGACGAGCAAGGTCTTCGAGTCAGGTTCCATAATTTTGGTGACAGCCCTACATCTTCTGTCGCGATATACACAGTGGAGGCAGAAAACAAATACTAGCTATAATTTTCACAGCTTTTCCATAAGAATGGCCATATCATTGGGCTTGAATAGGGACCTCCCCTCGTCCTTCAGTGATAGCAGCATTCTGGAACAAAGACGCCGAATTTGGTGGTCTGTCTACTCTTGGGAGATCCAATTGTCCCTGCTTTATGGTCGATCCATCCAGCTTTCTCAGAATACAATCTCCTTCCCTTCTTCTGTCGACGATGTGCAGCGTACCACAACAGGTCCCACCATATATCATGGCATCATTGAAACAGCAAGGCTCTTACAAGTTTTCACAAAAATCTATGAACTAGACAAAACAGTAACTGCAGAAAAAAGTCCTATATGTGCAAAAAAATGCTTGATGATTTGTAATGAGATTGAGGAGGTTTCGAGACAGGCACCAAAGTTTTTACAAATGGATATTTCCACCACCGCTCTAACCAATTTGTTGAAGGAACACCCTTGGCTATCCTTTACAAGATTCGAACTGAAGTGGAAACAGTTGTCTCTTATCATTTATGTATTAAGAGATTTTTTCACTAATTTTACCCAGAAAAAGTCACAACTAGAACAGGATCAAAATGATCATCAAAGTTATGAAGTTAAACGATGCTCCATCATGTTAAGCGATGCAGCACAAAGAACTGTTATGTCTGTAAGTAGCTATATGGACAATCATAATGTCACCCCATATTTTGCCTGGAATTGTTCTTATTACTTGTTCAATGCAGTCCTAGTACCCATAAAGACTCTACTCTCAAACTCAAAATCGAATGCTGAGAATAACGAGACCGCACAATTATTACAACAAATTAACACTGTTCTGATGCTATTAAAAAAACTGGCCACTTTTAAAATCCAGACTTGTGAAAAATACATTCAAGTACTGGAAGAGGTATGTGCGCCGTTTCTGTTATCACAGTGTGCAATCCCATTACCGCATATCAGTTATAACAATAGTAATGGTAGCGCCATTAAAAATATTGTCGGTTCTGCAACTATCGCCCAATACCCTACTCTTCCGGAGGAAAATGTCAACAATATCAGTGTTAAATATGTTTCTCCTGGCTCAGTAGGGCCTTCACCTGTGCCATTGAAATCAGGAGCAAGTTTCAGTGATCTAGTCAAGCTGTTATCTAACCGTCCACCCTCTCGTAACTCTCCAGTGACAATACCAAGAAGCACACCTTCGCATCGCTCAGTCACGCCTTTTCTAGGGCAACAGCAACAGCTGCAATCATTAGTGCCACTGACCCCGTCTGCTTTGTTTGGTGGCGCCAATTTTAATCAAAGTGGGAATATTGCTGATAGCTCATTGTCCTTCACTTTCACTAACAGTAGCAACGGTCCGAACCTCATAACAACTCAAACAAATTCTCAAGCGCTTTCACAACCAATTGCCTCCTCTAACGTTCATGATAACTTCATGAATAATGAAATCACGGCTAGTAAAATTGATGATGGTAATAATTCAAAACCACTGTCACCTGGTTGGACGGACCAAACTGCGTATAACGCGTTTGGAATCACTACAGGGATGTTTAATACCACTACAATGGATGATGTATATAACTATCTATTCGATGATGAAGATACCCCACCAAACCCAAAAAAAATATGTGCAAAAAAATGCTTGATGATTTGTAATGAGATTGAGGAGGTTTCGAGACAGGCACCAAAGTTTTTACAAATGGATATTTCCACCTTTATGGTCGATCCATCCAGCTTTCTCAGAATACAATCTCCTTCCCTTCTTCTGTCGACGATGTGCAGCGTACCACAACAGGTCCCACCATATATCATGGCATCATTGAAACAGCAAGGCTCTTACAAGTTTTCACAAAAATCTATGAACTAGACAAAACAGTAACTGCAGAAAAAAGTCCTATATGTGCAAAAAAATGCTTGATGATTTGTAATGAGATTGAGGAGGTTTCGAGACAGGCACCAAAGTTTTTACAAATGGATATTTCCACCAACTTCAAAGTTATCTCAATAATTTTCACCCCTACTGCCCTATCGTGCACTCACCGACGCTAATGATGTTGTATAATAACCAGATTGAAATC
([G][A][T][C])3,000,000,000
CytogeneticBand5-10 Mb
….TTGTCCTTCACTTTCACTAACAGTAGCAACGGTCCGAACCTCATAACAACTCAAACAAATTCTCA….
1 bpresolution
BACsYACs
100s to 1000s of Kb
(0.1-1 Mb)
CosmidsPlasmids
10s Of Kb
resolution
Physical maps
Genetic map of the Drosophila X chromosome
1913
Sturtevant, A. H. 1913. The linear arrangement of six sex- linked factors in Drosophila, as shown by their mode of association. Journal of Experimental Zoology, 14: 43-59.
ww
w.d
naft
b.or
g/dn
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Genetic map of the yeast genome, 1960
Hawthorne & Mortimer GENETICS 1960 45: 1085 - 1110
His- Trp-
Xa haploid a haploid
Trp-
His-
a/ a diploid
His-
Trp-
Trp-
His-His-
His-
Trp-
Trp-
twomeiotic
divisions
100% parental
meiosis
His- Trp-
Xa haploid a haploid
Trp-
His-
a/ a diploid
His-
Trp-
Trp-
His-His-
Trp-
twomeiotic
divisions
50% parental50% recombinant (non-parental)
His- Trp-
His-
Trp-
Trp-
His-His-
Trp-
twomeiotic
divisions
100% parental0% recombinant (non-parental)
Trp-
His-
His-
Trp-
Trp-
His-His-
Trp-
twomeiotic
divisions
50% recombinant
His- Trp-
His-
Trp-
Trp-
His-His-
Trp-
twomeiotic
divisions
0% recombinant
Trp-<50% recombinant
genes “linked”
>>
His-
His-
Trp-
Trp-
His-His-
Trp-
twomeiotic
divisions
50% parental50% recombinant (non-parental)
His- Trp-
Tetratype
His-
Trp-
Trp-
His-His-
His-
Trp-
Trp-
twomeiotic
divisions
100% parental
Parental ditype
Mortimer & Hawthorne GENETICS 53: 165-173 1966
50% recombinants0% recombinants
40% recombinants
16% recombinants T = 49 * 4 = 196 spores/2 = 98r
PD = 14 * 4 = 56 spores = 0r
NPD = 15 * 4 = 56 spores = 56r
308 spores 154r
Mortimer & Hawthorne GENETICS 53: 165-173 1966
c 19951966
CytogeneticBand
5-10 Mb
Genetic MapCm
YACs~1 Mb
BACs~150 Kb
λ clones~15 Kb
GENETICS 134: 81-150 (1993)
YAC Clones Cosmid Clones
Genome
the more pieces in the puzzle, the harder it is to assemble
Marra et al., 1997 High throughput fingerprint analysis of large-insert clones. Genome Res. 7:1072
Genome mapping
Meyers BC, Scalabrin S, Morgante M (2004) Nature Reviews Genetics 5: 578
“finishing”
Marra et al., 1997 High throughput fingerprint analysis of large-insert clones. Genome Res. 7:1072
“Finishing”
Genome mapping
Meyers BC, Scalabrin S, Morgante M (2004) Nature Reviews Genetics 5: 578
“finishing”
“Sequence-ready” BAC map
Green ED Nat Rev Genetics 2001 2:573-83
Genome maps
Meyers BC, Scalabrin S, Morgante M (2004) Nature Reviews Genetics 5: 578
CTAGTACTGTCG
CAGTGCTATTAG
200-500 bp
STS: SequenceTagged Sites
Closely linked STSs STSs farther apartclosely linked markers markers farther apart
T.A. Brown GENOMES 2 BIOS Scientific Publishers Ltd, 2002
Radiation hybrid cell lines
Cox DR et al. 1990 Radiation hybrid mapping: a somatic cell genetic method for constructing high resolution maps of mammalian chromosomes. Science 250: 245–250. PMID: 2218528
Radiation hybrid mapping
His-
Trp-
Trp-
His-His-
His-
Trp-
twomeiotic
divisions
50% recominant >> 0% recombinant
Trp-
Cox DR et al. 1990 Radiation hybrid mapping: a somatic cell genetic method for constructing high resolution maps of mammalian chromosomes. Science 250: 245–250. PMID: 2218528
Radiation hybrid mapping
CTAGTACTGTCG
CAGTGCTATTAG
200-500 bp
Human Molecular Genetics 2, Strachan and Read © 1999 Garland Science
STS content mapping
Eric Green, NHGRI
CytogeneticBand
5-10 Mb
YACs~1 Mb
BACs~150 Kb
STS mapping
fingerprint mapping
RFLPs
Donis-Keller H et al. A genetic map of the human genome. Cell. (1987); 51: 319–337 PMID: 3664638
Human Genome Genetic Map
198710 Mb resolution
probe
X
X
1
2
3haplotypes
Human Genome Genetic Map
1996<1 Mb resolution
SSLPS
Dib C et al. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. (1996) 380: 152–154 PMID: 8600387
Human Genome Genetic Map
“Sequence-ready” BAC map