Download Jan 26,2012 - Mapping(ppt)

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Transcript 
Genome mapping
Genome sequencing
Next Gen sequencing
Genomics = resources
genome maps 1980- 1998
genome clones
genome sequences1977- 2003
DNA microarrays
whole gene collections
functional genomics!
In the beginning…….
Genomics
=
DNA mapping
~ 1980 - 1998
http://home.comcast.net/~dmgt350/cytogenetics/images/ktype.gif
ATGAAGCTACTGTCTTCTATCGAACAAGCATGCGATATTTGCCGACTTAAAAAGCTCAAGTGCTCCAAAGAAAAACCGAAGTGCGCCAAGT
GTCTGAAGAACAACTGGGAGTGTCGCTACTCTCCCAAAACCAAAAGGTCTCCGCTGACTAGGGCACATCTGACAGAAGTGGAATCAAGGCT
AGAAAGACTGGAACAGCTATTTCTACTGATTTTTCCTCGAGAAGACCTTGACATGATTTTGAAAATGGATTCTTTACAGGATATAAAAGCA
TTGTTAACAGGATTATTTGTACAAGATAATGTGAATAAAGATGCCGTCACAGATAGATTGGCTTCAGTGGAGACTGATATGCCTCTAACAT
TGAGACAGCATAGAATAAGTGCGACATCATCATCGGAAGAGAGTAGTAACAAAGGTCAAAGACAGTTGACTGTATCGATTGACTCGGCAGC
TCATCATGATAACTCCACAATTCCGTTGGATTTTATGCCCAGGGATGCTCTTCATGGATTTGATTGGTCTGAAGAGGATGACATGTCGGAT
GGCTTGCCCTTCCTGAAAACGGACCCCAACAATAATGGGTTCTTTGGCGACGGTTCTCTCTTATGTATTCTTCGATCTATTGGCTTTAAAC
CGGAAAATTACACGAACTCTAACGTTAACAGGCTCCCGACCATGATTACGGATAGATACACGTTGGCTTCTAGATCCACAACATCCCGTTT
ACTTCAAAGTTATCTCAATAATTTTCACCCCTACTGCCCTATCGTGCACTCACCGACGCTAATGATGTTGTATAATAACCAGATTGAAATC
GCGTCGAAGGATCAATGGCAAATCCTTTTTAACTGCATATTAGCCATTGGAGCCTGGTGTATAGAGGGGGAATCTACTGATATAGATGTTT
TTTACTATCAAAATGCTAAATCTCATTTGACGAGCAAGGTCTTCGAGTCAGGTTCCATAATTTTGGTGACAGCCCTACATCTTCTGTCGCG
ATATACACAGTGGAGGCAGAAAACAAATACTAGCTATAATTTTCACAGCTTTTCCATAAGAATGGCCATATCATTGGGCTTGAATAGGGAC
CTCCCCTCGTCCTTCAGTGATAGCAGCATTCTGGAACAAAGACGCCGAATTTGGTGGTCTGTCTACTCTTGGGAGATCCAATTGTCCCTGC
TTTATGGTCGATCCATCCAGCTTTCTCAGAATACAATCTCCTTCCCTTCTTCTGTCGACGATGTGCAGCGTACCACAACAGGTCCCACCAT
ATATCATGGCATCATTGAAACAGCAAGGCTCTTACAAGTTTTCACAAAAATCTATGAACTAGACAAAACAGTAACTGCAGAAAAAAGTCCT
ATATGTGCAAAAAAATGCTTGATGATTTGTAATGAGATTGAGGAGGTTTCGAGACAGGCACCAAAGTTTTTACAAATGGATATTTCCACCA
CCGCTCTAACCAATTTGTTGAAGGAACACCCTTGGCTATCCTTTACAAGATTCGAACTGAAGTGGAAACAGTTGTCTCTTATCATTTATGT
ATTAAGAGATTTTTTCACTAATTTTACCCAGAAAAAGTCACAACTAGAACAGGATCAAAATGATCATCAAAGTTATGAAGTTAAACGATGC
TCCATCATGTTAAGCGATGCAGCACAAAGAACTGTTATGTCTGTAAGTAGCTATATGGACAATCATAATGTCACCCCATATTTTGCCTGGA
ATTGTTCTTATTACTTGTTCAATGCAGTCCTAGTACCCATAAAGACTCTACTCTCAAACTCAAAATCGAATGCTGAGAATAACGAGACCGC
ACAATTATTACAACAAATTAACACTGTTCTGATGCTATTAAAAAAACTGGCCACTTTTAAAATCCAGACTTGTGAAAAATACATTCAAGTA
CTGGAAGAGGTATGTGCGCCGTTTCTGTTATCACAGTGTGCAATCCCATTACCGCATATCAGTTATAACAATAGTAATGGTAGCGCCATTA
AAAATATTGTCGGTTCTGCAACTATCGCCCAATACCCTACTCTTCCGGAGGAAAATGTCAACAATATCAGTGTTAAATATGTTTCTCCTGG
CTCAGTAGGGCCTTCACCTGTGCCATTGAAATCAGGAGCAAGTTTCAGTGATCTAGTCAAGCTGTTATCTAACCGTCCACCCTCTCGTAAC
TCTCCAGTGACAATACCAAGAAGCACACCTTCGCATCGCTCAGTCACGCCTTTTCTAGGGCAACAGCAACAGCTGCAATCATTAGTGCCAC
TGACCCCGTCTGCTTTGTTTGGTGGCGCCAATTTTAATCAAAGTGGGAATATTGCTGATAGCTCATTGTCCTTCACTTTCACTAACAGTAG
CAACGGTCCGAACCTCATAACAACTCAAACAAATTCTCAAGCGCTTTCACAACCAATTGCCTCCTCTAACGTTCATGATAACTTCATGAAT
AATGAAATCACGGCTAGTAAAATTGATGATGGTAATAATTCAAAACCACTGTCACCTGGTTGGACGGACCAAACTGCGTATAACGCGTTTG
GAATCACTACAGGGATGTTTAATACCACTACAATGGATGATGTATATAACTATCTATTCGATGATGAAGATACCCCACCAAACCCAAAAAA
AATATGTGCAAAAAAATGCTTGATGATTTGTAATGAGATTGAGGAGGTTTCGAGACAGGCACCAAAGTTTTTACAAATGGATATTTCCACC
TTTATGGTCGATCCATCCAGCTTTCTCAGAATACAATCTCCTTCCCTTCTTCTGTCGACGATGTGCAGCGTACCACAACAGGTCCCACCAT
ATATCATGGCATCATTGAAACAGCAAGGCTCTTACAAGTTTTCACAAAAATCTATGAACTAGACAAAACAGTAACTGCAGAAAAAAGTCCT
ATATGTGCAAAAAAATGCTTGATGATTTGTAATGAGATTGAGGAGGTTTCGAGACAGGCACCAAAGTTTTTACAAATGGATATTTCCACCA
ACTTCAAAGTTATCTCAATAATTTTCACCCCTACTGCCCTATCGTGCACTCACCGACGCTAATGATGTTGTATAATAACCAGATTGAAATC
([G][A][T][C])
3,000,000,000
Physical maps
resolution
5-10 Mb
Cytogenetic
Band
100s to 1000s
of Kb
(0.1-1 Mb)
BACs
YACs
10s
Of Kb
Cosmids
Plasmids
….TTGTCCTTCACTTTCACTAACAGTAGCAACGGTCCGAACCTCATAACAACTCAAACAAATTCTCA…
.
1 bp
resolution
www.dnaftb.org/dnaftb/ concept_11/con11bio.html
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.
Genetic map of the yeast genome, 1960
Hawthorne & Mortimer GENETICS 1960 45: 1085 - 1110
His-
X
a haploid
a/a diploid
HisTrp-
Trpa haploid
meiosis
His-
His-
His-
TrpHis-
two
meiotic
divisions
Trp-
Trp-
100% parental
Trp-
His-
X
a haploid
a/a diploid
HisTrp-
Trpa haploid
HisHis-
His-
Trptwo
meiotic
divisions
His-
Trp-
Trp-
Trp-
50% parental
50% recombinant (non-parental)
HisHis-
His-
TrpHis-
two
meiotic
divisions
Trp-
Trp-
Trp-
100% parental
0% recombinant (non-parental)
HisHis-
His-
Trptwo
meiotic
divisions
His-
Trp-
Trp-
Trp-
50% recombinant
HisHis-
His-
TrpHis-
two
meiotic
divisions
<50% recombinant
>>
genes “linked”
0% recombinant
Trp-
Trp-
Trp-
Tetratype
His-
His-
His-
Trptwo
meiotic
divisions
His-
Trp-
Trp-
Trp-
50% parental
50% recombinant (non-parental)
Parental ditype
His-
His-
His-
TrpHis-
two
meiotic
divisions
Trp-
Trp-
100% parental
Trp-
50% recombinants
0% 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
1966
Mortimer & Hawthorne GENETICS 53: 165-173 1966
c 1995
5-10 Mb
Cytogenetic
Band
Cm
Genetic Map
YACs
~1 Mb
BACs
~150 Kb
λ clones
~15 Kb
GENETICS 134: 81-150 (1993)
the more pieces in the puzzle, the harder it is to assemble
Genome
YAC Clones
Cosmid Clones
Marra et al., 1997 High throughput fingerprint analysis of large-insert clones. Genome Res. 7:1072
Genome mapping
“finishing”
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
Genome mapping
“finishing”
Meyers BC, Scalabrin S, Morgante M (2004) Nature Reviews Genetics 5: 578
“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
STS: SequenceTagged Sites
CTAGTACTGTCG
CAGTGCTATTAG
200-500 bp
closely
Closelylinked
linkedmarkers
STSs
markers
fartherapart
apart
STSs farther
Radiation hybrid
cell lines
T.A. Brown GENOMES 2 BIOS Scientific Publishers Ltd,
Radiation hybrid mapping
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
HisHis-
His-
TrpHis-
Trp-
two
meiotic
divisions
Trp-
Trp-
50% recominant >> 0% recombinant
Radiation hybrid mapping
CTAGTACTGTCG
CAGTGCTATTA
G
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
STS content mapping
Human Molecular Genetics 2, Strachan and Read © 1999 Garland Science
Eric Green, NHGRI
Cytogenetic
Band
5-10 Mb
YACs
STS mapping
~1 Mb
BACs
fingerprint mapping
~150 Kb
probe
X 1
haplotypes
2
3
RFLPs
Human Genome
Genetic Map
1987
10 Mb resolution
Donis-Keller H et al. A genetic map of the human genome. Cell. (1987); 51: 319–337 PMID: 3664638
X
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
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