genome mapping genome sequencing next gen sequencing

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

aftb/

con

cept

_11/

con1

1bio

.htm

l

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