BIOL 311 Human Genetics
Fall 2006
Lecture: Genomics
Reading: Chap. 8 pp. 210-221
Outline:
1. The path to the genome project
2. Human genetic map
3. Mapping genes and markers to chromosomes
4. Physical mapping
5. Sequencing strategies
Lecture:
1. The path to the human genome project
One of the most important discoveries of science in this century is the deduction of the
entire base sequence of the human genome. The draft sequence was completed in June
2000 and now the sequence of the entire genome is essentially complete.
Milestones: Box 8.3
1956 Human cells shown to contain 46 chromosomes
1977 Sanger developed dideoxy sequencing
1981 Sander published complete sequence of human mitochondrial DNA
1990 Human genome project launched as $3 billion, 15 year project
1992 French group published first human genetic linkage map
1995 Lander et al. published first detailed physical map of the human genome
1999 First human chomosome, #22, completely sequenced
2000 Draft of human genome announced by Celer and International Human Gene
Sequencing Consortium
2001 Papers in Science and Nature on draft sequence
2003 Human genome project completed
2. Human genetic map
a. Gene mapping
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


only a few hundred genes known in early days of genome project
genes vary in length, location
therefore need more sites for detailed map
b. RFLP markers
 segments of DNA that vary in sites for restriction enzymes
 can be far apart
 not easy to type
c. microsatellite markers (SSR) simple sequence repeats
 informative, easy to type
 dispersed throughout the genome
 example: CACACA…
o
GTGTGT…
 Also used in forensic analysis
3. Mapping genes and markers to chromosomes
a. FISH: fluorescence in situ hybridization
 Fluorescently tagged DNA probe
 Incubate with lysed cells with denatured chromosomes on a slide
b. Somatic Cell Hybrids
Box 8.4
[locate image]
Fuse human cell with mouse or hamster cell in presence of PEG to form heterokaryon
random loss of most human chromosomes, while all rodent chromosomes are kept
create hybrid panel--different cell lines retaining particular human chromosomes or parts
of chromosomes
Test for presence of protein or enzyme produced by particular gene and presence of a
particular human chromosome
OR
Carry out a Southern blot of DNA from a panel probed with a particular cDNA or gene
probe.
c. Radiation Hybrids
Map genes to particular segment of a chromosome
[locate image]
Human cells are exposed to a lethal dose of radiation
Radiation induces chromosome breaks
Irradiated human cells are fused with rodent cells
Genetic selection (thymidine kinase +) with dominant selectable marker used to identify
rodent cells that have retained some human chromosome fragments
Compare pattern of hybridization of unmapped DNA sequence to that of known STS
(sequence tagged sites--unique DNA sequences)
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4. Physical mapping
Box 8.5
 determine number of bases separating DNA markers
 partial digest of genomic DNA cut occasionally at restriction sites
 clone fragments into large capacity vector (YAC, BAC, PAC)
 align overlapping clones to create a "contig"
overlaps are based on restriction sites
location of markers referred as STS=sequence tagged site
5. Sequencing strategies for the genome project
a. International Human Genome Project
US Human Genome Project/Francis Collins
Fig. 8.3
Used physical maps to align fragments
b. Celera
US Company/Craig Venter
"shotgun" approach
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