Computational Molecular Biology
Biochem 218 – BioMedical Informatics 231
[Link]
The Human Genome Project
Doug Brutlag
Professor Emeritus
Biochemistry & Medicine (by courtesy)
Maeve’s Office Hours
• Monday and Friday 3:30 to 5:00 PM
• Beckman Center B403A
• Please Email Maeve to set up an
appointment if you want to meet with
her.
– maeveo@[Link]
• Take the elevator to the fourth floor of
Beckman and turn left. The hallway
leads directly to the lab B403 and my
office is inside the lab at B403A.
Current Topics in Genome Analysis 2010
[Link]
Hierarchical Sequencing vs.
Whole Genome Shotgun Sequencing
from Gibson & Muse, A Primer of Genome Science
[Link]
© Gibson & Muse A Primer of Genome Science
The Human Genome Project:
How should we do it?
• Weber, J. L., & Myers, E. W. (1997). Human whole-genome shotgun seque
ncing.
Genome Res, 7(5), 401-409.
– [Link]
on&list_uids= 9149936
– Use multiple length clones 2 kb, 10 kb and 50 kb
– Use clone end sequencing generating mate-pairs
– Able to use long clones to leap over repeated regions
– Clone length permits one to measure length of repeated regions.
– Will find more polymorphisms (SNPs)
– Costs less
– BAC clone artifacts
• Differential amplification
• BACs not stable in bacteria will be lost.
• Repeated regions will recombine and be lost
• Green, P. (1997). Against a whole-genome shotgun. Genome Res, 7
(5), 410-417.
– [Link]
uids=9149937
– Preferred clone-by-clone BAC sequencing
– Distributed versus monolithic organization
– BACs linked to genetic maps
– Costs less (sequence 4x human genome)
– Finishing simplified and fewer gaps
– Haplotyping automatic
– Longer repeat regions lengths measured
History of Whole Genome Assembly
1997
Let’s sequence
the human
genome with the
shotgun strategy
That is
impossible, and a
bad idea anyway
Phil Green
Gene Myers
Thanks to Serafim Batzoglou
Public Human Genome Project Strategy
[Link]
Contig Formation as Mapping Progresses
Lander & Waterman 1988
[Link]
Public Genome Assembly Process
BAC and PAC Libraries in
Public Human Genome Project
[Link]
=11237011
Total Genome Sequence Information 2001
[Link]
Comparing Chromosome 2 Sequence Versus
Genetic Maps
[Link]
Synteny
Between
Human and
Mouse
[Link]
bMed&dopt=Citation&list_uids=11237011
Celera Sequencing
[Link]
Celera Scaffolds
[Link]
Celera Assembler
Chromosome 21:
Public vs Celera Assemblies
[Link]
Chromosome 8: Public vs. Celera
[Link]
Finishing
Strategy
for the
Public
Genome
Project
[Link]
Citation&list_uids=15496913
Finished Sequence in 2004 (Build 35)
[Link]
Chromosome 7: Draft versus Finished Sequence
[Link]
496913
Substitutions in BAC Overlaps withBAC
s from Same or Different Libraries
Gaps in BAC Overlaps withBACs fro
m Same or Different Libraries
Duplications and Deletions
in the Human Genome
Percentage of Chromosomes Duplicated
[Link]
t_uids=15496913
Available Next Generation
Sequencing Technologies
• Illumina – Solexa
– [Link]
• Illumina Technology
– [Link]
• 454 Life Sciences
– [Link]
• 454 Life Sciences Technology
– [Link]
• Applied Biosystems Inc. (ABI) SOLID Sequencing
– [Link]
• ABI SOLID Sequencing Technology
– [Link]
SystemSequencing/OverviewofSOLiDSequencingChemistry/[Link]
Next Generation Sequencing
Technologies in Development
• Pacific BioSciences
– [Link]
• Pacific BioSciences Technology
– [Link]
• Helicos
– [Link]
• Helicos Technology
– [Link]
/[Link]
• Complete Genomics
– [Link]
• Complete Genomics Technology
– [Link]
