Transcript Genome Project History.ppt

DNA Sequencing and the
Human Genome Project
•History
•Technology
•Analysis
History
• Timeline
– 1953
James Watson and Francis Crick discover the double helical
structure of DNA ( Nature ).
– 1972
Paul Berg and co-workers create the first recombinant DNA
molecule ( PNAS ).
– 1977
Allan Maxam and Walter Gilbert (pictured) at Harvard University
and Frederick Sanger at the U.K. Medical Research Council
(MRC) independently develop methods for sequencing DNA
( PNAS , February; PNAS , December).
History (cont’d)
– 1980
David Botstein of the Massachusetts Institute of Technology, Ronald Davis of Stanford
University, and Mark Skolnick and Ray White of the University of Utah propose a method to
map the entire human genome based on RFLPs (American Journal of Human Genetics ).
– 1984
Charles Cantor and David Schwartz of Columbia University develop pulsed field
electrophoresis
MRC scientists decipher the complete DNA sequence of the Epstein-Barr virus, 170 kb
– 1985
Kary Mullis and colleagues at Cetus Corp. develop PCR , a technique to replicate
vast amounts of DNA
– 1986
Sydney Brenner, DOE, Renato Dulbecco, CSH Symposium all publicly advocate a
human genome project. Not everyone convinced!
History (cont’d)
– 1986
Leroy Hood and Lloyd Smith of the California Institute of
Technology and colleagues announce the first automated
DNA sequencing machine
– 1987
An advisory panel suggests that DOE should spend $1 billion on
mapping and sequencing the human genome over the next 7
years-and that DOE should lead the U.S. effort. DOE's
Human Genome Initiative begins.
David Burke ,Maynard Olson , and George Carle of Washington
University in St. Louis develop YACs (left) for cloning,
increasing insert size 10-fold
DuPont scientists develop a system for rapid DNA sequencing
with fluorescent chain-terminating dideoxynucleotides
(Marv Caruthers, in Biochem, one of the patent holders)
Applied Biosystems Inc. puts the first automated sequencing
machine, based on Hood's technology, on the market.
History (cont’d)
– 1988
NIH establishes the Office of Human Genome Research and snags
Watson (pictured) as its head. Watson declares that 3% of the genome
budget should be devoted to studies of social and ethical issues.
– 1989
Olson ,Hood ,Botstein , and Cantor outline a new mapping strategy, using
STSs.
DOE and NIH start a joint committee on the ethical, legal, and social
implications of the HGP.
NIH office is elevated to the National Center for Human Genome Research
(NCHGR), with grant-awarding authority
History (cont’d)
– 1990
NIH and DOE publish a 5-year plan. Goals include a complete genetic map, a physical map with
markers every 100 kb, and sequencing of an aggregate of 20 Mb of DNA in model organisms
by 2005
NIH and DOE restart the clock, declaring 1 October the official beginning of the HGP. Cost per
base ~$0.75
David Lipman, Eugene Myers (CU CS Department!), and colleagues at the National Center for
Biotechnology Information (NCBI) publish the BLAST algorithm for aligning sequences
–
1991
NIH biologist J. Craig Venter announces a strategy to find expressed genes, using
ESTs (Science ). A fight erupts at a congressional hearing 1 month later, when
Venter reveals that NIH is filing patent applications on thousands of these partial
genes.
History (cont’d)
– 1992
Watson resigns as head of NCHGR
Venter leaves NIH to set up The Institute for Genomic Research
(TIGR), William Haseltine heads its sister company, Human
Genome Sciences, to commercialize TIGR products.
Britain's Wellcome Trust enters the HGP with $95 million
Mel Simon of Caltech and colleagues develop BACs for cloning
U.S. and French teams complete the first physical maps of
chromosomes: David Page of the Whitehead Institute and
colleagues map the Y chromosome; Daniel Cohen of the Centre
d'Etude du Polymorphisme Humain (CEPH) and Généthon and
colleagues map chromosome 21
U.S. and French teams complete genetic maps of mouse and human:
mouse, average marker spacing 4.3 cM , Eric Lander and
colleagues at Whitehead; human, average marker spacing 5 cM,
Jean Weissenbach and colleagues at CEPH
History (cont’d)
– 1993
Francis Collins of the University of Michigan is named director of
NCHGR.
NIH and DOE publish a revised plan for 1993-98. The goals include
sequencing 80 Mb of DNA by the end of 1998 and completing the
human genome by 2005. Cost per base target $0.10/base
finished.
The Wellcome Trust and MRC open the Sanger Centre at Hinxton
Hall, south of Cambridge, U.K. Led by John Sulston
The GenBank database officially moves from Los Alamos to NCBI,
ending NIH's and DOE's tussle over control
– 1994
Jeffrey Murray of the University of Iowa, Cohen of Généthon, and
colleagues publish a complete genetic linkage map of the human
genome, with an average marker spacing of 0.7 cM
History (cont’d)
– 1995
Venter and Claire Fraser of TIGR and Hamilton Smith of Johns Hopkins publish
the first sequence of a free-living organism, Haemophilus influenzae , 1.8 Mb
Patrick Brown of Stanford and colleagues publish first paper using a printed glass
microarray of complementary DNA (cDNA) probe
Researchers at Whitehead and Généthon (led by Lander and Thomas Hudson at
Whitehead) publish a physical map of the human genome containing 15,000
markers
– 1996
NIH funds six groups to attempt large-scale sequencing of the human genome.
Affymetrix makes DNA chips commercially available.
An international consortium publicly releases the complete genome sequence of the
yeast S. cerevisiae
History (cont’d)
– 1997
Fred Blattner ,Guy Plunkett , and University of Wisconsin,
Madison, colleagues complete the DNA sequence of E. coli , 5 Mb
–
1998
NIH announces a new project to find SNPs
Phil Green (pictured) and Brent Ewing of Washington University and colleagues
publish a program called phred for automatically interpreting sequencer data.
Both phred and its sister program phrap (used for assembling sequences) had
been in wide use since 1995.
PE Biosystems Inc. introduces the PE Prism 3700 capillary sequencing machine
Venter announces a new company named Celera and declares that it will
sequence the human genome within 3 years for $300 million
In response, the Wellcome Trust doubles its support for the HGP to $330
million, taking on responsibility for one-third of the sequencing
History (cont’d)
– 1998
NIH and DOE throw HGP into overdrive with a new goal of creating a "working draft"
of the human genome by 2001, and they move the completion date for the
finished draft from 2005 to 2003.
Sulston of the Sanger Centre and Robert Waterston of Washington University and
colleagues complete the genomic sequence of C. elegans (100mb).
– 1999
NIH again moves up the completion date for the rough draft, to spring 2000
Ten companies and the Wellcome Trust launch the SNP consortium, with plans to
publicly release data quarterly
NIH launches a project to sequence the mouse genome, devoting $130 million over 3
years
British, Japanese, and U.S. researchers complete the first sequence of a human
chromosome, number 22
History (cont’d)
– 2000
Celera and academic collaborators sequence the 180-Mb genome of the
fruit fly Drosophila melanogaster
Because of disagreement over a data-release policy, plans for HGP and
Celera to collaborate disintegrate amid considerable sniping.
HGP consortium led by German and Japanese researchers publishes the
complete sequence of chromosome 21
At a White House ceremony, HGP and Celera jointly announce working
drafts of the human genome sequence, declare their feud at an end,
and promise simultaneous publication
An international consortium completes the sequencing of the first plant,
Arabidopsis thaliana 125 Mb
HGP and Celera's plans for joint publication in Science collapse; HGP
sends its paper to Nature
TADA!!
2001
The HGP consortium
publishes its working
draft in Nature (15
February), and Celera
publishes its draft in
Science (16 February).
Technology
Aspects of Sequencing
Genomes
• Sequencing method
• Cloned DNA
• Clone/Sequence Assembly
Sequencing Methods
• “Sanger” chain termination
method; >90% of all sequencing
– Relies on ability of DNA
polymerase to incorporate
nucleotide analogs while
synthesizing template driven DNA
Dideoxynucleotidebased Sequencing
Automating Sanger
Sequencing
Other Automated
Methods
• Hybridization method
– Hybridize to oligos on a chip
• Affymetrix can do 30K resequence
• Limited by number of features and
hybridization specificity
• Single molecule methods
– Pore-base - threads DNA through
molecular pore in membrane - bases
determined by changes in conductance
– Mass spec - best for small molecules
now like SNPs
Most-used hardware
• ABI 377 - gel based - 96 lanes a
pop - read length ~500bp - run
time ~4-16h => ~40,000
bases/run X 3 runs/day =
120,000
• ABI 3700 - Capillary based - 48
capillaries - read length ~500bp run time ~40 minutes => 950,
Whaddaya determine
the sequence of?
Given chemistry and hardware to
read ~500bp in a row what gets
sequenced?
Clones
• Large insert clones
– YACs (Yeast Artificial Chromosomes
• Useful for mapping ~1mb inserts
• Unstable during construction and propagation
• Not useful for sequencing
– BACs (Bacterial Artificial Chromosomes)
• ~150kb insert
• Extremely stable and easy to propagate
• Gold standard for sequencing targets and chromosomescale maps
– Cosmids
• ~50kb insert
• Extremely stable and easy to propagate
• Useful for sequencing but too small for chromosome maps
Sequence-ready clones
• Plasmids
–
–
–
–
–
1-10kb insert capacity
High copy number
Easy to sequence bi-directionally
Automated clone picking/DNA isolation possible
Examples: pUC18, pBR322
• Single-stranded Bacteriophage
– 1-5kb insert capacity
– Grows at high copy as plasmid and is shed into medium as
single stranded DNA phage
– Easy to isolate, pick, sequence
– Easy to automate
– M13 is used almost exclusively