Human genome project

„ Read about the human genome project

at
http://www.ornl.gov/sci/techresources/
Human_Genome/home.shtml
 Genomes that have already
been sequenced
„ Phage ΦX174 1977 „ Drosophila 2000
„ Mycoplasma genitalium „ Caenorhabditis elegans
1995 1998
„ Haemophilus „ Arabidopsis thaliana
2001
influenzae 1995
„ Rice 2002
„ Yeast 1996
„ Anopheles gambiae
„ E. coli 1997 2002
„ Human genome 2003
What is the human genome
project
„ International 13 year effort (began
October 1990)
„ 30,000 genes
„ 3 billion DNA base pairs
„ Coding regions only 2% of the genome
 Early reactions

“It endangers all of The idea of trudging

us, especially the through the genome
young researchers” sequence by sequence
David Botstein does not command
Science, 1986 wide and enthusiastic
support in the UK.
Sydney Brenner, 1986
Support builds
The sequence of the human
genome would perhaps be the
most powerful tool ever developed
to explore the mysteries of human
development and disease
Leroy Hood, 1987
The project starts!

It is essentially immoral
not to get it [the human
genome sequence] done
as fast as possible.
James Watson 1990
Goals of The Human Genome
Project
„ Identify all the approx. 30,000 genes
„ Determine the sequences of the 3
billion bps public databases
„ Develop faster more efficient
sequencing technologies
„ Tools for data analysis
„ Address ethical, legal, and social issues
(ELSI)
Who is the U.S. Human
Genome Project?
„ National Center for Human Genome
Research
„ Department of Energy Ari Patrinos

„ National Institutes of Health Francis

Collins
Where
„ DOE Joint Genome Institute
„ 3 DOE national labs
„ Baylor College of Medicine
„ Sanger Centre
„ Washington University Genome
Sequencing Center
„ Whitehead Institute/MIT Center for
Genome Research
Where locally?
„ University of Washington Genome
Center

„ University of Washington
Multimegabase Sequencing Center
Whose?
„ A reference sequence - not an exact
match for any one person
„ Blood (female) or sperm (male)
samples taken from a large number of
donors.
„ Ethnically diverse
„ Few samples processed
„ Names protected
Patents?
„ 1987 Walter Gilbert announces plans to
start Genome Corp. with goal of
sequencing and copyrighting the human
genome and selling data for profit
 Patents

I am
horrified

James Watson 1991

 An Independent Genome
Project? 1998

„ Celera Genomics Corporation CEO

Craig Venter

„ Proposes to sequence human genome

in 3 years for $3 million

„ Invented new sequencing technologies

 A Truce
„ Sequencing Progress
Draft Sequence:
Completed June 26,
2000

„ Joint announcement
by Venter and
Collins
 Current Status of HGP
AREA GOAL ACHIEVED DATE ACHIEVED

Genetic Map 2- to 5-cM 1-cM resolution September 1994

resolution map map (3,000
(600 – 1,500 markers)
markers)

Physical Map 30,000 STSs 53,000 STSs October 1998

DNA Sequence 95% of gene- 99% of gene- April 2003

containing part of containing part of
human sequence human sequence
finished to finished to
99.99% accuracy 99.99% accuracy
AREA GOAL ACHIEVED AREA

Human 100,000 mapped 3.7 million mapped February 2003

Sequence human SNPs human SNPs
Variation

Gene Full-length human 15,000 full-length March 2003

Identification cDNAs human cDNAs

Model Complete genome Finished genome April 2003

Organisms sequences of sequences of E. coli,
E. coli, S. cerevisiae, S. cerevisiae,
C. elegans, C. elegans,
D. melanogaster D. melanogaster, plus
whole-genome drafts
of several others,
including C. briggsae,
D. pseudoobscura,
mouse and rat
Functional Genomics
ELSI
„ Research informed public policy

„ 40 states in the US have passed genetic

non discrimination bills

„ 3000 judges went through 20

workshops on fundamentals of genetics
Beyond the human genome
project?
„ Genomics
„ Proteomics
„ Genomics-based medicine
„ Hereditary factors in heart disease
„ Cancer
„ Diabetes
„ Schizophrenia
„ Individualized medicine
 Recent events in HGP
„ The DNA sequence and analysis of human
chromosome 13
A Dunham et al.
Nature 428, 522-528 (2004)
„ Chromosome 13 is the largest acrocentric
human chromosome.
„ Lowest gene density of all chromosomes
Medically interesting genes on
chromosome 13

BRCA2 RB1

DAOA locus associated with bipolar

disorder and schizophrenia.
 Disease localisation Sequence OMIM
Gene containing reference
gene
ATP7B Wilsons Disease 13q14.3-q21.1 AL162377 606882
AL138821

BMIQ2 Quantitative trait for body mass index 13q14 Not cloned 606643

BRCA2 Breast cancer 2,early onset 13q12.3 AL442512 600185

AL137247

BRCA3 Breast cancer 3 13q21 Not cloned 605365

CLN5 Ceroid-lipofuscinosis, Neuronal-5 13q21.1- AL355879 608102

q32

BRCD1 Breast cancer, ductal 13 Not cloned 211410

D13S25 B-cell chronic lymphocytic leukaemia 13q14 Not cloned 109543

DDX26 Non small cell lung cancer 13q14.12- AL137780 604331

q14.2 AL354820

EDNRB Hirschsprung Disease 13q22 AL139002 131244

ENUR1 Nocturnal Enuresis 13q13-q14.3 Not cloned 600631

ERCC5 Xeroderma pigmentosum 13q33 AL157769 133530

F10 Factor X deficiency 13q34 AL137002 227600

F7 Factor VII deficiency 13q34 AL137002 227500

FGF14 Fibroblast growth factor 14 13q34 AL160153 601515

FLT3 Decreased survival in Acute myeloid leukaemia 13q12 AL356575 136351

AL445262
AL356915

FOXO1A Alveolar 13q14.1 AL133318 136533

rhabdomyosarcoma AL355132

DAOA Schizophrenia 13q34 AL359751 607408

GER Gastroesophageal reflux 13q14 Not cloned 109350

GJA3 Cataract, zonular 13q11 AL138688 121015

pulverulent-3

GJB2 Deafness, autosomal 13q11 AL138688 121011

recessive-1

GJB6 Deafness, autosomal 13q12 AL355984 604418

dominant-3

HTR2A Psycotic illness 13q14-q21 AL136958 182135

AL160397

ING1 Squamous cell carcinoma, 13q34 AL157820 601566

head and neck

IPF1 Pancreatic aqenesis, 13q12.1 AL353195 600733

maturity-onset diabetes
IRS2 Noninsulin-dependent 13q34 AL162497 600797
diabetes mellitus

ITM2B Dementia 13q14 AL139322 603904

LDLR Cholesterol lowering factor 13q Not cloned 604595

LIG4 LIG4 syndrome 13q22-q34 AL157762 601837

MBS1 Moebius syndrome 13q12.2-q13 Not cloned 157900

MCOR Congenital microcoria 13q31-32 Not cloned 156600

PAPA2 Postaxial polydactyl, 13q21-q32 Not cloned 602085

TypeA2

PCCA Propioninacidemia 13q32 AL356575 232000

AL355338
AL136526
AL353697
PHF11 Asthma,atopic hypersensitivity 13q14.1 AL139321 607796

RB1 Retinoblastoma 13q14.1- AL136960 180200

q14.2 AL392048

RFXAP Bare lymphocyte syndrome 13q14 AL159973 601861

RHOK Oguchi disease-2 13q34 Partialy Contained in BX537316 180381

RIEG2 Rieger syndrome 13q14 Not cloned 601499

Chromosome 19
„ April 2004

„ Most Gene rich of all

How do you sequence a whole
genome?
 Vectors for large scale
genome projects
„ YACS Yeast Artificial Chromosomes
„ Megabase!

„ BACS Bacterial Artificial Chromosomes

„ Vector 6.9 kbps
„ Insert average 150 kb
YACS
BACS
How do you sequence a whole
genome?
„ Clone by Clone
„ requires a map

„ Shotgun sequencing Figure 24.7

Maps
„ Genetic map
„ determined from recombination
frequencies

„ Physical map
„ based on physical distances
„ the physical location of a particular
cloned sequence of DNA
Genetic markers - landmarks
on the map
„ Morphological markers
„ scorable phenotypes e.g. hemophilia,
wrinkled pea

„ Physical markers
„ RFLPs, CAPS, VNTR, STS
Critical to the success of the HGP clone
by clone sequencing strategy was
development of a physical map of the
human genome placing molecular
markers on this map.
STS = sequence tagged sites were
particularly used.
One of a kind
markers not
duplicated
anywhere else in
the genome
 Current Status of HGP
AREA GOAL ACHIEVED DATE ACHIEVED

Genetic Map 2- to 5-cM 1-cM resolution September 1994

resolution map map (3,000
(600 – 1,500 markers)
markers)

Physical Map 30,000 STSs 53,000 STSs October 1998

DNA Sequence 95% of gene- 99% of gene- April 2003

containing part of containing part of
human sequence human sequence
finished to finished to
99.99% accuracy 99.99% accuracy
 Physically mapping whole
chromosomes

Large scale mapping cytogenetics

FISH

Somatic cell hybrid mapping

STS mapping figure 24.6

Fine mapping
 Mapping a whole genome
„ Recognizing
chromosomes
„ Somatic Cell hybrid mapping

„ Locate DNA fragment to particular

chromosome
Locate markers to
chromosomes

A is on 1

B is on 7

C is on 5
 Radiation hybrid map

•Map based on the co-occurrence of

markers in a panel of radiation hybrid
cell lines, resulting in an ordering of
markers along a chromosome
backbone.
 Radiation hybrids
„ Irradiate with X rays before fusion
Chromosome 10 C 1 2 3 4 5 M

1 2 3 4 5
Fine structure mapping
„ STS mapping
„ Used to order BAC clones
„ Generate contigs
„ Principle:
„ If the same STS marker can be PCR
amplified from two clones the clones
overlap
CLONE STS
A B C D E
1 + + + - -
2 + - + - +
3 + + - + -
4 - + - + -

2 E C A
1 B

4 D