Ranchi: July 9, 2006

Impact of Genomics
on human health
Seyed E. Hasnain

UNIVERSITY OF HYDERABAD
What distinguishes modern Human from
its predecessors (300,000yrs)

Their ability to make and use complex tools !

The dazzling leap in technology influenced

human evolution in every field
“(DNA technology) The most awesome and
powerful tool acquired by man since the
splitting of atoms”

- The Time Magazine (USA)

CDFD
The Milestones in DNA Technology in the last 50 years:
•1953: Double helix structure of DNA discovered.

•1973: Cohen and Boyer “cut & paste” segments of DNA and
reproduce (clone) the new DNA in bacteria.

•1976: The first working synthetic gene was developed.

•1977: The first human protein (somatostatin) was produced.

•1982: Recombinant human insulin was marketed.

•1983: Polymerase chain reaction (PCR) technique was conceived.

•1985: Human growth hormone produced in bacterium was marketed.

•1990: Human Genome Project (HGP), was launched.

•1995: The first full gene sequence of a living organism was completed for
the bacterium, Haemophilus influenzae.

•2000: First draft of human genome sequence was completed.

•2003: The final sequence of the human genome was produced.

The discovery that started it all!!

1953
Molecular Biology Overview

Cell Nucleus

Chromosome

Protein Gene (mRNA), Gene (DNA)

single strand
 The Central Dogma of life
Translation

DNA makes RNA makes Protein

Transcription

•DNA as gene
•The concept of ‘junk’ DNA
From Chromosomes
to Proteins
 Recombinant DNA
•Recombinant DNATechnology/
Transgenics/ GMOs and GM Food
Technology and Sequencing
•Molecular Diagnostics and Genetic Medicine

•Stem cells

•Cloning

•DNA Fingerprinting or Genomic profiling

Fruits of the gene technology revolution

Speaking the language of DNA Recombinant Technology
Cohen and Boyer gave the first break through in Recombinant technology

EcoRI Ligase
PAUL BERG: A pioneer
in the field of RECOMBINANT
DNA TECHNOLOGY

Developed a Biochemical Method for Inserting New

Genetic Information into SV40 DNA

Circular SV40 DNA Molecules Containing Lambda

Phage Genes and the Galactose Operon of E. coli.
 Recombinant DNA Technology
Genetic Engineering of Microorganisms

GMO

Ananda Chakraborty and US patent

 Applications of Genetic engineering
Microbial systems Transgenic animals
• GMOs for Food and Dairy • Biopharmaceuticals
• GMOs for environmenta • Human proteins and
• Recombinant therapeutics humanised organs
• Recombinant enzymes • Heterologous proteins of medical
• Therapeutic Biomolecules and surgical importance
• Recombinant vaccines • Animal models of cancer, allergy
• Proteins, Neutraceuticals and ageing
• Cosmetic products
 What does the DNA contain????

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Revealing the information...

Technological innovations to sequence the Human
and other genomes
….. One of the largest endeavors in the history
of mankind CDFD
 1977- Maxam and Gilbert (US) and Sanger (UK)
Independently developed methods for sequencing DNA

Slow rate of sequencing

(250bp/day) and the complex genomes

Improvement in technology was the key

Advanced Molecular Biological techniques and computational

Biology bridged the gap (6000 times enhancement in sequencing rate)
 Technology in full swing
sequencing by ‘synthesis nanotechnology’ approach

Sequencing genomes in Sequencing genomes in

weeks and months hours!!
 Genome Projects
Model organisms

C. elegans
E. coli (bacteria) (nematode) worm)

Saccharomyces cerevisae
(brewer’s yeast)
50 years after the double helix story…...
 Post-genomic issues
Vast number of genes have no known function
Human 40 - 60%
Arabidopsis 48%
Leishmania 52%
H. pylori >50%
M. tuberculosis 40%

The question of numbers

No clue as to which set of genes are expressed in a

given time, given tissue, given environmental
conditions

Shift from qualitative biology to quantitative biology

No clue as to how the genes cross-talk

Post Genomic Efforts: From data to knowledge

High throughput technologies

Rapid accumulation of biological data

Key Methods to analyse the vast amount of genomic data

Structural genomics Functional genomics

Comparative genomics

Proteomics Pharmacogenomics
Computational Biology Harvesting the genomic data
Arrival of BIOINFORMATICS

Genomes

GeneProducts

“ And that’s why we need a computer”

Structure and
Function • Scientific challenges

• Algorithmic challenges
Pathways &
Physiology • Computational Challenges
 Evolution of Informatics Tools
Submission

Hit Lead Lead CD

Target Concept Development Launch
Identifica- Identifica- Optimisa- Prenomi-
Identification Testing for launch Phase
tion tion tion nation

Launch

BioSuit
(India)

MouseBase
Biological Systems are several log More
complicated than Physical Systems!
 Make Connections: Build and
Visualize Relationships
Animal Models
Disease
Tissue
Histopath
Projects
Clinical Data
Time

Biomarker

Compounds Genes
Biomedial Image

Literature -Omic tools

Target

-omic data
The Rise of Systems Biology
Anticipated Benefits of the human genome
• Improved diagnosis of disease and intervention
- PCG example
• Earlier detection of genetic predispositions to disease
• Rational drug design
• Gene therapy
• Pharmacogenomics or "custom drugs”: SNP Profiling

CDFD
 •Recombinant DNATechnology/
Transgenics/ GMOs and GM Food

Diagnostics
•Molecular and Genetic
Diagnostics Medicines
and Genetic Medicine

•Stem cells

•Cloning

•DNA Fingerprinting or Genomic profiling

Fruits of the gene technology revolution

 Molecular Diagnostics
Another Breakthrough in Recombinant DNA Technology:
The Invention of Polymerase Chain reaction (PCR)

Invented by Kary Mullis

in 1983.

First published account

appeared in1985.

Awarded NobelPrize for

Chemistry in 1993.

Single molecule to 10 n molecules

(n = number of PCR cycles)
Microarray /gene chips in diagnostics
Measures global changes in gene expression
Automated ultra-high throughput screening
Technology for the future generation
Can measure mRNA expression levels of 10,000 genes
Can be used for genome wide mapping
Can be used to monitor time kinetic expression of genes
Useful for detecting SNPs, particularly important for
allelically heterologous genes as BRCA1
Identification of disease genes - mismatch scanning (GMS)
Identification of new drug targets
Microarrays: Biology's discovery platform

CDFD
 Genomics for diagnostic markers
Normal tissue Cancer tissue

cells Biopsy cells

mRNA

Subtractive methods

Only sequences that differ in

Cancer tissue
Proteomics in generating Diagnostic markers

Analytical
methods

Normal
tissue
Analytical
methods

Colon
cancer
tissue 2-D gel

Cumbersome Marker for cancer

Methods are under development
 Origin of Laser Desorption (LD)
During 1960’s it was demonstrated that the irradiation of low-mass
organic molecules with a high-intensity laser pulse leads to the formation
of ions that could be successfully mass analyzed – the origin of laser
desorption (LD)
Origin of MALDI-TOF
In 1987, Michael Karas and Franz Hillenkamp successfully
demonstrated the use of a matrix in LD to circumvent the mass
Limitation – origin of MALDI
Applications of MALDI-TOF
• Mass detection of peptides
• Peptide Sequencing
• SNPs detection
• Disease diagnosis
SELDI TOF – Surface Enhanced Laser Desorption
Ionisation – Time of flight
Varied chemical and biochemical surface allow differential capture of
proteins based on the intrinsic properties of the proteins

Patterns of masses are identified rather than actual identification

of the proteins

SELDI-TOF has been

successfully used to
detect peaks of proteins
differentially expressed
in sera of ovarian cancer
patients compared to
healthy individuals
Medicine in the Post Genomics era
- Better understanding of the disease
process

- Paradigm shift from preventive to

predictive medicine

- Generalized medicine vs personalized

medicine - Genetic Medicine
Why are we so different? SNP…..ss??

• Single nucleotide variations that occur when a

single nucleotide in the genome sequence is altered
• Occur once in app. every 1000 bases
• Two of every three SNPs involve in replacement of C with T
• Occur both in coding and non-coding regions of the genome
• Most SNPs have no effect on cell function but others
predispose people to disease or influence their response to drug
• About 300,000 SNPs in the human genome
 Pharmacogenomics
Study of the genetic basis for the differences
between the individuals in responses to drug.

• Optimum dose: Daily required dose varies

(e.g. 40-fold for propanolol or 20-fold for warfarin)

• Drug efficacy: (e.g. 30% of scizophrenics do not

respond to antipsychotics, Interferon B/G is effective
only in one out of three patients with multiple
sclerosis or HCC)

•Adverse drug reaction: In US alone, in 1994,

2.2.million of serious cases were reported and was
the 5th leading cause of death What can we gain?
Markers for early detection
Markers for efficacy
Markers for safety
 SNPs

0.1% frequency in the human genome

Bases at the Drug Efficiency of

polymorphic site metabolism medication

TACGTGG Fast High

TACATGG Slow Low

e. g. Cyp 2D6 locus vis-a-vis codein metabolism

 Genetic Variation and drug
responses
Gene Drug Consequences

CYP2C9 Warfarin Increased bleeding

CYP2C19 Omeprazole Rapid metabolism and decreased efficacy in peptic ulcer
UGT 1A1 Irinotecan Metabolism and toxicity of irinotecan
5-LO ABT-761 Efficacy of ABT-761 in asthma
Thiopurine
methyl transferase 6-mercaptopurine Toxicity and efficacy of 6-mercaptopurine in leukemia
Dopamine D3R Typ. neuroleptics Development of tardive dyskinesia in schizophrenics
CETP Pravastatin Efficacy of pravastatin in coronaty atherosclerosis
ADBR2 Salbutamol Efficacy of salbutamol in asthma
 •Recombinant DNATechnology/
Transgenics/ GMOs and GM Food

•Molecular Diagnostics and Genetic Medicine

Stem
•Stem cellsCells

•Cloning

•DNA Fingerprinting or Genomic profiling

Fruits of the gene technology revolution

 Embryonic stem (ES) cells
Applications of Embryonic Stem Cells
in Biotechnology and Medicine
¾ Single cell retains the ability to give
rise to precursor cells of different
human cell types (Heart, Brain,
Kidney, Lung, Ovary, Skin etc.)
 •Recombinant DNATechnology/
Transgenics/ GMOs and GM Food

•Molecular Diagnostics and Genetic Medicine

•Stem cells

Cloning
•Cloning

•DNA Fingerprinting or Genomic profiling

Fruits of the gene technology revolution

Cloning?
 After Dolley...

Next..? Human Cloning ?

Medical benefits
How successful is it to CLONE ?

Green - success

Yellow - very close

Red - not yet

 •Recombinant DNATechnology/
Transgenics/ GMOs and GM Food

•Molecular Diagnostics and Genetic Medicine

•Stem cells

•Cloning

DNA
•DNA Fingerprinting
Fingerprinting or Genomic profiling

Fruits of the gene technology revolution

 DNA Fingerprinting or Genome Profiling
DNA is the molecule of choice for forensic identification for the following
four reasons

1. Discrimination
No two people except identical twins (monozygotic) will
share the same genetic blueprint. Identical twins are
essentially clones.

2. Genetic Continuity
Different biological sources of DNA found at the
crime scene will share the identical pattern if they originate
from the same person regardless of the biological origin

3. Sensitivity
A few drops of blood, a buccal swab or a small semen stain
will generally contain ample amounts of DNA for forensic
4. Stability analysis.
extremely stable molecule capable of withstanding environmental insults both natural and
manmade.
 1 2 3 4

Case of the lost child

Paternity disputes

A case of inclusion
1. Mother
2 Biological child
3. Lost in the “Mela”
4. Father
 1 2 3
Mother is a mother is a fact,
father is a father is a belief

Maternity is also questioned!!

Two mothers claiming parenthood for
a single child!!

1. Biological Mother
2. Disputed Child
3. Suspected Mother
 One army officer was
suspected to be involved In
a murder case .
Blood stain of the victim
was recovered from the
barrel of his revolver due to
Locus Blood stain Blood stain
splashing of blood at the
recovered recovered
from from seat time when the deceased
revolver cover was shot
D8S1179 15 17 15 17

D21S11 28 29 28 29

D18S51 17 17 17 17

D3S1358

vWA
15

14
16

19
15

14
16

19
DNA on weapon
FGA 20 23 20 23

D5S818 11 13 11 13

D13S317 10 11 10 11

D7S820 8 10 8 10

Amelogenin (Gender Marker) X Y X Y

 DNA Fingerprinting
Criminal Identification and Forensics: cases of sexual abuse,
murders, robbery etc (Madhumita murder case)

Personal Identification: mass disaster and mass

fatality incidents
(Attack on World Trade Centre / The Kashmir issue:
distinguishing civilians from terrorists)

In Civil Cases : The Basmati rice dispute

Non human DNA testing: The black buck case

DNA Technology: Not only justice but justice in time
DNA
analysis of
14,249
body parts
of 2,795
people

Use of DNA in criminal investigations can drastically reduce the time

consumed in judgement delivery
 DNA technology
Are we taking the human element out of it?
Questions regarding GENES and PRIVACY

? What if your blood sample for medical check-up is used for research or
other purposes without being informed?

? Genetic testing: what if it cause unnecessary stress and unwelcome

changes in personal relationships

? Should genetic testing be carried out where there is no treatment

available…as in albinism and dwarfism?
? What do you think about the following cases?
- genetic testing for insurance
- genetic testing for new employees
- genetic databanks for forensic use
- genetic databanks for institutionalized children

? Would it cause social biasness: what if people with ‘aggression genes’,

‘cancer genes’ or ‘mood-swing genes’ are considered the Bad Seeds!
We have recently advanced our knowledge of genetics to
the point where we can manipulate life in a way never
intended by nature.

We must proceed with the utmost caution in the

application of this new found knowledge.

LUTHER BURBANK

Time for legal system and science to work together

 DNA and the Law

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 The gene revolution is forcing judges to deal with
science in a way
they never had to before

Questions about the legal relationship between an egg

donor, her husband, person being cloned, a surrogate
mother and the resulting Child, legal rights , privileges
and immunities a cloned child could claim in a
jurisdiction that bans human reproductive cloning
While science in itself is often regarded as
being neutral, the application and products
of research may not be…
Make virus from written information- Bio terrorism!!

July, 2002: Polio virus “synthesized in the laboratory”,

based on the sequence available in print
The work raises alarming questions regarding Bio-terrorism

Challenges the meaning of the terms “extinct/eradication”

Other deadly viruses: Small pox, Ebola, Influenza - deadly

weapons

Vaccination should continue even though disease may no

longer exist
 Are we trying to play God or a Devil?

•Today it is Polio virus...

•Tomorrow it could be still more deadly form of HIV or Plague

•Day after tomorrow may be a human monster (Frankenstein?)

“It is humbling for me and awe-inspiring
to realize that we have caught the first
glimpse of our own instruction book,
previously known only to God”

- Francis Collins, NHGRI