Dr N A GanaiProfessor

Centre of Animal BiotechnologySKUAST-Kashmir

Contents Introduction to

Bioinformatics Complexity of life Size of genome Exponential growth in information

generation Why and how to handle this

information Definition of Bioinformatics?

Data bases Tools

Scope of Bioinformatics Anticipated benefits Ethical, Legal, and Social

Issues

Variation : Basis of evolution

What is Marker?

`̀

Marker is a piece of Marker is a piece of DNA molecule that is DNA molecule that is

associated with a associated with a certain trait of a certain trait of a

organismorganismMorphologicalMorphological

BiochemicalBiochemical

ChromosomalChromosomal

GeneticGeneticTypes of Types of MarkersMarkers

Animals are selected based on Animals are selected based on appearanceappearance

Eg. PIGMENTATIONEg. PIGMENTATION

Disadvantage: lack of polymorphismDisadvantage: lack of polymorphism

Animals are selected based on biochemical Animals are selected based on biochemical propertiesproperties

Eg. Hb, AMYLASE, BLOOD GROUPS ETC.Eg. Hb, AMYLASE, BLOOD GROUPS ETC.

Disadvantage:Disadvantage: Sex limitedSex limitedAge dependentAge dependentInfluenced by environmentInfluenced by environmentIt covers less than 10% of genomeIt covers less than 10% of genome

Animals are selected based on Animals are selected based on structural & numerical variationsstructural & numerical variations

Eg. Structural and Numerical VariationsEg. Structural and Numerical VariationsStructural- Structural- Deletions, Insertions etc.Deletions, Insertions etc.Numerical-Numerical- Trisomy, Monosomy, Nullysomy Trisomy, Monosomy, Nullysomy

Disadvantage: low polymorphismDisadvantage: low polymorphism

Molecular Marker

Revealing variation at a DNA level

Characteristics:Co-dominant expressionNondestructive assayComplete penetranceEarly onset of

phenotypic expression High polymorphism Random distribution

throughout the genome Assay can be automated

DNA isolated from any tissue eg. Blood, hair etc.

DNA isolated at any stage even during foetal life

DNA has longer shelf-life readily exchangeable b/w labs

Analysis of DNA carried out at early age/ even at the embryonic

Stage irrespective of sex.

Molecular Markers

Single locus markerSingle locus marker

Multi-locus markerMulti-locus marker

RFLP

Microsatellite

STS

DNA Fingerprinting

AFLP

RAPD

SNPs

DNA is not merely a molecule with a pattern; it is a code, a language, and an

information storage mechanism

Size of Human Genome Each cell carries: 3.2 billion base pairs

A code you need to write in 500 books, each book of 500 pages

Length of DNA in adult man: The total length of DNA present in one adult

human is calculated as: (length of 1 bp)(number of bp per cell)(number of cells in

the body)(0.34 × 10-9 m)(6 × 109)(1013)2.0 × 1013 meters

That is the equivalent of nearly 70 trips from the earth to the sun and back.

Human Genome Project• HGP: International research

effort• Began 1990, completed

2003

• Biggest ever project in life sciences

• 20 labs participated world around

• Next steps for ~30,000 genes– Function and regulation of all

genes– Significance of variations

between people– Cures, therapies, “genomic

healthcare”

Genomics

Transcriptomics

Proteomics Metabolomi

cs

Year Base Pairs Sequences1982 680,338 606

1983 2,274,029 2,427

1984 3,368,765 4,175

1985 5,204,420 5,700

1986 9,615,371 9,978

1987 15,514,776 14,584

1988 23,800,000 20,579

1989 34,762,585 28,791

1990 49,179,285 39,533

1991 71,947,426 55,627

1992 101,008,486 78,608

1993 157,152,442 143,492

1994 217,102,462 215,273

1995 384,939,485 555,694

1996 651,972,984 1,021,211

1997 1,160,300,687 1,765,847

1998 2,008,761,784 2,837,897

1999 3,841,163,011 4,864,570

2000 11,101,066,288 10,106,023

2001 15,849,921,438 14,976,310

2002 28,507,990,166 22,318,883

2003 36,553,368,485 30,968,418

2004 44,575,745,176 40,604,319

2005 56,037,734,462 52,016,762

2006 69,019,290,705 64,893,747

2007 83,874,179,730 80,388,382

2008 99,116,431,942 98,868,465

Av. Growth in data generation :

5400 times per year

Exponential Growth in Biological Databases:High throughput Technologies

PCR : by Kary Mullis 1983 - an employee of Cetus Corporation, a biotechnology firm in CaliforniaAwarded the Nobel Prize for the discovery of PCR in 1993

Microarray Technology

Real-Time PCR

DNA Chips

Sequencing

Sanger method : 1975Chain Termination Method

Maxam Gilbert : 1977Chemical Modification Method

Next Generation: 1994High Throughput Parallel sequencingEntire genome can be sequenced in a matter of weeks

History of DNA Sequencing

Avery: Proposes DNA as ‘Genetic Material’

Watson & Crick: Double Helix Structure of DNA

Holley: Sequences Yeast tRNAAla

1870

1953

1940

1965

1970

1977

1980

1990

2002

Miescher: Discovers DNA

Wu: Sequences Cohesive End DNA

Sanger: Dideoxy Chain TerminationGilbert: Chemical Degradation

Messing: M13 Cloning

Hood et al.: Partial Automation

• Cycle Sequencing • Improved Sequencing Enzymes• Improved Fluorescent Detection Schemes

1986

• Next Generation Sequencing•Improved enzymes and chemistry•Improved image processing

Adapted from Eric Green, NIH; Adapted from Messing & Llaca, PNAS (1998)

1

15

150

50,000

25,000

1,500

200,000

50,000,000

Efficiency(bp/person/year)

15,000

100,000,000,000 2008

The Genome Sequence is at hand…so?

“The good news is that we have the human genome. The bad news is it’s just a parts list”

What Next???

We need to know every part, its function and

application

What is Bioinformatics?

The newest, fastest growing specialty in the life sciences that integrates biotechnology and computer science.

Computers aid to collect, analyze, and interpret biological information at the molecular level.

Understand a living cell and how it functions at molecular level

Develop data basses and computational tools Databases to:

Store all the data (information) related to Genomics, Transcriptomics, preoteomics, Metabolomics

Tools to To mine (analyze) databases to generate knowledge

to better understand the living systems

Goal of Bioinformatics

Anticipated Benefits of Genome Research & Bioinformatics

Molecular Medicine : Gene Testing , Pharmacogenomics Gene Therapyimprove diagnosis of diseasedetect genetic predispositions to diseasecreate drugs based on molecular informationuse gene therapy and control systems as drugsdesign “custom drugs” (pharmacogenomics) based on individual genetic profiles

Huntigton disease (an inherited neurodegenerative disorder)

Symptoms:uncontrollable dance-like (choreatic) movements,mental disturbance,personality changes and intellectual impairment

repeats of the trinucleotide CAG,corresponding to polyglutamine blocks in the corresponding protein, huntingin

11-28 CAG repeats -->normal

29-34 CAG repeats---->likely to develop disease

35-41 CAG repeats develop mild symptoms

morethan 41 CAG repeats suffer full huntington disease

Diagnosis of disease and disease risk

Microbial Genomics rapidly detect and treat pathogens in clinical

practice develop new energy sources (biofuels) monitor environments to detect pollutants protect citizenry from biological and chemical

warfare clean up toxic waste safely and efficiently

DNA Identification (Forensics)identify potential suspects whose DNA may match evidence left at crime scenes

exonerate persons wrongly accused of crimes

establish paternity and other family relationships

identify endangered and protected species as an aid to wildlife officials (could be

detect bacteria and other organisms that may pollute air, water, soil, and food

match organ donors with recipients in transplant programs

determine pedigree for seed or livestock breeds 

Benefits: …contined

Agriculture, Livestock Breeding, and Bioprocessing

grow disease-, insect-, and drought-resistant crops

breed healthier, more productive, disease-resistant farm animals

grow more nutritious produce

develop biopesticides

incorporate edible vaccines incorporated into food products

develop new environmental cleanup uses for plants like tobacco

Benefits …cont .

ELSI: Ethical, Legal, and Social Issues

• Privacy and confidentiality of genetic information.

• Fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others.

• Psychological impact, stigmatization, and discrimination due to an individual’s genetic differences.

• Reproductive issues including adequate and informed consent and use of genetic information in reproductive decision making.

• Clinical issues including the education of doctors and other health-service providers, people identified with genetic conditions, and the general public about capabilities, limitations, and social risks; and implementation of standards and quality‑control measures.

Health and environmental issues concerning genetically modified foods (GM) and microbes.

Commercialization of products including property rights (patents, copyrights, and trade secrets) and accessibility of data and materials.