Genome sequencing the human genome project speaker joy scaria biological sciences group
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Genome Sequencing & the Human Genome Project Speaker- Joy Scaria Biological Sciences Group. “Today we are initiating an unending study of human biology. Whatever else [happens]…. It will be an adventure, a priceless endeavor” -Norton Zinder.

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Genome sequencing the human genome project speaker joy scaria biological sciences group

Genome Sequencing & the Human Genome ProjectSpeaker- Joy Scaria Biological Sciences Group


Today we are initiating an unending study of human biology whatever else happens

“Today we are initiating an unending study

of human biology. Whatever else [happens]….

It will be an adventure, a priceless endeavor”

-Norton Zinder

Comparisons

Manhattan Project

Apollo programme


Today we are initiating an unending study of human biology whatever else happens

Genome Size

Human genome- 3 Billion nucleotides(3.2Gb)

E.coli – 4.7 million Nucleotides

E. coli genome – 300 pages of a 1000 page book

D.melanogaster- 10 books (8 Chromosomes)

Human – 200 books( 200, 000 pages)


Today we are initiating an unending study of human biology whatever else happens

Origin of the project

No one is certain as to who first suggested the idea

First serious proposal was by Robert Sinsheimer

Renato Dulbecco who was in attendance told this to

J.D. Watson at CSHL

DOE Scientists were made aware of Sinsheimer’s

proposal

Charles Delisi Head of DOE’s Health & Environmental

Research convened a metting and offered Los Alamos

And Livermore labs to start the project


Today we are initiating an unending study of human biology whatever else happens

Celera Vs Government project

The cDNA dispute and patent claims

Craig Ventor Establishes Celera

Celera database is paid while the other is free


Whose genome is being sequenced

Whose genome is being sequenced?

  • the first reference genome is a composite genome from several different people

  • generated from 10-20 primary samples taken from numerous anonymous donors across racial and ethnic groups

Male or Female ???


Today we are initiating an unending study of human biology whatever else happens

Whose Money ??

Major participant is US government

Totally 20 Groups from UK, Japan, France

Germany and China are involved

Celera is a private company


Human genome project

Human Genome Project

Project goals are to

■ identify all the approximate 30,000 genes in human DNA,

■ determine the sequences of the 3 billion chemical base pairs that

make up human DNA,

■ store this information in databases,

■ improve tools for data analysis,

■ transfer related technologies to the private sector, and

■ address the ethical, legal, and social issues (ELSI) that may arise from

the project.

Recent Milestones:

■ June 2000 completion of a working draft of the entire human genome

■ February 2001 analyses of the working draft are published


Today we are initiating an unending study of human biology whatever else happens

Satellite projects


Today we are initiating an unending study of human biology whatever else happens

GenomeSequencing

Published/complete genomes = 173

Prokaryotic ongoing projects = 432

Eukaryotic ongoing genomes = 368

Total = 974 (data as on 20-07-04)

Many more on the way


Today we are initiating an unending study of human biology whatever else happens

Draft First Sequence later


Today we are initiating an unending study of human biology whatever else happens

Developing overlapping genomic clone library


Today we are initiating an unending study of human biology whatever else happens

Cloning in Bacteria


Today we are initiating an unending study of human biology whatever else happens

Robotic Assembly for HTG Sequencing


Today we are initiating an unending study of human biology whatever else happens

Determining the purity of DNA

To determine the DNA concentration, the eluted samples are transferred into

specially designed quartz glass microplates and the absorbancy at 260 nm and 320 nm


Today we are initiating an unending study of human biology whatever else happens

Sequencing

The robot is gripping a 384 well microplate (used for PCR or sequencing)

from a 384 well MJ PTC 225 Tetrad Block.


Today we are initiating an unending study of human biology whatever else happens

Automated liquid handling

The Hydras are used for all liquid handling steps,

e. g. setting up the PCR reaction, the purification, the sequencing, etc.


Today we are initiating an unending study of human biology whatever else happens

Station Fridge.

The fridge is for plates with contents (e. g. sequencing mix, PCR mix, etc.)

which have to be stored at +4 °C. The door is opened and closed pneumatically


Today we are initiating an unending study of human biology whatever else happens

Capillary Array Electrophoresis (CAE).

DNA samples are introduced into the 96-capillary array; as

the separated fragments pass through the capillaries, they are

irradiated all at once with laser light. Fluorescence is measured

by a charged coupled device that acts as a simultaneous multichannel

detector. (Inset circle at upper left: Closeup view of individual capillary

lanes with separated samples.


Today we are initiating an unending study of human biology whatever else happens

Technical Parlance

Raw sequence: Individual unassembled sequence reads,

produced by sequencing of clones containing DNA inserts.

Paired-end sequence: Raw sequence obtained from both

ends of a cloned insert in any vector, such as a plasmid or

bacterial artificial chromosome.

Finished sequence: Complete sequence of a clone or

genome, with an accuracy of at least 99.99% and no gaps

BAC clone: Bacterial artificial chromosome vector carrying a genomic

DNA insert, typically 100–200 kb. Most of the large-insert clones

sequenced in the project were BAC clones

Draft clone :A large-insert clone for which roughly half-shotgun

sequence has been produced.


Today we are initiating an unending study of human biology whatever else happens

Predraft clone: A large-insert clone for which some shotgun sequence

is available, but which does not meet the standards for inclusion in the

collection of draft clones.

Contig The result of joining an overlapping collection of sequences

or clones.

Scaffold: The result of connecting contigs by linking information from paired-end reads from plasmids, paired-end reads from BACs, known messenger RNAs or other sources. The contigs in a scaffold are ordered

and oriented with respect to one another

STS :Sequence tagged site, corresponding to a short (typically less than 500 bp) unique genomic locus


Today we are initiating an unending study of human biology whatever else happens

Common Sources of STSs

Expressed sequence tags (ESTs) are short sequences obtained

by analysis of complementary DNA (cDNA) clones.

Complementary DNA is prepared by converting mRNA into

double-stranded DNA and is thought to represent the sequences

of the genes being expressed.

Simple sequence length polymorphisms (SSLPs) are arrays of

repeat sequences that display length variations. SSLPs that are

polymorphic and have already been mapped by linkage analysis

are particularly valuable because they provide a connection

between genetic and physical maps.

Random genomic sequences


Today we are initiating an unending study of human biology whatever else happens

SNP :Single nucleotide polymorphism

RFLP: Restriction fragment length polymorphism


Today we are initiating an unending study of human biology whatever else happens

What does the project reveal ?

Gene Numbers- Celera estimates 26000,

Public project puts it as 3100

Genome is laden with repeat sequences

But Puffer fish Genome virtually lacks any

Human repetitive sequences are old and enfeebled

While Mouse repeats are dynamic

More than 1.4 million SNPs has been found

Origin of genome- From evolutionary past

Only 94 of 1,278 protein families are vertebrate specific


Today we are initiating an unending study of human biology whatever else happens

Why did evolution favor Males

No sexuality in lower kingdoms

Hermaprodites are perfect animals

After all Why do we need males?

Instead of being parasites on females why do

they just go away?


Today we are initiating an unending study of human biology whatever else happens

Total number of genes 252

SRY is mapped on Y.p11.3

It is just 896bp


Today we are initiating an unending study of human biology whatever else happens

Question of Mitochondrial Eve

Medical research

Artificial intelligence and many more…


Next step in genomics

Next Step in Genomics

• Transcriptomics involves large‑scale analysis of messenger RNAs

(molecules that are transcribed from active genes) to follow when, where,

and under what conditions genes are expressed.

• Proteomics—the study of protein expression and function—can bring

researchers closer than gene expression studies to what’s actually

happening in the cell.

• Structural genomics initiatives are being launched worldwide to

generate the 3‑D structures of one or more proteins from each protein

family, thus offering clues to function and biological targets for drug design.

• Knockout studies are one experimental method for understanding the

function of DNA sequences and the proteins they encode. Researchers

inactivate genes in living organisms and monitor any changes that could

reveal the function of specific genes.

• Comparative genomics—analyzing DNA sequence patterns of humans

and well‑studied model organisms side‑by‑side—has become one of the

most powerful strategies for identifying human genes and interpreting their

function.


Today we are initiating an unending study of human biology whatever else happens

References

http://www.nature.com/genomics/human/papers/409860a0_fs_1.html

http://www.celera.com/therapeutics/home.cfm?ppage=genomics

http://vector.cshl.org/

http://www.ornl.gov/hgmis/

Nature : Vol.409, No.6822., 15 Feb 2001


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