What Is Genomics?
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What Is Genomics?. Genomics is the study of how the entire genome of a species functions as a unit and evolves over time. It is the study of life’s blueprint, life’s diversity, and life’s history. Bioinformatics: Analyses the information content of genomes.

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What Is Genomics?

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What is genomics

What Is Genomics?

Genomics is the study of how the entire genome of a species functions as a unit and evolves over time.

It is the study of life’s blueprint, life’s diversity, and life’s history.

Bioinformatics:Analyses the information content of genomes.

Comparative Genomics: Compares genome sequences with each other to infer evolutionary relationships and mechanisms of evolution.

Functional Genomics: Probes how genomes function, as a whole, to give rise to organisms.

Ecological Genomics: Understands how genomes, and the organisms they encode, fill specific environmental niches.


What is genomics

>500 complete microbial genomes

730 in progress


What is genomics

Why Sequence Whole Genomes?

  • To speed characterization of genes mapped by linkage

  • To obtain a "parts list" for what makes up an organism.

  • To discover what sets of genes make organisms (and each of us) similar to and different from one another.

  • To understand our evolutionary heritage. Our genomes are a reflection of our recent and ancient origins.


What is genomics

Dideoxy “chain termination” DNA sequencing-

Sanger v1, continued


What is genomics

Dideoxy “chain termination”

DNA sequencing-

Sanger v2 !!

Fred Sanger, SECOND Nobel Prize

in 1980 (Chemistry; his first was in

1958 for methods for determining

amino acid sequences in proteins).

Made easily robotfriendly.

High throughput DNA sequencing has

allowed the sequencing of whole

Genomes.

This has driven the Genomics revolution.


What is genomics

The Next Gen Technologies:

Pyrosequencing (454, Roche)

Oil emulsion:

1 template/bead

Sheared and ssDNA

Polony: clonal amplification

Polony + enzyme beads

Picoliter plate

First of the ‘parallel’ sequencing platforms.


What is genomics

Sequencing-by-synthesis

Pyrosequencing

3’ATCGTTGCACGTCGACGTA

5’TAGCAAC

G

dGTP

PPi

ATP sulfurylase

ATP

Luciferase

400K reads X 400 bases = 16-20 Mb in 4 hrs!

So, 125 Mb is only 6 runs for 1X coverage!


What is genomics

The Next Gen Technologies: Illumina (Solexa)

Sequence by synthesis – one base at a time

Each base has a different color

Each base has a reversible terminator


What is genomics

The Next Gen Technologies: Illumina (Solexa)

3’

5’

G

C

T

A

C

G

T

A

C

T

A

C

C

5’

C

C

G

A

T

A

A

A

C

G

T

T

T

A

T

G

G

G

C

1

2

3

4

5

6

7

8

9

Base calling

Image acquisition

TGCTACGAT …

Sample preparation

DNA

Cluster growth

Single molecule array

Sequencing

5 million clusters / channel; 8 channels / flow cell

= 40 million reads times ~35 cycles (bases)

= 120 billion bases in 3 days (1.2Gb)


What is genomics

Technology Development drives Biology


What is genomics

First, we've learned that we have a lot to learn

Over 35% of genes in ANY organism (including Human)

have no deducible function!


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