BioinformaticsKick Ass Cool Stuff

Bioinformatics

Def.: where the rubber meets the road (i.e., where computer science meets biology)

"The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.”

Central Dogma: DNA -----> RNA -----> protein

? What is a genome ?

Total amount of the DNA found within one complete set of chromosomes

M. Cummings, 2000

? How much DNA is in the human

genome ?

3 billion base pairs of DNA

?Size of the Human Genome?

GenBank has over 30 billion bases and is doubling every year

How do we access and analyze the data?

?What are the challenges?

10 sets of encyclopedias, 32 volumes each, but only 4 letters: ATGC

Background Info on the HGP

Begun in 1990

15 year project

Background Info on the HGP

Federal and private funding

Multinational project

DOE and NIH at an estimated cost of $3 billion.

Purposes of HGP

Determine the sequences of the 3 billion chemical base pairs that make up human DNA,

Identify all the 100,000 genes in human DNA,

M. Cummings, 2000

M. Cummings, 2000

Mapped Human Diseases

M. Cummings, 2000

Chromosome 4 Chromosome 17 Huntington diseaseHuntington disease Breast cancer (BRCA1)Breast cancer (BRCA1)

Chromosome 5 Chromosome 19 Familial polyposisFamilial polyposis Myotonic dystrophyMyotonic dystrophy

Chromosome 7 Chromosome 21 Cystic fibrosisCystic fibrosis Amyotrophic lat. sclerosisAmyotrophic lat. sclerosis

Chromosome 13 X Chromosome RetinoblastomaRetinoblastoma Duchene Musc. dystrophyDuchene Musc. dystrophy

Fragile-X syndromeFragile-X syndrome

Chromosome 13 Polycystic kidney diseasePolycystic kidney disease

Benefits from HGP: Molecular Medicine

Earlier detection of genetic predispositions to disease

Gene therapy

Improved diagnosis of disease

http://www.ornl.gov/hgmis/project/benefits.html

Disease Identification: Microarray Technology

Hartl and Jones, 2000

Benefits of HGP: Microbial Genomics

New energy sources (biofuels)

Environmental monitoring to detect pollutants

Protection from biological and chemical warfare

Toxic waste cleanup

http://www.ornl.gov/hgmis/project/benefits.html

Benefits of HGP:DNA Forensics (Identification)

Establish paternity and other family relationships

Identify crime and catastrophe victims

Exonerate persons wrongly accused of crimes

Identify potential suspects whose DNA may match evidence left at crime scenes

http://www.ornl.gov/hgmis/project/benefits.html

Agriculture

Livestock Breeding (MARC)

Bioprocessing

http://www.ornl.gov/hgmis/project/benefits.html

Other benefits of HGP