Public Consortium
Celera Genomics
Sequence Genomes
Find Genes
Establish Function and Disease Mechanism
Drug Candidates
Cure
Genetic Mapping, Mutation Detection
Diagnostics/ Prognostics
Gene Therapy
“Sequence the 3 billion (+) base pairs of human DNA and identify all genes contained in the human genome”
DNA Sequence ‘Reads’ Need 60,000,000 of them!!
Time Line of the Human Genome Project
BCM-HGSC: Sequencing Throughput 2,000,000
Today 1.9 M reads
1,800,000 1,600,000 1,400,000 1,200,000 1,000,000 800,000 600,000 400,000 200,000 0 Jan-00
May-00
Sep-00
Jan-01
May-01
Sep-01
Jan-02
May-02
Standard Molecular Biology techniques – running agarose gels.
CS-Packard DNA Production Robotic Systems (x 3)
Multiplexed (104) Capillary Array for Electrophoresis
State of the Art - ABI 3700 “Prism” DNA Sequencer
US $300,000 Each! A room full of 3700 Sequencers – total price tag of US $22.5 Million
“State of the Art”: Assembly Whole Genome Shotgun (WGS)
BAC by BAC Versus
-Front end loaded, - Tractable Assembly Problem
-Efficient front end, - Huge Assembly Problem BCMHGSC
Linux Farm
Very small changes in technology have had a huge impact on the HGP….. Imagine what a large change in technology would do…
The Future: More Genomes!! Rat, Mouse, Rabbit, Dog, Chimp, Rhesus, Zebrafish, Fugu, Hamster, Cow, Sheep, Pig, Chicken, Honey Bee, Silk Worm, Shark, Dolphin, Whale, Frog, Sea Urchin, Sea Squirt, Sea Turtle, Salmon, Hydra, Wallaby, Platypus, Rice, Wheat, Maize, Sorgum, Soy, Banana, Poplar, Potato, Corn, Sea Turtle, Wheat, Pine ……….
COMPLETE (HETEROZYGOUS) MUTATION DETECTION ABI 370: Universal Primer Tag PCR
exon
13,000 OMIM - 10,000 Entries
BCMHGSC
Dextrocardia and Situs Inversus
Disorders of laterality occur in 2 – 3 per 10,000 live births
Pulmonary valve stenosis mutations
BCMHGSC
SCREENING 160 SPORADIC PATIENTS IN NODAL SIGNALING PATHWAY RECEPTORS TYPE 1 (ALK2 “ACVR1” ALK4 “ACVR1B”; ALK7 (mouse) TYPE 2 (ActRIIA “ACVR2”; ActRIIB “ACVR2b”)
NODAL + LEFTYA competing for receptor components EGF-CFC Co-Factor Proteins Cripto and Cryptic Interacts with ALK4 receptor
INTRACELLULAR MEDIATORS, SMAD2, SMAD3, SMAD4
SMADS INTERACTS w/ TGIF to repress pathway
Human mutations in all loci marked in read
SMADS INTERACTS w/ FAST1 to activate gene
Target Genes: PITX2 + NODAL + LEFTYB
Epigenetics/Methylation
Epigenix web site
Genomic DNA can be different in Different cells of the same person…..
BCM-HGSC
~ 230 Personnel