Historical costs to sequence the 3 billion bp of a human genome two vendorscompetition $3 billion...
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Transcript of Historical costs to sequence the 3 billion bp of a human genome two vendorscompetition $3 billion...
historical costs to sequence the 3 billion bp of a human genome
two vendors competition
costs to sequence a human genome
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1989 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009
year sequenced
log
10 (
US
do
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$3 billion
$300 million
$300,000
Gordon Moore
BGI Offers Next-Gen Sequencing Service: Kicks Off 100-Genome Sequencing Project [8 January 2008]
Knome, BGI Forge Sequencing Alliance; GATC Spins Off Personal Genomics Unit [January 15 2008]
1 million SNPs580,000 SNPs
whole genome
BGI-Shenzhen
Emperor’s Yan and Huang were the first rulers of ancient China, so modern Chinese say that they are descendants of YanHuang.
The panda is a Chinese national treasure and the logo for the World Wildlife Fund. While not the first endangered species to be sequenced (chimp was first), it will be the first with a conservation focus.
Whole genome shotgun assembly is non-trivial for 35 bp reads even with paired end information and 50x redundancy.
YanHuang and the panda genome (raising awareness for the new technologies)
Nature: 17 January 2008 Science: 25 January 2008
BGI-Shenzhen and allies in the US and UK will be sequencing 1000 human genomes in the next 3 years
expressed gene sequences of 1000 medicinal plants for only $2 million
There are 96 plant species with more than 20,000 expressed sequence tags (ESTs), but most are crop plants. If we count only medicinal plants, generously defined to include makers of secondary metabolites with purported health benefits, such as lycopene for tomatoes and resveratrol for grapes, there are 16 plant species with more than 20,000 ESTs. If we use a strict definition of medicinal, there are just 4 plant species with more than a mere 5000 ESTs. They are artemesia, Madagascar periwinkle, gingko, and ginseng.
the triad of biological causation
human genome
gene hunts vs synthetic biology
environmental factors
questionnaires vs molecular detection
infectious agentscultures vs
metagenomics
http://www.cancer.gov/cancertopics/factsheet/Risk/BRCA
Among individuals of Ashkenazi Jewish descent, researchers have found that about 2.3 percent have an altered BRCA1 or BRCA2 gene. This frequency is about 5 times higher than that of the general population.
http://www.who.int/mediacentre/factsheets/fs297/en/index.html
One-fifth of cancers worldwide are due to chronic infections, mainly from hepatitis B viruses HBV (causing liver), human papilloma viruses HPV (causing cervix), Helicobacter pylori (causing stomach), schistosomes (causing bladder), the liver fluke (bile duct) and human immunodeficiency virus HIV (Kaposi sarcoma and lymphomas).
we can cure, eradicate, or at least treat almost all infectious diseases
metagenomics: DNA sequencing analysis of viral and microbial worlds
without requiring a pure culture
we have little information on the vast majority of viral and microbial species because of our inability to culture them in the lab; the estimate is fewer than 1% have been cultured
classical methods
known sequence grow as a pure culture
molecular biologytargeted
amplification
biological sample
metagenomics
partial purification (e.g.
by size)
just sequence it
biological sample
metagenomics of the “virome”
human specimen
0.45 m filter
viral particles
DNA RNA
virome sequence
tangential flow filter, high speed centrifuge
viral genomes (103 bp) are very small compared to bacterial (106 bp) or human (109 bp) genomes and it helps to remove non-viral contamination
February 6, 2008 (10.1056/NEJMoa073785)
A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases
Gustavo Palacios, Julian Druce, Lei Du, … and W. Ian Lipkin
Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York; Victorian Infectious Diseases Reference Laboratory, Victoria, Australia; 454 Life Sciences, Branford, CT; Centers for Disease Control and Prevention, Atlanta.
Viral and bacterial cultures; polymerase-chain-reaction assays for known pathogens; viral and panmicrobial microarrays revealed no plausible candidates.
However, BLASTX analysis of the deduced proteins for 94,043 reverse transcribed sequences revealed 14 fragments consistent with Old World arenaviruses.
22 February 2008: Vol. 319. no. 5866, pp. 1096 - 1100
Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
Huichen Feng, Masahiro Shuda, Yuan Chang, Patrick S. Moore
Molecular Virology Program, University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Suite 1.8, Pittsburgh, PA 15213, USA.
99.4% of 382,747 tumor derived sequences aligned to human RefSeq RNA, mitochondrial, assembled chromosomes, or immunoglobulin sequences. Two sequences were used to define a previously unknown human polyomavirus.
proof of causation and other steps after candidate pathogen is identified
metagenomics of idiopathic inflammatory diseases is a high-risk extremely-high-payoff activity, but there is a low-risk moderately-high-payoff activity that will put Alberta “on the map” internationally
disease tissue
viral fragment
genome sequence
compound screening
develop diagnostics
population case-controls
develop treatments
genome synthesis
develop vaccines
synthesis costs $0.50 per bp
computationally accelerated