historical costs to sequence the 3 billion bp of a human genome

1. Gordon Moore $3 billion $300 million two vendors $300,000 competition historical costs to sequence the 3 billion bp of a human genome

2. 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] Google BGI-Shenzhen 580,000 SNPs 1 million SNPs whole genome competition for the personal genome heats up

3. 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. Emperor’s Yan and Huang were the first rulers of ancient China, so modern Chinese say that they are descendants of YanHuang. YanHuang and the panda genome (raising awareness for the new technologies)

4. Science: 25 January 2008 Nature: 17 January 2008 BGI-Shenzhen and allies in the US and UK will be sequencing 1000 human genomes in the next 3 years

5. 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. expressed gene sequences of 1000 medicinal plants for only $2 million

6. gene hunts vs synthetic biology human genome infectious agents environmental factors cultures vs metagenomics questionnaires vs molecular detection the triad of biological causation

7. 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

8. classical methods metagenomics biological sample biological sample grow as a pure culture known sequence partial purification (e.g. by size) targeted amplification molecular biology just sequence it 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 metagenomics: DNA sequencing analysis of viral and microbial worlds without requiring a pure culture

9. tangential flow filter, high speed centrifuge 0.45 m filter viral particles 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 DNA RNA virome sequence human specimen metagenomics of the “virome”

10. 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.

11. 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.

12. synthesis costs $0.50 per bp genome synthesis develop vaccines disease tissue viral fragment genome sequence population case-controls develop diagnostics compound screening develop treatments computationally accelerated 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 proof of causation and other steps after candidate pathogen is identified