Transcript lecture28_Sequencing.. - University of Alberta

historical costs to sequence the
3 billion bp of a human genome
Gordon Moore
costs to sequence a human genome
10
log10 (US dollar)
9
8
$3 billion
7
$300 million
6
5
$300,000
two vendors
4
1989
1991
1993
1995
1997
1999 2001
year sequenced
2003
competition
2005
2007
2009
BGI Offers Next-Gen Sequencing Service: Kicks Off 100Genome Sequencing Project [8 January 2008]
Knome, BGI Forge Sequencing Alliance; GATC Spins Off
Personal Genomics Unit [January 15 2008]
Google
580,000 SNPs
BGI-Shenzhen
1 million SNPs
whole genome
YanHuang and the panda genome
(raising awareness for the new technologies)
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 nontrivial for 35 bp reads even with paired end
information and 50x redundancy.
BGI-Shenzhen and allies in the US and UK will be
sequencing 1000 human genomes in the next 3 years
Nature: 17 January 2008
Science: 25 January 2008
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
gene hunts vs
synthetic biology
human
genome
infectious
agents
environmental
factors
cultures vs
metagenomics
questionnaires vs
molecular detection
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
classical methods
metagenomics
biological sample
biological sample
grow as a
pure culture
molecular biology
known sequence
targeted
amplification
partial purification
(e.g. by size)
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 of the “virome”
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
human specimen
DNA
RNA
virome
sequence
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
synthesis costs
$0.50 per bp
genome
synthesis
disease
tissue
viral
fragment
genome
sequence
population
case-controls
compound
screening
develop
vaccines
develop
diagnostics
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