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Grass Roots Genomics: Using Hong Kong's Emblem to Crack Exobytes of Data
@SCEdmunds@BauhiniaGenome
#HKGenome
The language of heredity & evolutionWatson & Crick (based on data from Franklin) crack structure
http://www.bbc.co.uk/schools/gcsebitesize/science/add_ocr_pre_2011/growth_development/genesrev1.shtml
Fred Sanger figures out how to read it…
https://blogs.scientificamerican.com/the-curious-wavefunction/winning-two-nobel-prizes-revolutionizing-genomics-turning-down-knighthoods-
the-legacy-of-fred-sanger-1918-2013/
AKA dideoxy chain-termination
https://en.wikipedia.org/wiki/Sanger_sequencing#/media/File:Sanger-sequencing.svg
So DOE wants to read it all…
V
Then it becomes a race…
A brief history of genomics…
Source: http://www.genome.gov/Images/press_photos/highres/38-300.jpg
Human Genome Project: 1990-2003. 1 Genome = $3 Billion
Post-Human Genome Project
1st Gen
2nd (next) Gen
Source: http://www.genome.gov/sequencingcosts/ (with apologies)
2nd (next) Gen
Next-Gen Sequencing
AKA
Sequencing-by-Synthesis
3rd Generation: AKA Single Molecule Seq
Real-time, FRET, Nanopore, Semiconductor Sequencing…
http://www.nature.com/nbt/journal/v28/n5/full/nbt0510-426.html
Genome Assembly: piecing together the overlap
Seq Tech Read Length Accuracy Cost per Mbp
Sanger Seq 400-900bp 99.9% $2400
Solexa/Illumina 50-500bp 99.9% $0.05-$0.15
PacBio Up to 40kb 87% $0.13–$0.60
Nanopore Up to 300Kbp ~90% $0.11 - 0.5
https://en.wikipedia.org/wiki/DNA_sequencing#High-throughput_methodshttp://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html
Genome(-ish) Assembly (the cheap version)
http://www.nature.com/nrd/journal/v12/n5/full/nrd3979.html
eDNA & metabarcoding in the field for biodiversity studies,
clinical sequencing in the clinic. Used in ebola & zika crises.
Produces real-time data, can diagnose infectious disease in
minutes.
Genomics TNG. Nanopores: the final frontier.
In situ sequencing: ebola, zika & beyond
Nanopores meet Open Hardware: Quantum Sequencing?
Methylomics
Histone Modifications
Chromatin profiling
ncRNA
E is for EPIGENOMICS
Metagenomics & the microbiome
Single Cell Sequencing
Ancient DNA Sequencing
Omes & more omes!
The skills needed for the 21st century
"by 2025, it is possible that as many as 25% of the population in developed nations and half of that in less-developed nations will have their genomes sequenced”
Big Data: Astronomical or Genomical?http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1002195
GENOMICS IN HONG KONG
BGI HK Chamber O’Illumina’sThe LHC of Biology?
20PB of storage
Made in Hong Kong
Hong Kong’s R&D spend is lowData: WorldBank
Hong Kong could invest in R&D
• HK runs a surplus (unlike everyone else)
• US spend on Human Genome (1988-2003) returned $1.98 in economic output for every $1.00 spent
• US spend on genomics (1993-2010) returns $2.01 for every $1.00 spent
• General public R&D spend in UK returns about £1.20 for every £1.00 spent
http://bit.ly/1jTzB3R
Hong Kong’s focus…“The plot earmarked for expansion of Hong Kong Science Park might now be used to build apartment blocks instead. Is the government backing down on its commitment to project Hong Kong as a major technology hub?” http://bit.ly/1TxCRj3
Hong Kong’s focus…“The plot earmarked for expansion of Hong Kong Science Park might now be used to build apartment blocks instead. Is the government backing down on its commitment to project Hong Kong as a major technology hub?” http://bit.ly/1TxCRj3
WORKING AROUND THE SYSTEM
Breaking the funding bottleneck
Biggest crowdfunding successes
The “Peoples Parrot”Puerto Rican Parrot Genome Project (Amazona vittata )
Rarest parrot, national bird of Puerto Rico
Community funded from artworks, fashion shows, beer brands, crowdfunding…
Genome annotated by students in community college as part of bioinformatics education
Paper and Data published in GigaScience and GigaDB
Taras K Oleksyk, et al., (2012) A Locally Funded Puerto Rican Parrot (Amazona vittata) Genome Sequencing Project Increases Avian Data and Advances Young Researcher Education. GigaScience 2012, 1:14Steven J. O’Brien. (2012): Genome empowerment for the Puerto Rican parrot – Amazona vittata. GigaScience 2012, 1:13Oleksyk et al., (2012): Genomic data of the Puerto Rican Parrot (Amazona vittata) from a locally funded project. GigaScience. http://dx.doi.org/10.5524/100039
CHANGING THE SYSTEM
Brought to you by: HKCUHK
…and the people of Hong Kong
An emblematic genome project
A historical mystery that needs solving
?
Botanical and Afforestation Department, 1903: "The mysterious origin of the tree and its magnificent flowers at once arrest the interest. … So far, all efforts to identify them with any foreign species have failed"
Plant genomics #101Why hybrids changed the world?
An icon that needs protecting
Useful Bauhinia?
Latin name
Common name
(Nepal) Edible use Other use
Bauhinia purpurea Tanki
Flowers and young shoots eaten as vegetable. Leaves used as fodder.
Bauhinia valii BhorlaPods eaten as vegetable.
Fruits edible.
Stem bark used to make ropes.Leaves used to make umbrella
Traditional plates for ritual functions.
Bark juice used as fermenting material and to cure blood
dysentery.
Bauhinia variegata Koiralo
Young shoots and leaves eaten as vegetable. Flowers eaten as vegetable or used
to make pickle. N/A
Useful Bauhinia?
A puzzle that needs assembling
With Parts Made in (BGI) Hong Kong
Building skills and awareness in HK
Building skills and awareness in HK
….in the news
http://www.scmp.com/magazines/post-magazine/article/1875917/unique-project-sequence-genome-hong-kong-bauhinia-tree
CNN “On China” covering the Bauhinia Genome project, 27th April 2016
https://youtu.be/TyJBALA0da0
Building skills and awareness in HK
….on TV
Building skills and awareness in HK
….in the art galleries
Building skills and awareness in HK
….in the art galleries
A project that needs supporting
@bauhiniagenome #bauhinawatchhttps://www.facebook.com/BauhiniaGenome
http://bauhiniagenome.hk/
http://igg.me/at/bauhiniahttps://www.paypal.me/HKSSS
https://www.patreon.com/BauhiniaGenome
Follow us:
What next for the peoples GMO?
Education: #bauhiniawatch
Education: school outreach
Education: (OER) teaching materials
https://www.oercommons.org/courseware/lesson/9147/overview
Education: reproducible research
Education: lets make genomes!(or at least 4 x transcriptomes)
Education: lets share rich metadata
http://dx.doi.org/10.5524/100245
Next: lets analyse (OPEN) data
Next: lets empower HK BioCoders
http://www.oreilly.com/biocoder/
“We’re at the start of a revolution that will transform our lives as radically as the computer revolution of the 70s. The biological revolution will touch every aspect of our lives: food and health, certainly, but also art, recreation, law, business, and much more.”
Next: lets embrace Hong Kong’s DNA
http://www.scmp.com/lifestyle/article/2017906/biohackers-diy-biologists-out-barcode-all-hong-kongs-plants-insects-and
Finally: what can you do to help?
• Spread the word.
• Phenotype: #bauhiniawatch.
• Donate towards whole genomes.
• Help with fundraising.
• Learn & help with genome assembly.
Thank you for listening!
