Grass Roots Genomics: Using Hong Kong's Emblem to Crack Exobytes of Data. Bauhina Genome speaking at M-Labs in Hong Kong on the 28th November 2016

1. Grass Roots Genomics: Using Hong Kong's
Emblem to Crack Exobytes of Data
@SCEdmunds
@BauhiniaGenome
#HKGenome

2. The language of heredity & evolution
Watson & Crick (based on data from Franklin) crack structure
http://www.bbc.co.uk/schools/gcsebitesize/science/add_ocr_pre_2011/growth_develop
ment/genesrev1.shtml

3. 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/

4. AKA dideoxy chain-termination
https://en.wikipedia.org/wiki/Sanger_sequencing#/media/File:Sanger-sequencing.svg

5. So DOE wants to read it all…

6. V
Then it becomes a race…

7. 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

8. Post-Human Genome Project
1st Gen
2nd (next) Gen
Source: http://www.genome.gov/sequencingcosts/ (with apologies)

9. 2nd (next) Gen
Next-Gen
Sequencing
AKA
Sequencing-by-
Synthesis

10. 3rd Generation: AKA Single Molecule Seq
Real-time, FRET, Nanopore, Semiconductor Sequencing…
http://www.nature.com/nbt/journal/v28/n5/full/nbt0510-426.html

11. 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_methods
http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html

12. Genome(-ish) Assembly (the cheap version)
http://www.nature.com/nrd/journal/v12/n5/full/nrd3979.html

13. 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.

14. In situ sequencing: ebola, zika & beyond

15. Nanopores meet Open Hardware: Quantum Sequencing?

16. Methylomics
Histone Modifications
Chromatin profiling
ncRNA
E is for EPIGENOMICS

17. Metagenomics & the microbiome

18. Single Cell Sequencing

19. Ancient DNA Sequencing

20. Omes & more omes!

21. 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

22. GENOMICS IN HONG KONG

23. BGI HK Chamber O’Illumina’s
The LHC of Biology?
20PB of storage

24. Made in Hong Kong

25. Hong Kong’s R&D spend is low
Data: WorldBank

26. 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

27. 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

28. 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

29. WORKING AROUND THE SYSTEM

30. Breaking the funding bottleneck

31. Biggest crowdfunding successes

32. 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, 1:14
Steven J. O’Brien. (2012): Genome empowerment for the Puerto Rican parrot – Amazona vittata. GigaScience 2012, 1:13
Oleksyk 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

33. The “Peoples Parrot”
https://youtu.be/Hr43ZXP9NGw

34. CHANGING THE SYSTEM

35. Brought to you by: HK CUHK
…and the people of Hong Kong

36. An emblematic genome project

37. 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"

38. Plant genomics #101
Why hybrids changed the world?

39. An icon that needs protecting

40. 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 Bhorla
Pods 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

41. Useful Bauhinia?

42. A puzzle that needs assembling

43. With Parts Made in (BGI) Hong Kong

44. Building skills and awareness in HK

45. 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

46. CNN “On China” covering the Bauhinia Genome project, 27th April 2016
https://youtu.be/TyJBALA0da0
Building skills and awareness in HK
….on TV

47. Building skills and awareness in HK
….in the art galleries

48. Building skills and awareness in HK
….in the art galleries

49. A project that needs supporting
@bauhiniagenome #bauhinawatch
https://www.facebook.com/BauhiniaGenome
http://bauhiniagenome.hk/
http://igg.me/at/bauhinia
https://www.paypal.me/HKSSS
https://www.patreon.com/BauhiniaGenome
Follow us:

50. What next for the peoples GMO?

51. Education: #bauhiniawatch

52. Education: school outreach

53. Education: (OER) teaching materials
https://www.oercommons.org/courseware/lesson/9147/overview

54. Education: reproducible research

55. Education: lets make genomes!
(or at least 4 x transcriptomes)

56. Education: lets share (OPEN) data
http://dx.doi.org/10.5524/100245

57. Education: lets share rich metadata
http://dx.doi.org/10.5524/100245

58. Next: lets analyse (OPEN) data

59. 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.”

60. 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

61. 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!