Our -Omics Odyssey
K. Thomas Pickard
Founder, StartCodon
2015 TCGC Short Course
Personal Genomics: Variant Analysis and In...
Topics
• Getting started
• DIY sequencing
• Data sharing
2
Getting started for $5,000
3
Which is more valuable?
4
The report or the data?
Now what?
• Adult-aged daughter with autism
• Family trio sequencing
• Search for genetic clues
5
Genomics provides clues ...
DIY Sequencing
1. Raise money
2. Find a sequencing company
3. Contact doctor and order blood draw
4. Show up at lab with k...
1. Launch a campaign
7
Source: https://experiment.com/projects/searching-for-genetic-clues-in-autism-with-family-trio-sequ...
Blog about it
8
Raised
$1,850 in
less than
24 hours
Source: http://genomedad.com
2. Find a sequencing company
9
10
Source: http://www.amazon.com/gp/product/B0015TEDS0
3. Blood draw
4. Make it look right and
no one asks questions
5. Sh...
6. Download data
11
About 325GB per person (FASTQ, BAM, VCF, indexes)
• Amazon to Amazon copy: 10GBytes/hour
• Amazon to H...
7. Analyze results: Family Trio Sequencing
Methods
1. Looked at de novo and compound hets
52 variants total
2. Looked at autism gene databases
200 – 700 genes total
...
14
15
Mom
Dad
Proband
Location: HRC
16
Location: HRC
Proband
Mom
Dad
Autism gene databases
• Autworks
http://autworks.hms.harvard.edu/
• KU Autism Database
http://wren.bcf.ku.edu/
• Lancet se...
18
Location: 16p11.2
Dad
Mom
Proband
19
Location: 16p11.2
Dad
Mom
Proband
20
Dad
Mom
Proband
Location: 16p11.2 (deletion)
21
Location: NXRN1 (insertion)
Dad
Mom
Proband
22
Location: NXRN1 (deletion)
Dad
Mom
Proband
Take home lessons / to-dos
1. Run trio samples through the same pipeline
2. Beware of false positive de novo variants
3. P...
Autism spectrum disorders
• Disease prevalence:
World: 1%
• 20% explained by genetics
• U.S. 2M people  > 6 types  300k ...
Schizophrenia
• Disease prevalence:
World: 1% (with little variation)
• Disease types: 7 or more
• U.S. 3.5M people  7 ty...
Diabetes
• Disease prevalence:
World: 4% to 40%
U.S.: 10%
• Disease types: 30+
• U.S.: 30M people  30 types  1M per type...
Common disease  rare disease
• 300k autism spectrum disorder patients
50 patients per hospital  1 in 1,000
• 500k schizo...
Making genomes useful
GA4GH: 320+ organizations enabling
genomic data sharing
28
Beacon Project: Test the willingness of
i...
Summary
• Personal genomics is real
• Think “homebrew computers” in the mid-‘70s
• Some dark alleys, but not all
• Data sh...
Special Thanks
30
For the use of
Thank you
K. Thomas Pickard
ktpickard [at] startcodon.org
@kthomaspickard
www.linkedin.com/in/kthomaspickard
Blog: www.gen...
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TCGC15-Our-Omics-Odyssey

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Finding genetic clues in autism with family trio sequencing - preliminary findings presented at the 2015 Clinical Genome Conference in San Francisco.

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TCGC15-Our-Omics-Odyssey

  1. 1. Our -Omics Odyssey K. Thomas Pickard Founder, StartCodon 2015 TCGC Short Course Personal Genomics: Variant Analysis and Interpretation with Public Data June 22, 2015
  2. 2. Topics • Getting started • DIY sequencing • Data sharing 2
  3. 3. Getting started for $5,000 3
  4. 4. Which is more valuable? 4 The report or the data?
  5. 5. Now what? • Adult-aged daughter with autism • Family trio sequencing • Search for genetic clues 5 Genomics provides clues to autism for about 1 in 5 individuals Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756414/
  6. 6. DIY Sequencing 1. Raise money 2. Find a sequencing company 3. Contact doctor and order blood draw 4. Show up at lab with kit 5. Overnight samples 6. Download data 7. Analyze results 8. Give talk 6
  7. 7. 1. Launch a campaign 7 Source: https://experiment.com/projects/searching-for-genetic-clues-in-autism-with-family-trio-sequencing
  8. 8. Blog about it 8 Raised $1,850 in less than 24 hours Source: http://genomedad.com
  9. 9. 2. Find a sequencing company 9
  10. 10. 10 Source: http://www.amazon.com/gp/product/B0015TEDS0 3. Blood draw 4. Make it look right and no one asks questions 5. Ship it!
  11. 11. 6. Download data 11 About 325GB per person (FASTQ, BAM, VCF, indexes) • Amazon to Amazon copy: 10GBytes/hour • Amazon to Home (150Mbits/sec): 4GBytes/hour Source: https://www.dnanexus.com/
  12. 12. 7. Analyze results: Family Trio Sequencing
  13. 13. Methods 1. Looked at de novo and compound hets 52 variants total 2. Looked at autism gene databases 200 – 700 genes total 3. Looked at autism gene “hot spots” 16p11.2, NRXN1 13 Source: http://www.ncbi.nlm.nih.gov/pubmed/22228009
  14. 14. 14
  15. 15. 15 Mom Dad Proband Location: HRC
  16. 16. 16 Location: HRC Proband Mom Dad
  17. 17. Autism gene databases • Autworks http://autworks.hms.harvard.edu/ • KU Autism Database http://wren.bcf.ku.edu/ • Lancet series on autism (April 2015) http://dx.doi.org/10.1016/S1474-4422(15)00044-7 • Simons Foundation Autism Research Initiative http://sfari.org/ 17
  18. 18. 18 Location: 16p11.2 Dad Mom Proband
  19. 19. 19 Location: 16p11.2 Dad Mom Proband
  20. 20. 20 Dad Mom Proband Location: 16p11.2 (deletion)
  21. 21. 21 Location: NXRN1 (insertion) Dad Mom Proband
  22. 22. 22 Location: NXRN1 (deletion) Dad Mom Proband
  23. 23. Take home lessons / to-dos 1. Run trio samples through the same pipeline 2. Beware of false positive de novo variants 3. Pay attention to carrier status 4. Perform CNV analysis 23
  24. 24. Autism spectrum disorders • Disease prevalence: World: 1% • 20% explained by genetics • U.S. 2M people  > 6 types  300k per type 24 Sources: http://www.cdc.gov/ncbddd/autism/documents/asd_prevalence_table_2013.pdf http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756414/ Autistic activist Temple Grandin
  25. 25. Schizophrenia • Disease prevalence: World: 1% (with little variation) • Disease types: 7 or more • U.S. 3.5M people  7 types  500k per type 25 Source: http://www.ncbi.nlm.nih.gov/pubmed/25219520 Nobel laureate John Nash
  26. 26. Diabetes • Disease prevalence: World: 4% to 40% U.S.: 10% • Disease types: 30+ • U.S.: 30M people  30 types  1M per type 26 Sources: http://care.diabetesjournals.org/content/29/suppl_1/s43.full.pdf http://healthintelligence.drupalgardens.com/content/prevalence-diabetes-world-2013
  27. 27. Common disease  rare disease • 300k autism spectrum disorder patients 50 patients per hospital  1 in 1,000 • 500k schizophrenic patients 80 patients per hospital  1 in 625 • 1M diabetes patients 170 patients per hospital  1 in 300 27  Rare disease: 1 in 1,500 Source: http://www.cdc.gov/datastatistics/
  28. 28. Making genomes useful GA4GH: 320+ organizations enabling genomic data sharing 28 Beacon Project: Test the willingness of international sites to share data Source: https://genomicsandhealth.org/
  29. 29. Summary • Personal genomics is real • Think “homebrew computers” in the mid-‘70s • Some dark alleys, but not all • Data sharing is critical for insights 29
  30. 30. Special Thanks 30 For the use of
  31. 31. Thank you K. Thomas Pickard ktpickard [at] startcodon.org @kthomaspickard www.linkedin.com/in/kthomaspickard Blog: www.genomedad.com 31

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