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Should I be dead?
a very personal genomics
Neil Saunders
Digital Productivity
www.csiro.au
personal genomics: Slide 2 of 20
personal genomics pipelines
- we need reports that patients and clinicians can use
personal genomics: Slide 3 of 20
personal genetics is already reality
http://genomesunzipped.org/2011/06/3747.php
personal genomics: Slide 4 of 20
introduction to 23andme
https://www.23andme.com
Who Should Have Access to Your DNA?
https...
personal genomics: Slide 5 of 20
data visualization at 23andme
personal genomics: Slide 6 of 20
23andme “raw data”
rs4477212 1 82154 AA
rs3094315 1 752566 AA
rs3131972 1 752721 GG
rs125...
personal genomics: Slide 7 of 20
promethease + SNPedia
http://www.snpedia.com/index.php/Promethease
personal genomics: Slide 8 of 20
ensembl variant effect predictor (VEP)
http://www.ensembl.org/info/docs/tools/vep/index.h...
personal genomics: Slide 9 of 20
converting 23andMe data to VCF
personal genomics: Slide 10 of 20
VCF conversion attempt #1 - 23andme2vcf.pl
https://github.com/arrogantrobot/23andme2vcf
...
personal genomics: Slide 11 of 20
VCF conversion attempt #2 - plink
990 762 / 991 786 lines converted (but with issues)
sa...
personal genomics: Slide 12 of 20
VCF conversion attempt #3 - python script
(not tried)
https://github.com/hammer/personal...
personal genomics: Slide 13 of 20
VCF conversion attempt #4 - bcftools
(not tried)
http://samtools.github.io/bcftools/bcft...
personal genomics: Slide 14 of 20
VCF conversion attempt #5 - the winner
973 306 / 991 786 lines converted
http://apol1.bl...
personal genomics: Slide 15 of 20
running the VEP - summary output
personal genomics: Slide 16 of 20
parsing VEP output
you can read this later
personal genomics: Slide 17 of 20
visualization of stop-gained variants
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personal genomics: Slide 18 of 20
so should I be dead?
yes and so should you
“All genomes are dysfunctional: broken genes ...
personal genomics: Slide 19 of 20
summary
a growing “hacker community” around personal genomics data
no shortage of inspir...
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Should I be dead? a very personal genomics

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Presentation for CSIRO Bioinformatics FOAM meeting, Melbourne, February 12-13 2015

Publié dans : Sciences
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Should I be dead? a very personal genomics

  1. 1. Should I be dead? a very personal genomics Neil Saunders Digital Productivity www.csiro.au
  2. 2. personal genomics: Slide 2 of 20 personal genomics pipelines - we need reports that patients and clinicians can use
  3. 3. personal genomics: Slide 3 of 20 personal genetics is already reality http://genomesunzipped.org/2011/06/3747.php
  4. 4. personal genomics: Slide 4 of 20 introduction to 23andme https://www.23andme.com Who Should Have Access to Your DNA? https://medium.com/backchannel/who-should-have-access-to-your-dna-6830fbf8dc79
  5. 5. personal genomics: Slide 5 of 20 data visualization at 23andme
  6. 6. personal genomics: Slide 6 of 20 23andme “raw data” rs4477212 1 82154 AA rs3094315 1 752566 AA rs3131972 1 752721 GG rs12562034 1 768448 GG rs12124819 1 776546 AA rs11240777 1 798959 GG rs6681049 1 800007 CC rs4970383 1 838555 AC rs4475691 1 846808 CT rs7537756 1 854250 AG
  7. 7. personal genomics: Slide 7 of 20 promethease + SNPedia http://www.snpedia.com/index.php/Promethease
  8. 8. personal genomics: Slide 8 of 20 ensembl variant effect predictor (VEP) http://www.ensembl.org/info/docs/tools/vep/index.html
  9. 9. personal genomics: Slide 9 of 20 converting 23andMe data to VCF
  10. 10. personal genomics: Slide 10 of 20 VCF conversion attempt #1 - 23andme2vcf.pl https://github.com/arrogantrobot/23andme2vcf in vcf 946 275 not in reference 30 734 DI 26 DD 161 II 689 D 36 I 112 - - 13 752 total 991 785 in raw data 991 786
  11. 11. personal genomics: Slide 11 of 20 VCF conversion attempt #2 - plink 990 762 / 991 786 lines converted (but with issues) sau103@spanxc-nh ˜/vep/data $ grep -v "ˆ#" vcf/plink19.vcf | head -4 | sort 1 752566 rs3094315 A . . . . GT 0/0 1 752721 rs3131972 G . . . . GT 0/0 1 768448 rs12562034 G . . . . GT 0/0 1 776546 rs12124819 A . . . . GT 0/0 sau103@spanxc-nh ˜/vep/data $ grep -v "ˆ#" vcf/23andme2vcf.vcf | head -4 | sort chr1 752566 rs3094315 g A . . . GT 1/1 chr1 752721 rs3131972 A G . . . GT 1/1 chr1 776546 rs12124819 A . . . . GT 0/0 chr1 798959 rs11240777 g . . . . GT 0/0 http://www.snpedia.com/index.php/User:Donwulff
  12. 12. personal genomics: Slide 12 of 20 VCF conversion attempt #3 - python script (not tried) https://github.com/hammer/personal-genome-analysis/tree/master/scripts
  13. 13. personal genomics: Slide 13 of 20 VCF conversion attempt #4 - bcftools (not tried) http://samtools.github.io/bcftools/bcftools.html
  14. 14. personal genomics: Slide 14 of 20 VCF conversion attempt #5 - the winner 973 306 / 991 786 lines converted http://apol1.blogspot.com.au/2013/08/impute-apoe-and-apol1-with-23andme.html #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Neil_Saunders 1 82154 rs4477212 A G . . . GT 0/0 1 752566 rs3094315 G A . . . GT 1/1 1 752721 rs3131972 A G . . . GT 1/1 1 768448 rs12562034 G A . . . GT 0/0 1 776546 rs12124819 A G . . . GT 0/0
  15. 15. personal genomics: Slide 15 of 20 running the VEP - summary output
  16. 16. personal genomics: Slide 16 of 20 parsing VEP output you can read this later
  17. 17. personal genomics: Slide 17 of 20 visualization of stop-gained variants 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X 0 Mb 50 Mb 100 Mb 150 Mb 200 Mb 250 Mb clinical significance benign likely_pathogenic not_provided not_provided,not_provided other pathogenic pathogenic,other Genomic location of my stop_gained variants
  18. 18. personal genomics: Slide 18 of 20 so should I be dead? yes and so should you “All genomes are dysfunctional: broken genes in healthy individuals” “A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes” http://genomesunzipped.org/2012/02/all-genomes-are-dysfunctional-broken-genes-in-healthy-individuals.php http://www.sciencemag.org/content/335/6070/823.full
  19. 19. personal genomics: Slide 19 of 20 summary a growing “hacker community” around personal genomics data no shortage of inspiration for reporting and visualization tools the challenge is interpretation for non-specialists

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