Personal Genomes: what can I do with my data?

Revolutionizing Biology with Personal Genomes Melanie Swan Research Fellow MS Futures Group +1-650-681-9482 @LaBlogga [email_address] www.melanieswan.com March 26, 2010 NASA AMES Project information: DIYgenomics.org Slides: http://slideshare.net/LaBlogga/slideshows Image credit: http://www-nmr.cabm.rutgers.edu/photogallery/proteins/gif/dna.gif

Agenda ,[object Object],[object Object],[object Object],DIYgenomics.org Image credit: http://current.com/1u8qe4c

Numerous useful applications of genomics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Reference: “Cheating is so 1999: A reporter spends a year searching for the athletic holy grail: a sports gene,” Assael , Shaun, ESPN The Magazine, Oct. 6, 2009, http://www.genome.duke.edu/education/seminars/journal-club/documents/Assael_2009.pdf

Direct-to-Consumer genomics landscape DIYgenomics.org $2,500 $999 Single/few condition Multiple condition Whole genome Cost 1 Whole genome: $68,500; exome: $24,500 Offering Breadth Public studies (specific diseases or traits) (common diseases) Matchmaking ScientificMatch $1,995 GenePartner $10-$99 Paternity Genelex $200-$475 Identigene $149-$399 Pregnancy Screening Counsyl $349 Nutrigenomics APO E Gene Diet $389 Inherent Health $99 Coriell 15 conditions Scripps (Navigenics) 28 conditions Pers. Genome Proj. Conditions undisclosed Harvard Med. Sch. Genetic disorders, Predisposition DNA Direct $200-$3,500 Matrix Genomics $199-$799 Drug sensitivity, Knome Illumina $48,000 $350,000 $99,500 $68,500 1 23andme 141 conditions Navigenics 28 conditions Gene Essence 84 conditions $1,000 $429 Genome-wide health offerings $2,000 $1,195 $299 Genomics 71 conditions Pathway $ deCODEme 49 conditions $985

Example: Breast cancer – Navigenics DIYgenomics.org Source: http://www.navigenics.com/demo/for_scientists/d/breast_cancer

Example: Breast cancer – deCODEme DIYgenomics.org Source: http://demo.decodeme.com/health-watch/details/BCRS

Example: Breast cancer – 23andme DIYgenomics.org Source: https://www.23andme.com/you/journal/breastcancer/techreport

Example: Breast cancer – Pathway Genomics DIYgenomics.org Source: https://www.pathway.com

Side-by-side comparison: breast cancer ,[object Object],DIYgenomics.org Source: http://www.diygenomics.org/, http://melanieswan.com/documents/multigenic_analysis.xls Markers reviewed by consumer genomic services for breast cancer

Why risk interpretation can vary by consumer genomic service ,[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Source: Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010, in press. Image credit: http://www.tigerteamconsulting.com/TTC_Site/sectors_binf.jsp

1. Differences in population average lifetime risk DIYgenomics.org Source: Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010, in press. http://melanieswan.com/documents/multigenic_analysis.xls Population average lifetime risk in DTC genomic services

2. Differences in SNP/loci selection criteria ,[object Object],DIYgenomics.org Source: Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010, in press. http://melanieswan.com/documents/multigenic_analysis.xls Loci overlap for three DTC Genomic Companies

3. Differences in risk assignment methodology ,[object Object],[object Object],[object Object],DIYgenomics.org Source: Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010, in press. http://melanieswan.com/documents/multigenic_analysis.xls Risk Allele Quantification by DTC Genomic Companies

Genomics comparison scorecard DIYgenomics.org 1 Conditions, genes, variants, underlying research references, and methodology white paper(s) available on public website ,[object Object],Consumer genomic service # Cond-itions Cost Report Data access Visible research quality 1 Updates deCODEme 49 $2,000  +   +  + 23andme 141 $429     Navigenics 28 $999    Pathway Genomics 71 $299  Gene Essence 84 $1,195 Coriell 7-15 public study PGP (Personal Genome Project) n/a public study

Consumer resource: AccessDNA.com DIYgenomics.org ,[object Object]

DIYgenomics.org genomics comparison ,[object Object],DIYgenomics.org 1. 20 conditions 2. Locus/SNP detail 3. Reference detail 4. PubMed detail Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan Source: http://www.diygenomics.org

Early sequencing technology ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Sources: http://www.phgfoundation.org/tutorials/dna/5.html, http://www.genomicseducation.ca/files/images/information_articles/sequencing.gif

Contemporary (2 nd -gen) sequencing technology ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Source: http://www.wellcome.ac.uk/News/2009/Features/WTX056032.htm Illumina sequencing 1 2 3

3 rd -generation sequencing ,[object Object],DIYgenomics.org Sources: http://www.pacificbiosciences.com/video_lg.html, http://www.sciencemag.org/cgi/content/abstract/323/5910/133, Science 2 January 2009: Vol. 323. no. 5910, pp. 133 – 138, DOI: 10.1126/science.1162986 Phospholinked nucleotides DNA polymerase wrapped around DNA chain Label fluoresces as cleaved 1 2 3 Zero-mode waveguide reads sequence 4

4 th -generation sequencing technology ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Sources: http://www.nanoporetech.com/sequences, http://www.youtube.com/watch?v=wvclP3GySUY Oxford Nanopore Technologies Ion Torrent

DNA sequencing and genetic variation DIYgenomics.org ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Image credit: http://im.encyklopedie.seznam.cz/wiki_cz//image/27/119427-180px-dna-snp.svg.png

Contemporary research in genomics DIYgenomics.org ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Image credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg

Moore’s Law in life sciences: Carlson curves DIYgenomics.org ,[object Object],[object Object],[object Object],[object Object],[object Object],Source: http://www.synthesis.cc/carlson_DNA_cost_curves_Sept_09.jpg

Example: what to do with your data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Source: http://www.wired.com/wiredscience/2009/10/genetically-bad-driving 1 Ribeiro, L. et. Al., The brain-derived neurotrophic factor rs6265 (Val66Met) polymorphism and depression in Mexican-Americans. Cellular, Molecular and Developmental Neuroscience. May 8, 2007.

Finding your BDNF data, variant rs6265 DIYgenomics.org ,[object Object]

Consumer genomics enables peer research DIYgenomics.org

15 citizen science genomic projects http://diygenomics.pbworks.com DIYgenomics.org

Project #1: MTHFR mutation & Vit B12 deficiency http://diygenomics.pbworks.com/MTHFR DIYgenomics.org

Project #2: Longevity and genomics BU Centenarian study, Alzheimer’s disease DIYgenomics.org Source: Green RC, Roberts JS. The Impact and Utility of Personalized Genomic Information: Insights from the REVEAL Study. Page 30. Consumer Genetics Show. Hynes Convention Center, Boston, MA, June 9-11, 2009. http://cancercontrol.cancer.gov/od/phg/presentations/Green.pdf ,[object Object],[object Object]

DIYbio: self-genotyping DIYgenomics.org DNA Extraction Sources: http://www.instructables.com/id/5_minute_DNA_Extraction_in_a_Shot_Glass, http://www.boston.com/news/science/articles/2009/05/11/do_it_yourself_genetic_sleuthing, DNA 2.0 Gene Designer, https://www.dna20.com/index.php?pageID=220, http://openwetware.org/wiki/User:Jonathan_Cline/Notebook/Melaminometer DNA Design Melaminometer Hemochromatosis self-test Katherine Aull

Next-generation citizen science ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Microbiome Phenotype Environment Genotype Preventive medicine health data streams

Societal impact of genomics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Image credit: "Primo Posthuman“, Natasha Vita-More, 1997.

Personal genome analysis startups / tools ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Sources: http://openthoughtspace.pbworks.com/Personal-Genome-Analysis

Resources ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DIYgenomics.org Image credit: http://www.rsc.org/images/DNA-scrunching-350_tcm18-68641.jpg

Thank you! Melanie Swan Research Fellow MS Futures Group +1-650-681-9482 @LaBlogga [email_address] www.melanieswan.com Slides: http://slideshare.net/LaBlogga/slideshows Creative Commons 3.0 license Image credit: http://www-nmr.cabm.rutgers.edu/photogallery/proteins/gif/dna.gif

Personal Genomes: what can I do with my data?

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