Open human genome dataOpen up! – Open Data and Open AccessAnnual TKT/CLIDP Symposium University of Turku, 13th May, 2016Marja Pirttivaara, PhD, MBA (social and healthcare management)

Duodecim 2006;122:63–8http://www.terveysportti.fi/xmedia/duo/duo95417.pdf

Plus Prof. Jussi Huttunen’s hilarious comment…

Marja Pirttivaara, 13th May 2016

One important milestone in my own genome data journey…

Human genome: abt 3 billion pairs of nucleotides.

Variants are Single Nucleotide Polymorphisms, SNPs.

Basics of genome and cost of sequencing

Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing

Program (GSP) Available at: www.genome.gov/sequencingcosts. Accessed 13th May, 2016.

13th May, 2016, Marja Pirttivaara

Human genome – human evolution

“The human genome is contained in chromosomes that are present in almost every cell in our bodies. It is composed of approximately 3.2 billion nucleotides. When cells replicate to form germ cells that will contribute to the next generation, mutations occur. As a result of these mutations, about 50 to 200 new substitutions exist in every new individual that is born. These substitutions accumulate in the genome over time to the extent that roughly one nucleotide in a thousand differs between two human genomes today, whereas roughly one nucleotide in a hundred differs between a human and a chimpanzee genome. In addition, duplicated DNA sequences differ both between individuals and between species.”

Svante Pääbo: The Contribution of Ancient Hominin Genomes from Siberia to Our Understanding of Human Evolution, Herald of the Russian Academy of Sciences, Vol 85 No. 5, 2015

http://www.eva.mpg.de/documents/RussianAcadSciences/Paeaebo_Contribution_HeraldRussAcadSci_2015_2226501.pdf

13th May, 2016, Marja Pirttivaara

Why DNA tests and genome data?

© Marja Pirttivaara

• Healthcare: screening, diagnosis, prevention, medication and care, personalized medicine…

• Research & development: bioinformatics, genetics, genomics, medicine, health care, pharmacogenetics, ancientDNA, human migration…

• Forensic science

• Direct-to-consumer tests (DTC): ancestry, health etc

www.genome.gov

13th May, 2016, Marja Pirttivaara

• KardioKompassi is FIMM’s first preventative health care pilot project utilizing personal genetic risk information and returning it to the participants.

• Cardio-vascular diseases, appr. 50 snips chosen.

• Partners: FIMM, Finnish Red Cross Blood Services and the Finnish Innovation Fund Sitra.

• Aim: study the ways of providing people with health-risk information based on genetic research data, the ways this information is used in preventive healthcare and its usefulness with respect to individual health behaviour.

• In this project, the transfer of genetic information to an individual’s personal online health account was also being tested for the first time in Finland.

• The application developed during the project is further developed and utilized in new research projects.

Kardiokompassi – unique Finnish pilot

Marja Pirttivaara, 13th May 2016

“Many, many more individuals will have to make their personal genomes publicly available before we begin to get a real feeling of where we want to go.”

"I am homozygous for the “10” variant of the P450 drug metabolizing gene, CYP2P6 . As a result, I metabolize beta-blockers much more slowly than most other Caucasians. Before I take this knowledge, my use of beta-blockers to control my blood pressure caused me to constantly fall asleep at inappropriate moments. Instead of a daily pill, I now take one every week….”

James Watson: Living with my personal

genome

Ref:http://www.futuremedicine.com/doi/pdf/10.2217/pme.09.62

Picture: http://www.fraxa.org/fraxa/advisors/

Marja Pirttivaara 13th May 2016

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Open data, open science, mydata, big data, big science, open tools – and open minds

The Opportunity Project in the US

“..they've challenged the nation to ask not what your country can code for you, but ask what you can code for your country.” …

What I saw at the launch of The Opportunity Project yesterday suggested a shift in an approach that has promise. Instead of simply dumping a data set onto Data.gov and challenging people to use it, the White House worked with over 30 tech companies and nonprofits to develop prototypes of new tools or add features to existing platforms…”

People

ToolsData

http://www.techrepublic.com/article/president-obamas-new-open-data-initiative-could-help-cities-help-themselveshttps://www.whitehouse.gov/the-press-office/2016/03/07/fact-sheet-white-house-launches-opportunity-project-utilizing-open-data

13th May, 2016, Marja Pirttivaara

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Genome data in open databases

• Primary nucleotide sequence databases:

• GenBank (NCBI / NIH, USA) http://www.ncbi.nlm.nih.gov/genbank/

• EMBL (European Bioinformatics Institute) European Nucleotide Archive http://www.ebi.ac.uk/ena

• DDBJ, DNA Data Bank of Japan (National Institute of Genetics) http://www.ddbj.nig.ac.jp/

• Meta databases

• Genome databases

• Protein sequence databases

• Proteomics databases

• Protein structure databases

• Protein model databases

• RNA databases

• Carbohydrate structure databases

• Protein-protein and other molecularinteractions

• Signal transduction pathway databases

• Metabolic pathway and Protein Functiondatabases

• Microarray databases

• Exosomal databases

• Mathematical model databases

• PCR and quantitative PCR primer databases

• Phenotype databases

• Specialized databases

• Taxonomic databases

• Wiki-style databases

• Metabolomic Databases

• ETC

13th May, 2016, Marja Pirttivaarahttps://en.wikipedia.org/wiki/List_of_biological_databases

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Biobanks

• Biobank is ”clinical samples + data + informed consent” according to theFinnish biobank regulation.

• Globally, biobanks will form a global

evolving network of actors and actions: samples, labs & testing, data storage, consents, data sharing, tools, cooperation, competences…

• Ethics!

“Biobank is a collection of biological samples and data gathered with the donor’s consent for future medical research and product development for healthcare and health promotion purposes.”

“Your consent could be crucial for the development of new medicines and treatments. Your sample could change the world!”

http://www.biopankki.fi/

www.genome.gov 13th May, 2016, Marja Pirttivaara

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Open data deserves open tools: tools for genome data

Autosomal DNA tools

• http://isogg.org/wiki/Autosomal_DNA_tools

Y-DNA tools

• http://isogg.org/wiki/Y-DNA_tools

Mitochondrial DNA Tools

• http://isogg.org/wiki/MtDNA_tools

CSC Bioinformatics Tools

• https://research.csc.fi/bioscience-programs

BLAST finds regions of similarity between biological sequences

• http://blast.ncbi.nlm.nih.gov/Blast.cgi

BEAST Bayesian evolutionary analysis bysampling trees (Markov Chain Monte Carlo simulation)

• http://beast2.org/

R language

• https://www.r-project.org/

13th May, 2016, Marja Pirttivaara

1213th May, 2016, Marja Pirttivaara

Philip E. Bourne: Open data in a Global Ecosystem, Nov. 2015http://www.slideshare.net/pebourne/open-data-in-a-global-ecosystem

• Family Tree DNA / Gene by Gene

www.familytreedna.com

• 23andMe

www.23andme.com

• Ancestry

www.ancestry.com

• National Geographic

http://genographic.nationalgeographic.com

The Big Four in DTC

Marja Pirttivaara 13th May 2016

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Donation of mtDNA to the NIH NCBI GenBank

Marja Pirttivaara 13th May 2016http://www.ncbi.nlm.nih.gov/

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SNPedia and Promethease

• SNPedia is the Database

• Promethease is a Program to Personalize

• Upload a file of genotypes with dbSNP IDs and Promethease makes a personalized report

• It uses SNPedia to find and compliethe scientific literature specific to your DNA.

• Personal data is not stored, shared or sold.

• http://www.snpedia.com/index.php/SNPedia• https://www.snpedia.com/index.php/Promethease• https://www.promethease.com/• Antonio Regalado: How a Wiki Is Keeping Direct-to-

Consumer Genetics Alive, MIT Technology Review 2014 www.technologyreview.com/featuredstory/531461/how-a-wiki-is-keeping-direct-to-consumer-genetics-alive/

Marja Pirttivaara 13th May 2016Map of SNPedia usage in Finland, thx Mike Cariaso, SNPedia

16Sitra • Name • 13.5.2016 •

Example from a personalized Promethease report

What do people want to know?

●What will I die from? When will I die?

●What diseases am I at higher risk for, and by how much?

●What diseases might my children inherit?

●Are some drugs better than others for me? Or worse?

●Who can explain all this to me?

●Will my health-care providers understand it?

Thx to Mike Cariaso and Greg Lennon, SNPedia

Marja Pirttivaara 13th May 2016

Stanford course Gene 210 – Genomics and

Personalized Medicine

Marja Pirttivaara 13th May 2016

Course includes analysis of own DTC genome data and SNPedia writinghttp://web. stanford.edu/class/gene210/web/html/welcome.htmlhttp://www.snpedia.com/index.php/Rs1800497

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National Genome Strategy: Improving health through the use of genomic data

Marja Pirttivaara 13th May 2016http://stm.fi/en/genomicdata

• Who owns the data?

• Who can use the data?

• Informed consent

• Trust

• Transparency

• Incidental findings

• Right to know and right not to know.

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Privacy and ethics

13th May, 2016, Marja Pirttivaara

www.genome.gov

New cooperation, new cultures, new skills,

new methodologies, new tools, new emphasis,

new modes of discovery...

New era

Marja Pirttivaara 13th May 2016www.genome.gov

• sitra.fi

• Facebook.com/SitraFund

• @SitraFund

• @Marja_P

Building a successful Finland for tomorrow