fbpx
Wikipedia

OpenSNP

January 01, 1970

openSNP is an open source website where users can share their genetic information.[1] Users upload their genes, including gender, age, eye color, medical history, Fitbit data. With a focus on user patient-led research (PLR), there is potential to redefine the way health research is conducted.

"It promises to be a vital supplement to standard research: it can focus on conditions that are neglected by standard research, such as rare diseases or side effects, and can draw on a broader range of data and deliver outcomes more rapidly. It can also be a way of realising valuable forms of social interaction and support in cases where members of a community conduct PLR together, for example, patients suffering from the same illness."[2]

The name of the project is inspired by single nucleotide polymorphism (SNP), which is a DNA variation at a specific location on a strand. Scientists have discovered that there is a correlation between certain SNPs and genetic predispositions such as Mendelian disease.[3]

The code of the project is on GitHub and the CSS is licensed under the Apache 2.0 license.[1]

Potential risks edit

Since openSNP is an open-sourced social network that is readily available on the internet, there have been questions raised surrounding privacy issues and other risks.[4] Though the sign-up page warns potential users of the record lasting forever, participants must decide for themselves whether the benefits outweigh the pitfalls. As health research continues to progress, more and more scientific analysis places a greater role on PLR, leading to increased demands for a new social contract to secure conditions for participants.[2] Human participant research not only places subjects into potentially harmful situations, but also can lead to other risks such as exploitation and self-experimentation under non-controlled environments. There is also the risk of biases and distortions "arising from self-reporting and self-collected data". However, at this current state and time, the effects of genetic discrimination are unknown due to the lack of evidence.[5]

"Till date no systematic evaluation of the true value of anonymity with respect to the cost of genome information and insight has been assessed in real-life settings. This would require appropriate availability of information including caveats to whole genome assessment and analysis"[6]

Still, with the rise of open genomic research, privacy protection frameworks need strengthened efforts beyond "traditional legal and organizational safeguards", technical solutions such as data encryption, and mutual understanding.[7] In a study of an article done through the University of San Diego School of Law, Sejin Ahn discovered that perhaps the most critical solution that needs to be strengthened is the legislative ban on re-identification and anti-discrimination protection. Ahn explains that these remedies must be addressed and updated in order to protect participants from privacy breaches.[8]

A survey of users of the site found that while most respondents 'were well aware of the privacy risks of their involvement in open genetic data sharing and considered the possibility of direct, personal repercussions troubling, they estimated the risk of this happening to be negligible'.[9]

Potential benefits edit

The website provides a proof-of-concept mechanism for allowing anyone to be involved in any stage of genomics research. This model allows partnerships to form which can be independent of governments, academia or for-profit organisations and is a way of creating the enabling conditions for anyone to access, influence and get involved in every stage of the genomics research cycle.[10] The model reflects the value that users of such sites attach to sharing data as 'contributing to the common good of research'.[9]

The transparent open-source code arguably allows greater scrutiny and oversight than similar closed-source projects.[11]

History edit

The website was founded by German biologist, Bastian Greshake.

In 2012, Greshake sent a vial of his saliva to 23andMe, a genomics company, to study his own DNA. His results suggested that he was at risk of prostate cancer, and then recommended to his father to receive a medical examination as well. The doctor found a growing tumor in his father's prostate and was able to catch it early. After receiving his results, he posted them on GitHub, hoping to find other users willing to share their personal genetic makeup. Upon realizing that many people were unwilling or did not include a lot of information that was necessary for scientific research, Greshake created openSNP.[12]

"Maybe there are people who are interested in publishing their genetic information on the web to make it available, but those people don't have the opportunity,"[12]

Though Greshake acknowledges that there are services that allow people to test their own genes and discover inherent predispositions, they are often expensive, or difficult to access. In 2013, the Food and Drug Administration (FDA) forced company 23andMe to stop marketing their spit-box screening tests due to lack of scientific evidence. However, in 2015, the FDA eased their restrictions and stated that carrier screening tests would not have to undergo preliminary review.[13]

Greshake hopes that by making openSNP accessible and simple, it will not only attract the public to get interested in their genetic makeup, but also to take it down innovative avenues, such as turning openSNP data into music.[14]

Timeline edit

  • September 2011 — openSNP is released.[15]
  • September 2012 — Fitbit data inclusion feature added, seeing as obesity is correlated with specific SNPs.[16]
  • May 2014 — The website reached 1000 genotypings.
  • September 2015 — Crowdfunding campaign started on Patreon platform.[17]
  • February 2016 — Code of Conduct is created that outlines appropriate behavior and general guidelines.[18]
  • August 2016 — openSNP was a participant of Google Summer of Code.[19]

References edit

  1. ^ a b "openSNP". opensnp.org. Retrieved 20 November 2016.
  2. ^ a b Vayena, Effy; Brownsword, Roger; Edwards, Sarah Jane; Greshake, Bastian; Kahn, Jeffrey P; Ladher, Navjoyt; Montgomery, Jonathan; O'Connor, Daniel; O'Neill, Onora; Richards, Martin P; Rid, Annette; Sheehan, Mark; Wicks, Paul; Tasioulas, John (April 2016). "Research led by participants: a new social contract for a new kind of research". Journal of Medical Ethics. 42 (4): 216–219. doi:10.1136/medethics-2015-102663. PMC 4819634. PMID 25825527.
  3. ^ Greshake, Bastian (2014). "openSNP–A Crowdsourced Web Resource for Personal Genomics". PLOS ONE. 9 (3): e89204. Bibcode:2014PLoSO...989204G. doi:10.1371/journal.pone.0089204. PMC 3960092. PMID 24647222.
  4. ^ "The Social Network for People Who Want to Upload Their DNA to the Internet". Fusion. Retrieved 20 November 2016.
  5. ^ Angrist, Misha (2014). "Open Window: When Easily Identifiable Genomes and Traits Are in the Public Domain". PLOS ONE. 9 (3): e92060. Bibcode:2014PLoSO...992060A. doi:10.1371/journal.pone.0092060. PMC 3960179. PMID 24647311.
  6. ^ Scaria, Vinod (2014). "Personal genomes, participatory genomics and the anonymity-privacy conundrum". Indian Academy of Sciences. 93 (3): 917–20. doi:10.1007/s12041-014-0451-3. PMID 25572254. S2CID 2983269.
  7. ^ Vayena, Effy (2016). "Between Openness and Privacy in Genomics". PLOS Medicine. 13 (1): e1001937. doi:10.1371/journal.pmed.1001937. PMC 4710519. PMID 26757154.
  8. ^ Ahn, Sejin (1 September 2015). "Whose Genome Is It Anyway?: Re-identification and Privacy Protection in Public and Participatory Genomics". San Diego Law Review. 52 (3): 751.
  9. ^ a b Haeusermann, Tobias; Greshake, Bastian; Blasimme, Alessandro; Irdam, Darja; Richards, Martin; Vayena, Effy (9 May 2017). "Open sharing of genomic data: Who does it and why?". PLOS ONE. 12 (5): e0177158. Bibcode:2017PLoSO..1277158H. doi:10.1371/journal.pone.0177158. PMC 5423632. PMID 28486511.
  10. ^ (PDF). 28 November 2017. Archived from the original (PDF) on 28 November 2017. Retrieved 28 November 2017.
  11. ^ "Why Open Source Software is More Secure Than Commercial Software". Mend. Retrieved 12 April 2023.
  12. ^ a b "This Guy Is the Mark Zuckerberg of Open-source Genetics". Fusion. Retrieved 20 November 2016.
  13. ^ "FDA eases access to at-home DNA screening test". Retrieved 20 November 2016.
  14. ^ The Sound Of Bastian Greshake, retrieved 20 November 2016
  15. ^ "openSNP". openSNP. Retrieved 20 November 2016.
  16. ^ "Obesity - SNPedia". snpedia.com. Retrieved 20 November 2016.
  17. ^ "openSNP is creating Science | Patreon". Patreon. Retrieved 20 November 2016.
  18. ^ "gedankenstuecke/snpr". GitHub. Retrieved 20 November 2016.
  19. ^ "openSNP: Linking Phenotypes to SNPs in openSNP - 2016 - Google Summer of Code Archive". summerofcode.withgoogle.com. Retrieved 20 November 2016.

January 01, 1970
opensnp, opensnp, open, source, website, where, users, share, their, genetic, information, users, upload, their, genes, including, gender, color, medical, history, fitbit, data, with, focus, user, patient, research, there, potential, redefine, health, research. openSNP is an open source website where users can share their genetic information 1 Users upload their genes including gender age eye color medical history Fitbit data With a focus on user patient led research PLR there is potential to redefine the way health research is conducted It promises to be a vital supplement to standard research it can focus on conditions that are neglected by standard research such as rare diseases or side effects and can draw on a broader range of data and deliver outcomes more rapidly It can also be a way of realising valuable forms of social interaction and support in cases where members of a community conduct PLR together for example patients suffering from the same illness 2 The name of the project is inspired by single nucleotide polymorphism SNP which is a DNA variation at a specific location on a strand Scientists have discovered that there is a correlation between certain SNPs and genetic predispositions such as Mendelian disease 3 The code of the project is on GitHub and the CSS is licensed under the Apache 2 0 license 1 Contents 1 Potential risks 2 Potential benefits 3 History 4 Timeline 5 ReferencesPotential risks editSince openSNP is an open sourced social network that is readily available on the internet there have been questions raised surrounding privacy issues and other risks 4 Though the sign up page warns potential users of the record lasting forever participants must decide for themselves whether the benefits outweigh the pitfalls As health research continues to progress more and more scientific analysis places a greater role on PLR leading to increased demands for a new social contract to secure conditions for participants 2 Human participant research not only places subjects into potentially harmful situations but also can lead to other risks such as exploitation and self experimentation under non controlled environments There is also the risk of biases and distortions arising from self reporting and self collected data However at this current state and time the effects of genetic discrimination are unknown due to the lack of evidence 5 Till date no systematic evaluation of the true value of anonymity with respect to the cost of genome information and insight has been assessed in real life settings This would require appropriate availability of information including caveats to whole genome assessment and analysis 6 Still with the rise of open genomic research privacy protection frameworks need strengthened efforts beyond traditional legal and organizational safeguards technical solutions such as data encryption and mutual understanding 7 In a study of an article done through the University of San Diego School of Law Sejin Ahn discovered that perhaps the most critical solution that needs to be strengthened is the legislative ban on re identification and anti discrimination protection Ahn explains that these remedies must be addressed and updated in order to protect participants from privacy breaches 8 A survey of users of the site found that while most respondents were well aware of the privacy risks of their involvement in open genetic data sharing and considered the possibility of direct personal repercussions troubling they estimated the risk of this happening to be negligible 9 Potential benefits editThe website provides a proof of concept mechanism for allowing anyone to be involved in any stage of genomics research This model allows partnerships to form which can be independent of governments academia or for profit organisations and is a way of creating the enabling conditions for anyone to access influence and get involved in every stage of the genomics research cycle 10 The model reflects the value that users of such sites attach to sharing data as contributing to the common good of research 9 The transparent open source code arguably allows greater scrutiny and oversight than similar closed source projects 11 History editThe website was founded by German biologist Bastian Greshake In 2012 Greshake sent a vial of his saliva to 23andMe a genomics company to study his own DNA His results suggested that he was at risk of prostate cancer and then recommended to his father to receive a medical examination as well The doctor found a growing tumor in his father s prostate and was able to catch it early After receiving his results he posted them on GitHub hoping to find other users willing to share their personal genetic makeup Upon realizing that many people were unwilling or did not include a lot of information that was necessary for scientific research Greshake created openSNP 12 Maybe there are people who are interested in publishing their genetic information on the web to make it available but those people don t have the opportunity 12 Though Greshake acknowledges that there are services that allow people to test their own genes and discover inherent predispositions they are often expensive or difficult to access In 2013 the Food and Drug Administration FDA forced company 23andMe to stop marketing their spit box screening tests due to lack of scientific evidence However in 2015 the FDA eased their restrictions and stated that carrier screening tests would not have to undergo preliminary review 13 Greshake hopes that by making openSNP accessible and simple it will not only attract the public to get interested in their genetic makeup but also to take it down innovative avenues such as turning openSNP data into music 14 Timeline editSeptember 2011 openSNP is released 15 September 2012 Fitbit data inclusion feature added seeing as obesity is correlated with specific SNPs 16 May 2014 The website reached 1000 genotypings September 2015 Crowdfunding campaign started on Patreon platform 17 February 2016 Code of Conduct is created that outlines appropriate behavior and general guidelines 18 August 2016 openSNP was a participant of Google Summer of Code 19 References edit a b openSNP opensnp org Retrieved 20 November 2016 a b Vayena Effy Brownsword Roger Edwards Sarah Jane Greshake Bastian Kahn Jeffrey P Ladher Navjoyt Montgomery Jonathan O Connor Daniel O Neill Onora Richards Martin P Rid Annette Sheehan Mark Wicks Paul Tasioulas John April 2016 Research led by participants a new social contract for a new kind of research Journal of Medical Ethics 42 4 216 219 doi 10 1136 medethics 2015 102663 PMC 4819634 PMID 25825527 Greshake Bastian 2014 openSNP A Crowdsourced Web Resource for Personal Genomics PLOS ONE 9 3 e89204 Bibcode 2014PLoSO 989204G doi 10 1371 journal pone 0089204 PMC 3960092 PMID 24647222 The Social Network for People Who Want to Upload Their DNA to the Internet Fusion Retrieved 20 November 2016 Angrist Misha 2014 Open Window When Easily Identifiable Genomes and Traits Are in the Public Domain PLOS ONE 9 3 e92060 Bibcode 2014PLoSO 992060A doi 10 1371 journal pone 0092060 PMC 3960179 PMID 24647311 Scaria Vinod 2014 Personal genomes participatory genomics and the anonymity privacy conundrum Indian Academy of Sciences 93 3 917 20 doi 10 1007 s12041 014 0451 3 PMID 25572254 S2CID 2983269 Vayena Effy 2016 Between Openness and Privacy in Genomics PLOS Medicine 13 1 e1001937 doi 10 1371 journal pmed 1001937 PMC 4710519 PMID 26757154 Ahn Sejin 1 September 2015 Whose Genome Is It Anyway Re identification and Privacy Protection in Public and Participatory Genomics San Diego Law Review 52 3 751 a b Haeusermann Tobias Greshake Bastian Blasimme Alessandro Irdam Darja Richards Martin Vayena Effy 9 May 2017 Open sharing of genomic data Who does it and why PLOS ONE 12 5 e0177158 Bibcode 2017PLoSO 1277158H doi 10 1371 journal pone 0177158 PMC 5423632 PMID 28486511 Health Voices PDF 28 November 2017 Archived from the original PDF on 28 November 2017 Retrieved 28 November 2017 Why Open Source Software is More Secure Than Commercial Software Mend Retrieved 12 April 2023 a b This Guy Is the Mark Zuckerberg of Open source Genetics Fusion Retrieved 20 November 2016 FDA eases access to at home DNA screening test Retrieved 20 November 2016 The Sound Of Bastian Greshake retrieved 20 November 2016 openSNP openSNP Retrieved 20 November 2016 Obesity SNPedia snpedia com Retrieved 20 November 2016 openSNP is creating Science Patreon Patreon Retrieved 20 November 2016 gedankenstuecke snpr GitHub Retrieved 20 November 2016 openSNP Linking Phenotypes to SNPs in openSNP 2016 Google Summer of Code Archive summerofcode withgoogle com Retrieved 20 November 2016 Retrieved from https en wikipedia org w index php title OpenSNP amp oldid 1213556865, wikipedia, wiki, book, books, library,

article

, read, download, free, free download, mp3, video, mp4, 3gp, jpg, jpeg, gif, png, picture, music, song, movie, book, game, games.