Biology:Impute.me

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Impute.me. [1] was an open-source non-profit web application that allowed members of the public to use their data from direct-to-consumer (DTC) genetic tests (including tests from 23andMe and Ancestry.com) to calculate polygenic risk scores (PRS) for complex diseases and cognitive and personality traits.[2][3][4][5][6] In July 2022, Lasse Folkerson, initiator and operator of impute.me, took the website offline.[7][8]

impute.me
Content
DescriptionA polygenic risk score calculator for human diseases and traits
Data types
captured		single-nucleotide polymorphisms, genotypes, genes, variation
OrganismsHomo sapiens
Contact
Primary citationPMID 32714365
Miscellaneous
Software licenseGNU Lesser General Public License v3.0

Impute.me calculates PRSs, which are used to estimate the risk of developing complex diseases from the combined effects of numerous common single nucleotide polymorphisms in the human genome.[9][10]

It is intended for use by people who have obtained genetics data from a direct to consumer genetic testing company.[11][12] If they upload the files, the uploaded data is expanded into ungenotyped SNPs and the overlap with public GWAS summary statistics used to estimate risk.[2] The data is then subjected to analysis scripts including PRS calculations for approximately 2,000 traits and complex diseases.[2] PRSs are calculated based on the combined effect of all SNPs reported in the summary statistics of the underlying GWAS or of the top, genome-wide significant SNPs in the underlying GWAS.[2] The scores based on all SNPs are only available for about 20 complex diseases and traits.[2] Users can then make use of the web tool GenoPred[13] to translate their PRSs onto an absolute risk scale using summary statistics from the GWAS studies.[14]

Criticisms

Numerous criticisms has been raised against consumers accessing their own genetic information, including findings that more than 30% of direct-to-consumer related contacts to clinical genetics departments involve the use of imputed risk estimates and that third party genetics analysis site generally invoke science's power without accepting its limits, while failing to make clear the limitations and potential dangers.[15][16] In addition there are concerns that many people will react negatively to accessing their own polygenic risk scores, with findings that over 5% of users score over the threshold for potential post-traumatic stress disorder.[17] Notably, this criticism match the FDA-regulation imposed on the major direct-to-consumer genetics company 23andme.[18]

References

  1. ↑ "Impute.me". https://impute.me/. 
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Folkersen, Lasse; Pain, Oliver; Ingason, Andrés; Werge, Thomas; Lewis, Cathryn M.; Austin, Jehannine (2020). "Impute.me: An Open-Source, Non-profit Tool for Using Data From Direct-to-Consumer Genetic Testing to Calculate and Interpret Polygenic Risk Scores". Frontiers in Genetics 11: 578. doi:10.3389/fgene.2020.00578. ISSN 1664-8021. PMID 32714365. 
  3. ↑ "Design and user experience testing of a polygenic score report: a qualitative study of prospective users". BMC Med Genomics 14 (1): 238. October 2021. doi:10.1186/s12920-021-01056-0. PMID 34598685. 
  4. ↑ Ronald A (2020). "Editorial: Polygenic scores in child and adolescent psychiatry - strengths, weaknesses, opportunities and threats.". J Child Psychol Psychiatry 61 (5): 519–521. doi:10.1111/jcpp.13246. PMID 32304105. 
  5. ↑ Corpas M, Beck S, Glusman G, Shabani M (2021). "Editorial: Personal Genomes: Accessing, Sharing, and Interpretation.". Front Genet 12: 687584. doi:10.3389/fgene.2021.687584. PMID 34149819. 
  6. ↑ Zanardi R, Prestifilippo D, Fabbri C, Colombo C, Maron E, Serretti A (2021). "Precision psychiatry in clinical practice.". Int J Psychiatry Clin Pract 25 (1): 19–27. doi:10.1080/13651501.2020.1809680. PMID 32852246. https://pubmed.ncbi.nlm.nih.gov/32852246. 
  7. ↑ @ImputeMe. "We are undergoing an evolution to the next level of easy-to-access, high-quality genetic analysis.". https://twitter.com/ImputeMe/status/1547639111539822593.  Missing or empty |date= (help)
  8. ↑ @lassefolkersen. "Start spreading the news, I'm leaving today.". https://twitter.com/lassefolkersen/status/1547637066384560137.  Missing or empty |date= (help)
  9. ↑ Wray NR, Lin T, Austin J, McGrath JJ, Hickie IB, Murray GK (2021). "From Basic Science to Clinical Application of Polygenic Risk Scores: A Primer.". JAMA Psychiatry 78 (1): 101–109. doi:10.1001/jamapsychiatry.2020.3049. ISSN 2168-622X. PMID 32997097. https://pubmed.ncbi.nlm.nih.gov/32997097. 
  10. ↑ Murray GK, Lin T, Austin J, McGrath JJ, Hickie IB, Wray NR (2021). "Could Polygenic Risk Scores Be Useful in Psychiatry?: A Review.". JAMA Psychiatry 78 (2): 210–219. doi:10.1001/jamapsychiatry.2020.3042. PMID 33052393. https://pubmed.ncbi.nlm.nih.gov/33052393. 
  11. ↑ France2 (2018). "ADN pour tous". https://www.youtube.com/watch?v=xl10P__EAF4&t=3275s. 
  12. ↑ Vanzo RJ, Prasad A, Staunch L, Hensel CH, Serrano MA, Wassman ER (2020). "The Temple Grandin Genome: Comprehensive Analysis in a Scientist with High-Functioning Autism.". J Pers Med 11 (1): 21. doi:10.3390/jpm11010021. PMID 33383702. 
  13. ↑ "Converting Polygenic Score to Absolute Scale". https://opain.github.io/GenoPred/PRS_to_Abs_tool.html. 
  14. ↑ Template:Cite medRxiv
  15. ↑ "Impact of direct-to-consumer genetic testing on Australian clinical genetics services". Eur J Med Genet 63 (9): 103968. September 2020. doi:10.1016/j.ejmg.2020.103968. PMID 32502649. 
  16. ↑ "Public reactions to direct-to-consumer genetic health tests: A comparison across the US, UK, Japan and Australia". Eur J Hum Genet 28 (3): 339–348. March 2020. doi:10.1038/s41431-019-0529-8. PMID 31645768. 
  17. ↑ Peck L, Borle K, Folkersen L, Austin J (2021). "Why do people seek out polygenic risk scores for complex disorders, and how do they understand and react to results?". Eur J Hum Genet 30 (1): 81–87. doi:10.1038/s41431-021-00929-3. PMID 34276054. 
  18. ↑ Yim SH, Chung YJ (2014). "Reflections on the US FDA's Warning on Direct-to-Consumer Genetic Testing.". Genomics Inform 12 (4): 151–5. doi:10.5808/GI.2014.12.4.151. PMID 25705152. 

External links



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