Impute.me

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Impute.me 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. [1] [2] [3] [4] [5] In July 2022, Lasse Folkerson, initiator and operator of impute.me, took the website offline. [6] [7]

Contents

impute.me
Content
DescriptionA polygenic risk score calculator for human diseases and traits
Data types
captured		single-nucleotide polymorphisms, genotypes, genes, variation
Organisms Homo sapiens
Contact
Primary citation PMID   32714365
Access
Website[ dead link ] www.impute.me
Miscellaneous
License GNU 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. [8] [9]

It is intended for use by people who have obtained genetics data from a direct to consumer genetic testing company. [10] [11] 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. [1] The data is then subjected to analysis scripts including PRS calculations for approximately 2,000 traits and complex diseases. [1] 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. [1] The scores based on all SNPs are only available for about 20 complex diseases and traits. [1] Users can then make use of the web tool GenoPred [12] to translate their PRSs onto an absolute risk scale using summary statistics from the GWAS studies. [13]

Criticisms

Numerous criticisms have 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. [14] [15] 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. [16] Notably, this criticism match the FDA-regulation imposed on the major direct-to-consumer genetics company 23andme. [17]

References

  1. 1 2 3 4 5 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. PMC   7340159 . PMID   32714365.
  2. ↑ Brockman DG, Petronio L, Dron JS, Kwon BC, Vosburg T, Nip L, Tang A, O'Reilly M, Lennon N, Wong B, Ng K, Huang KH, Fahed AC, Khera AV (October 2021). "Design and user experience testing of a polygenic score report: a qualitative study of prospective users". BMC Med Genomics. 14 (1) 238. doi: 10.1186/s12920-021-01056-0 . PMC   8485114 . PMID   34598685.
  3. ↑ 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. S2CID   215810502.
  4. ↑ 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 . PMC   8213362 . PMID   34149819.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ↑ 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. S2CID   221347950.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ↑ @ImputeMe (July 14, 2022). "We are undergoing an evolution to the next level of easy-to-access, high-quality genetic analysis" (Tweet) – via Twitter.
  7. ↑ @lassefolkersen (July 14, 2022). "Start spreading the news, I'm leaving today" (Tweet) – via Twitter.
  8. ↑ Wray NR, Lin T, Austin J, McGrath JJ, Hickie IB, Murray GK; et al. (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. S2CID   222169651.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ↑ 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. S2CID   222351995.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ↑ France2 (2018). "ADN pour tous". YouTube .{{cite web}}: CS1 maint: numeric names: authors list (link)
  11. ↑ Vanzo RJ, Prasad A, Staunch L, Hensel CH, Serrano MA, Wassman ER; et al. (2020). "The Temple Grandin Genome: Comprehensive Analysis in a Scientist with High-Functioning Autism". J Pers Med. 11 (1): 21. doi: 10.3390/jpm11010021 . PMC   7824360 . PMID   33383702.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ↑ "Converting Polygenic Score to Absolute Scale". opain.github.io. Retrieved 2021-09-02.
  13. ↑ Pain, Oliver; Gillett, Alexandra C.; Austin, Jehannine C.; Folkersen, Lasse; Lewis, Cathryn M. (2022). "A tool for translating polygenic scores onto the absolute scale using summary statistics". European Journal of Human Genetics. 30 (3): 339–348. doi:10.1038/s41431-021-01028-z. medRxiv   10.1101/2021.04.16.21255481v1 .
  14. ↑ Millward M, Tiller J, Bogwitz M, Kincaid H, Taylor S, Trainer AH, Lacaze P (September 2020). "Impact of direct-to-consumer genetic testing on Australian clinical genetics services". Eur J Med Genet. 63 (9) 103968. doi:10.1016/j.ejmg.2020.103968. PMID   32502649.
  15. ↑ Charbonneau J, Nicol D, Chalmers D, Kato K, Yamamoto N, Walshe J, Critchley C (March 2020). "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. doi:10.1038/s41431-019-0529-8. PMC   7029038 . PMID   31645768.
  16. ↑ 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. PMC   8738734 . PMID   34276054.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  17. ↑ 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. PMC   4330248 . PMID   25705152.
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