Impute.me was an open-source non-profit
web application
A web application (or web app) is application software that is created with web technologies and runs via a web browser. Web applications emerged during the late 1990s and allowed for the server to dynamically build a response to the request, ...
that allowed members of the public to use their data from
direct-to-consumer (DTC) genetic tests (including tests from
23andMe
23andMe Holding Co. is an American personal genomics and biotechnology company based in South San Francisco, California. It is best known for providing a direct-to-consumer genetic testing service in which customers provide a saliva testing, sali ...
and
Ancestry.com
Ancestry.com LLC is an American genealogy company based in Lehi, Utah. The largest for-profit genealogy company in the world, it operates a network of genealogical, historical records, and related genetic genealogy websites. It is owned by The ...
) to calculate
polygenic risk scores (PRS) for complex diseases and cognitive and personality traits.
In July 2022, Lasse Folkerson, initiator and operator of impute.me, took the website offline.
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 genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...
in the
human genome
The human genome is a complete set of nucleic acid sequences for humans, encoded as the DNA within each of the 23 distinct chromosomes in the cell nucleus. A small DNA molecule is found within individual Mitochondrial DNA, mitochondria. These ar ...
.
It is intended for use by people who have obtained genetics data from a
direct to consumer genetic testing company.
If they upload the files, the uploaded data is expanded into ungenotyped SNPs and the overlap with public GWAS
summary statistics
In descriptive statistics, summary statistics are used to summarize a set of observations, in order to communicate the largest amount of information as simply as possible. Statisticians commonly try to describe the observations in
* a measure of ...
used to estimate risk.
The data is then subjected to analysis scripts including PRS calculations for approximately 2,000 traits and complex diseases.
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.
The scores based on all SNPs are only available for about 20 complex diseases and traits.
Users can then make use of the web tool GenoPred to translate their PRSs onto an
absolute risk Absolute risk (or AR) is the probability or chance of an event. It is usually used for the number of events (such as a disease) that occurred in a group, divided by the number of people in that group.
Absolute risk is one of the most understandabl ...
scale using summary statistics from the GWAS studies.
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.
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
Post-traumatic stress disorder (PTSD) is a mental disorder that develops from experiencing a Psychological trauma, traumatic event, such as sexual assault, domestic violence, child abuse, warfare and its associated traumas, natural disaster ...
.
Notably, this criticism match the FDA-regulation imposed on the major direct-to-consumer genetics company
23andme
23andMe Holding Co. is an American personal genomics and biotechnology company based in South San Francisco, California. It is best known for providing a direct-to-consumer genetic testing service in which customers provide a saliva testing, sali ...
.
References
External links
*
*{{dead link, date=October 2022
Open Source Codefork of Open Source Code
Genomics