Talk:Expression quantitative trait loci

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Medicine: Genetics

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Suggestions

This looks like a good start. It would be useful to also create a wikipedia page for eQTL and make it forward to this one. Also referencing needs to be tightened up a bit. The following URL is really useful, given a pubmed id it will generate the wiki text that needs to be inserted into the page:

http://diberri.dyndns.org/cgi-bin/templatefiller/?type=pubmed_id&id=17452784

Keep up the good work Alexbateman (talk) 10:00, 13 November 2009 (UTC)[reply]

Figures

Does anyone have a good figure that would illustrate the concept of an eQTL nad perhaps illustrate a specific example of an eQTL?

Perhaps something like shown on this webpage would be useful: http://www.scri.ac.uk/research/genetics/GenomeBiology/eQTL

It would be useful to have some subsections too. Perhaps these could include eQTL mapping, History of eQTL analysis, eQTLs implicated in disease.

Also does anyone know who first coined the term? Alexbateman (talk) 16:53, 13 November 2009 (UTC)[reply]

I've been looking for any nice illustrations in PLoS articles (as per Lars' suggestion) but haven't picked anything up yet - Wadhamite (talk) 20:50, 13 November 2009 (UTC)[reply]

History of eQTLs

I am hoping to flesh out this article eventually and add a history section. Right now it is all personal knowledge so I need to go back to basics and make sure I'm adding the citations to support it.

Basic outline for future reference:

QTL as a term is very old (1940s?), from back when "gene" still meant "unknown unit of inheritance" rather than the very specific definition it has now.
DNA sequencing (1970s onward) caused a rapid change in our understanding of genomics
During this period, there came a need to specify between more traditional QTL experiments (lots of cloning based methods) and the new, more direct measurements of phenotype like transcript abundance (eQTLs)
The term eQTL was first published around the 1990s-2000s*, but no specific person coined it**
Gene expression technically refers to any product of a gene, but because quantifying RNA levels is vastly easier that quantifying proteins (on a high-throughput, genome-wide scale), scientists generally use "expression" to mean "RNA", not protein.
Because of this, more specific QTL terms have continued to pop up including pQTLs, methylation QTLs, etc. The Illumina page on QTLs lists 5 kinds currently: https://www.illumina.com/techniques/popular-applications/qtl-analysis.html

*it appears eQTL is also used as an abbreviation for "equational" in some math textbooks, but the oldest verifiable use I could find was 2003. There's a possible usage in 1997 but I can't access the paper to confirm (too obscure for Sc*hub)

**Based on personal correspondence with colleagues, I know that several people were using the term before it was published, but no one seems really interested in claiming it. One of these authors emailed me that "it [was] not a creative thing just something that was easy to tag (anybody else would have done the same)". This is pretty common in my experience, scientific language just sort of evolves naturally and new concepts rarely come from a single person or eureka moment.

Bibliography

1996 short letter on mathematical limitations of cloning experiments https://pmc.ncbi.nlm.nih.gov/articles/PMC1914627/
1997 genetics paper using "EQTL" but couldn't access paper to verify the meaning of the acronym https://www.google.com/books/edition/Improving_the_Efficiency_of_Common_Bean/Ro2dtTP9t_cC?hl=en&gbpv=1&bsq=%22eqtl%22&dq=%22eqtl%22&printsec=frontcover
Science 2002, example of the transition from cloning/linkage based experiments to RNA transcript abundance https://www.science.org/doi/epdf/10.1126/science.1069516
Nature 2003, first use of eQTL I found on pubmed https://www.nature.com/articles/nature01434
PNAS 2005, using transcript abundance for QTL research but does not use "eQTL" https://doi.org/10.1073/pnas.0408709102
Nature Genetics 2008, several of same authors now using "eQTL" https://pmc.ncbi.nlm.nih.gov/articles/PMC2573859/ (disclosure: one of these authors is now my boss)

Abbey.thorpe (talk) 18:07, 17 October 2024 (UTC)[reply]