Very happy and proud to present: The GTEx papers. This set of 15 papers published today describes the final phase of this 10-year effort, providing the genomics community an atlas of genetic regulatory variants and a deep dive into the biology behind it. sciencemag.org/collections/ge…
In the main paper, co-led with @francoisaguet and @KArdlie, we introduce the data set of eQTLs and sQTLs in cis and trans from >15K samples from 49 tissues, analyze functional mechanisms, tissue- and cell-type specificity, GWAS interpretation, and more. science.sciencemag.org/content/369/65…
GTEx data resources including visualizations is available in @GTExPortal, dbGap/ANVIL, UCSC & elsewhere. We also put quite a bit of effort into making the main paper supplement readable & useful. It is LONG though - a TON of work went into this paper!
Huge thanks & congrats to my coauthors - above all @francoisaguet and also other lead analysts Alvaro Barbeira @rodbonazzola @arnsbr @stephanecastel Brian Jo @silvakasela @skimhellmuth @yanyu_liang Meritxell Oliva & @princyparsana. Also @KArdlie @hakyim @alexisjbattle!
I also want to thank people who built this consortium: @KArdlie, @dermitzakis @NancyGenetics @RodericGuigo, the analysis group over the years, @GTExPortal @NIH, sample collection & sequencing folks, above all donor families, & many others. It's been a pleasure and a privilege!
There is also a large number of companion papers from the consortium that dig deeper into specific questions and introduce novel data sets and methods. Full list here, and keep an eye on updates as additional papers get published. sciencemag.org/collections/ge…

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Tuuli Lappalainen

Tuuli Lappalainen Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @tuuliel

18 Jun
Daydreaming of a "cut the BS paperwork" campaign in academia. I think I could easily spend 10-20% more time on actual science if we could get rid of or streamline useless blurbs, reports, letters...for example:
Fluffy letters of support. Can we stop pretending that these expressions of enthusiasm and support are actually written by the signees? It's meaningless. Let's enforce a template that cuts the crap and only allows max 100 words of factual content.
Abstracts for invited seminars. These are so generic that they're useless for everyone involved. Title of the talk, name of the speaker, and maybe bio or google should be enough for people to decide if they want to attend the talk.
Read 8 tweets
30 May
No niin, maskiraportti luettu. TL;DR: Paljon hyvääkin aineistoa. Käsittely on kuitenkin rajattu niin kapeaksi, että muu lopputulos olisi tuskin ollut edes mahdollinen. Aineisto ei oikeuta jyrkkiä johtopäätöksiä, ja rapsan hyöty on suositusten teossa on hyvin rajallinen. Ketju:
Ensin hyvät asiat: Eri maiden toimenpiteistä on tehty hyödyllinen yhteenveto. Kirjallisuuskatsaus on oikein asiallista työtä valitun rajauksen puitteissa. Suurin osa puutteista mainitaan itse tekstissä, tosin tiivistelmä ja media jättää näiden käsittelyn vähälle.
Tosi iso ongelma on rajaus vain satunnaistettuihin kokeisiin. Se on tietty gold standard, mutta ei ainoa oikea tai kaikkiin asioihin sopiva tutkimusasetelma. Koska näiden tutkimusten määrä ja laatu on heikko ja muut on rajattu pois, niin ei ole ihme ettei todistusaineistoa löydy.
Read 10 tweets
15 May
Asiantuntijaryhmämme on julkaissut laajan muistion, jossa rohkaisemme hallitusta asettamaan määrätietoiset tavoitteet koronaepidemian tukahduttamiseksi. Tarjoamme monialaisen tilannekuvan, ja esitämme konkreettisia tavoitteita ja keinoja tämän työn tueksi. eroonkoronasta.fi
Tukahduttamisella tarkoitamme epidemian määrätietoista nitistystä nollan tuntumaan, kaikki ketjut jäljitykseen. Sitten yksittäistartunnat pidetään kurissa täsmätoimin. Tähän voisi päästä juhannukseksi, sitten helpottaisi. Tämä olisi parempi kuin nykytilassa rimpuilu pidempään.
Hybridistrategian keinoilla päästään jo pitkälle, jos toteutus on kunnianhimoinen. Suunta on jo oikea, lockdownia ei tarvita kunhan ei liikaa löysätä. Toimia voisi eriyttää paikallisesti. Maskien teho näyttää hyvältä. Esitämme seulontoja mahdolliseksi tulevaisuuden keinoksi
Read 6 tweets
13 Nov 19
Many labs, including mine, welcome postdocs with expertise in a more or less different field, but it's a riskier move - PIs need to consider every hire as an investment of finite time and resources, and PDs need to think of how to be productive & happy. Some thoughts: [thread]
PD candidates switching fields, make sure you know: 1) Why do you want to do this? Why this specific lab? Wanting to e.g. "learn computational skills" is not enough - labs need PDs who're interested in their research program, and PDs need to be excited about their research topic.
2) How will you be productive? Which of your skills are immediately applicable? Do you have an excellent track record of being a fast learner? It's a difficult sell if you ask a PI to spend ~$100K into you just learning but not producing, and you need papers the faster the better
Read 5 tweets
20 Aug 18
Our paper on modified penetrance of coding variants by cis-regulatory variation is out in @NatGenet! Huge thanks and congrats to @stephanecastel who led the analysis nature.com/articles/s4158… . 1/7
The hypothesis is that in individuals who’re heterozygous for a (rare) LoF coding variant, the phenotypic outcome (i.e. penetrance) can be affected by a cis-eQTL allele tweaking the “healthy” haplotype dosage. 2/7
The key analytical approach is asking whether rare predicted deleterious coding variants are randomly distributed on common eQTL haplotypes. We show that they’re not. 3/7
Read 7 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!

Follow Us on Twitter!