ASHG18 tweet summary day 1

Last updated on Mon, Feb 26, 2024 8 min read Conference

Today was the first day of the American Society of Human Genetics (ASHG) 2018 conference. The official hashtag for the conference is ASHG18 on Twitter. At first I was tweeting myself and checking both the top and the latest tweets. As the day progressed I started a Google Doc to take notes during talks. I was missing some details so I was relying on the latest tweets and copy-pasting the tweet links to my notes. At some point I told myself I should simply turn this collection of tweet links into a simple blog post. So here it is for day 1. You can consider it a curated list of the ASHG18 tweets. Although it’s incomplete because it only covers the talks I went to starting from the Presidential address.

The linked tweets are frequently from Eli Robertson¹ and Michael Hoffmann², but also from other Twitter users³.

So, without further ado, here we go:

Arrive in SD for @GeneticsSociety #ASHG18

Cab driver a Greek Orthodox Palestinian from Jerusalem
Tell him that I am here for genetics meeting

And his 1st ?: "Is the ancestry stuff accurate?...@Ancestry test told me that I'm 27% Greek and I know I am more than that."

😳
— Sek Kathiresan MD (@skathire) October 16, 2018

Award presentations

JL: Population → clan → family → patient. #ASHG18
— Michael Hoffman @michaelhoffman.bsky.social (@michaelhoffman) October 17, 2018

Sek also thanked all his mentees ^^.

#ASHG18: @gabecasis presenting the Curt Stern award to @skathire: “...be like Sek: think big, be enthusiastic, and self-examine”.
— Maria Chahrour (@MariaChahrour) October 17, 2018

Diversity

Thanks to @GeneticsSociety for expanding the code of conduct for #ASHG18. Let's make the meeting safe, productive, and fun! https://t.co/CLu84vonSD pic.twitter.com/lT4bycqHxG
— Michael Hoffman @michaelhoffman.bsky.social (@michaelhoffman) October 14, 2018

On the way to #ASHG18 to learn, meet, and share! interested in knowing how latent artifacts affect reconstruction of coexpression networks? Come to my talk on Fri, Room 6C#womeninSTEM #scientistMom
cc Claire Ruberman, .@jtleek @alexisjbattle @andrewejaffe @mike_schatz pic.twitter.com/n3VrclqHS3
— Princy Parsana (@princyparsana) October 16, 2018

3.75% of attendees are Hispanic at #ASHG18 (hosted in San Diego this year)

Would love to see more! I know @lcgunam is training a few dozen a year and @sacnas is helping thousands across science.

Let’s keep improving!#diversity
— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) October 16, 2018

Mine is simple. I don’t know everything @GeneticsSociety does to promote #diversity, but it’d be great if they took a 👀 at @rstudio’s diversity scholarship. Membership fee can be too prohibitive for scientists outside the US (if they manage to cover ✈️) https://t.co/nmZY7UrQUf
— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) October 16, 2018

Sek @skathire starts his #ASHG18 Curt Stern award presentation by briefly mentioning his immigration to the US story and highlighting it all in one word:

“possibility”

👏🏽🙌🏽
— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) October 17, 2018

Mitchel Cole

SNP crispr-cas9 perturbation study in blood cells.

#ashg18 Mitchel Cole describing genomewide CRISPR KO screen using red blood cell trait GWAS hits from our 2016 Cell paper using @uk_biobank & INTERVAL data: https://t.co/Ir4gk2rZ88
— Adam Butterworth (@aidanbutty) October 17, 2018

MC mentioned metaFDR for combining pvalues from 4 tests.

Priyanka Nakka

Uniparental disomy using 23andMe data. Seeking prevalence information in general population.

PN: Open questions: 1/What is the prevalence of UPD in general population (not ascertained for disease)? 2/What are rates of maternal UPD, paternal UPD, and subtypes in general population? 3/What phenotypes are associated with UPD? #ASHG18
— Michael Hoffman @michaelhoffman.bsky.social (@michaelhoffman) October 17, 2018

3 types that can be identified by 2 in silico methods.

PN: Used @23andMeResearch data, 5M+ customers, 80% consented for research. Computationally detect 3 subtypes of UPD (heterodisomy, isodisomy, or partial isodisomy) based on IBD between parent-child and ROH analysis. #ASHG18
— Charleston Chiang (@CharlestonCWKC) October 17, 2018

PN: In ~900k duos in the 23andMe database, find 199 individuals with UPD. Overall rate of 1/2000 - twice as common as previously thought & first estimate of UPD prevalence in general population #ASHG18
— 23andMe Research & Therapeutics (@23andMeResearch) October 17, 2018

PN: Problem distinguishing between UPD and consanguinity in parents. Trained logistic regression classifiers for each chromosome and population separately #ASHG18
— 23andMe Research & Therapeutics (@23andMeResearch) October 17, 2018

Mentioned PheWAS.

PN: Don’t know if you can get single cell data from 23andMe customers.

If you're interested in interning with us like Priyanka did, send me a DM! You can also check out the current job openings on our Research Team here: https://t.co/TlJVQjdjqT #ASHG18
— 23andMe Research & Therapeutics (@23andMeResearch) October 17, 2018

If like the previous question-asked you’re interested in single cell sequencing of sperm, you MUST check out @averydavisbell’s talk this Thursday at 9 am! #ASHG18
— Beryl Cummings (@beryl_bbc) October 17, 2018

I was too busy being a #proudPI to live tweet Priyanka Nakka’s talk about work with @23andMeResearch on identifying cases of uniparental disomy using IBD and runs of homozygosity. Find Priya during #ASHG18 to find out more!
— Sohini Ramachandran (@s_ramach) October 17, 2018

Jack A Kosmicki

Next up, my lab big brother @Jack_Kosmicki presenting on the latest in autism gene discovery on behalf of the Autism Sequencing Consortium #ASHG18
— Beryl Cummings (@beryl_bbc) October 17, 2018

mentioned pLl method

“@ksamocha does everything”. #ASHG18
— Eugene Gardner (@DrGeneUK) October 17, 2018

.@Jack_Kosmicki #ASHG18: Constraint scores (MPC for missense and pLI for loss-of-function) help identify de novo variants enriched in cases with autism.

Also thanks for the shout-outs, Jack. :)
— Kaitlin Samocha (@ksamocha) October 17, 2018

99 ASD genes

.@Jack_Kosmicki : 99 genes at FDR of 10%, 25 of which are genome-wide significant #ASHG18
— Beryl Cummings (@beryl_bbc) October 17, 2018

JK: 41/50 ASD-preferential genes have only 0-1 de novo missense or premature termination variants in ID/DD #ASHG18
— Michael Hoffman @michaelhoffman.bsky.social (@michaelhoffman) October 17, 2018

summary

JK: some de novo variants for autism are even more enriched in non-autistic intellectual/developmental delay. Others are ASD preferential. Stronger neg selection in ID/DD- than ASD-preferential genes. ID/DD-preferential genes associated with walking later. #ASHG18
— Daniel E. Weeks (@StatGenDan) October 17, 2018

Caitlin Bowen

Sorry, I left this talk early to see the poster talks (that I didn’t know had been delayed).

Wrap up

Poster talks

#ASHG18 “Poster Talks” starting in a few mins!! Get a sneak peek at some of the best data being presented this year @GeneticsSociety via these posters nominated to give brief talks. Here’s one from @Genomes2People @RobertCGreen: https://t.co/dEI5iOXCf9 Ballroom 6C pic.twitter.com/GIELxjyRps
— Genomes2People (@Genomes2People) October 17, 2018

Single cell composition and organs poster 2012 seemed interesting to me. I added to my calendar!

Acknowledgments

This blog post was made possible thanks to:

BiocStyle (Oleś, 2023)
blogdown (Xie, Hill, and Thomas, 2017)
knitcitations (Boettiger, 2021)
sessioninfo (Wickham, Chang, Flight, Müller et al., 2021)

as well as everyone who was tweeting! See you on Thursday!

ASHG-attending tweeps: hope to meet you at the #ASHG18 Tweetup! 7:30p Thursday, Garage Kitchen+Bar, 655 Fourth Ave. https://t.co/kfYRQSlTKt
— Michael Hoffman @michaelhoffman.bsky.social (@michaelhoffman) October 14, 2018

References

\[1\] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.12. 2021. URL: https://CRAN.R-project.org/package=knitcitations.

\[2\] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.28.0. 2023. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.

\[3\] H. Wickham, W. Chang, R. Flight, K. Müller, et al. sessioninfo: R Session Information. R package version 1.2.2. 2021. URL: https://CRAN.R-project.org/package=sessioninfo.

\[4\] Y. Xie, A. P. Hill, and A. Thomas. blogdown: Creating Websites with R Markdown. Boca Raton, Florida: Chapman and Hall/CRC, 2017. ISBN: 978-0815363729. URL: https://bookdown.org/yihui/blogdown/.

Reproducibility

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Eli Robertson creates great Twitter threads, so I frequently only link to the first tweet of the thread. ↩︎
Michael Hoffmann also writes multiple tweets per talk, though you’ll have to scroll through his timeline to find all the ones related to a talk. Unless I’m missing a way to make them into a thread. ↩︎
Some with a few followers, some with many. It didn’t matter. I was just checking the latest and saving the ones I liked the most. ↩︎

ASHG

Leonardo Collado-Torres

Investigator @ LIBD, Assistant Professor, Department of Biostatistics @ JHBSPH

#rstats @Bioconductor/🧠 genomics @LieberInstitute/@lcgunam @jhubiostat @jtleek @andrewejaffe alumni/@LIBDrstats @CDSBMexico co-founder