ASHG18 tweet summary day 2
This article is originally published at https://lcolladotor.github.io/
Continuing from my ASHG18 day 1 post, here’s my list of tweets from day 2. Note that I changed sessions a few times.
I have to say, digitally attending #ASHG18 by frantically refreshing the hashtag feed in my living room is...not quite the same. But maybe I'll get fish tacos for dinner.
— Julie Nadel (@JulieNadel) October 17, 2018
Turn down the lights and turn up the AC for the fuller remote #ASHG18 experience! ????
— Damien C-C (@dccc_phd) October 17, 2018
6E 10:30 am
Live tweet our #ASHG18 session on #SilentGenomes to hear what #Indigenous scientists are doing to change the narrative and push for more #IndiGenomics moderated by @KeoluFox and @NanibaaGarrison on Wed at 10:30am PT https://t.co/zI8NPXotop
— Nanibaa' Garrison (@NanibaaGarrison) October 16, 2018
Nanibaa’ Garrison
Check Claw et al paper at @NatureComms from @SINGConsortium
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
“A framework for enhancing ethical genomic research with Indigenous communities.” https://t.co/qBuDWGPIV4 #indigenomes #ASHG18
Maile Taualii
“Nobody wakes up thinking how can I harm indigenous populations!”
Maile Taualii: no one goes into research with the intent of harming indigenous communities, so why does this happen? Publish or Perish causes people to rush, skip steps. Ignorance of issues (not an excuse). “For their own good” mentality #ASHG18 #SilentGenomes #IndiGenomics
— Brooke LaFlamme (@Brooke_LaFlamme) October 17, 2018
Don't get distracted by the sexiness of genetic science! (Maile Taualii) #silentgenomes #ASHG18 #indigenomics
— Nanibaa' Garrison (@NanibaaGarrison) October 17, 2018
#ASHG18 #silentgenomes Maile directly addressing the "residue" of colonialism that is linked to culturally sustainable biomedical research today!
— Keolu Fox (@KeoluFox) October 17, 2018
Taualii: take-home messages
— Brooke LaFlamme (@Brooke_LaFlamme) October 17, 2018
1. There is no easy solution
2. Ignorance isn’t an excuse
3. Understand what is at risk
Think about whether your work is going to benefit the generations to come #SilentGenomes #IndiGenomics #ASHG18
Nadine Caron
Nadine Caron: addressing inequity in genomic diagnosis & research. #ASHG18
— Charleston Chiang (@CharlestonCWKC) October 17, 2018
Nadine Caron: "It is known that those who have the greatest health disparities, will actually benefit the least from new technologies and research" #ashg18 #silentgenomes
— John Hawks (@johnhawks) October 17, 2018
I think that Nadine Caron’s suggestions for First Nations and indigenous populations in Canada apply to other countries and underrepresented communities #IndiGenomics #silentgenome #ASHG18
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
Right @paleogenomics? https://t.co/7m5eWNpC8r
Agree!! That is an approach to follow with vulnerable communities. e.g. #Afromexicans, they are not only underrepresented but also have been sadly neglected for centuries.
— paleogenomics (@paleogenomics) October 17, 2018
Nadine Caron - access to research is an important determinant of health. Such a critical issue for health equity issues across the world. #silentgenomes #ASHG18
— Chris Gignoux (@popgenepi) October 17, 2018
Ngiare Brown
N Brown: Ancestry is not the same as culture. Genetic information today is increasingly commercialized and is creating another layer in an already tangled web #silentgenomes at #ASHG18
— Elena Sorokin (@ElenaSorokin) October 17, 2018
Dr. Ngiare Brown: “Some information cannot be individually owned.” Genomics research w/indigenous communities needs to involve to thinking beyond Western notions of consent. #SilentGenomes #ASHG18 #IndiGenomics
— Riley Taitingfong (@riley_ilyse) October 17, 2018
We too (Australia Aborigines) are excited about the sexiness of genetic research. So how do we make sure it gets done right? (Ngiare Brown) #SilentGenomes #ASHG18
— Nanibaa' Garrison (@NanibaaGarrison) October 17, 2018
Third time she mentioned “sexy research”. I thought that this term was frowned upon, maybe it’s not.
Maui Hudson
He made us laugh with his conflict of interest slide. No commercial interests. Just interest in indigenous genomics and helping others.
I like how Hudson is framing the scientific contribution of New Zealand: The genomic resources of Māori people are a unique resource, partnering with the community to enable them to be part of the conversation is essential to good science. #ashg18 #silentgenomes
— John Hawks (@johnhawks) October 17, 2018
Issue with open data. They want to control how the data is re-used. Like for imputation: what are they looking at? Is it something they agree?
Hudson is expressing, though not in so many words, a tension between the consultative approach, in which indigenous communities have a voice in how data are used, and what human geneticists have conceived as "open access" to genome data. #ashg18 #silentgenomes
— John Hawks (@johnhawks) October 17, 2018
I am struck by questions from audience members at #silentgenomes panel. Geneticists who are already working on projects with indigenous subjects, and they are ONLY NOW asking how they can seek involvement from those communities. #ashg18
— John Hawks (@johnhawks) October 17, 2018
These are well-intentioned, nice geneticists, I can see. But if you're asking a panel of indigenous scientists from other parts of the world to speak for the communities that you are working with, you're doing it wrong. Still, this is why #silentgenomes panel matters. #ashg18
— John Hawks (@johnhawks) October 17, 2018
6C 11:30 am
Kelly East
Kelly East of @hudsonalpha: data from Concert Genetics suggest on average, 10 new genetic testing products enter the market every day. #ASHG18
— Chris Gunter (@girlscientist) October 17, 2018
KE discussing how medical genetic testing is rapidly expanding both in types of tests and patients being tested. We don’t have enough genetic providers to handle this, and the ones we do have aren’t uniformly distributed. #ASHG18
— Avery Davis Bell PhD (@averydavisbell) October 17, 2018
(others made better tweets!)Kelly East wants to train MD, NP, PA so that they can understand genetics more and help patients too #ASHG18
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
K East: how do we bring more genetics services to everyone? 1. Make more providers. 2. Increase capacity of existing genetics providers. Or 3, her favorite: Train other healthcare providers to do genetics. #ASHG18
— Chris Gunter (@girlscientist) October 17, 2018
Solution to this KE is advocating is training non-genetic healthcare providers to do the genetics to help patients who will never make it to a genetic counselor. Many providers already interested in genetics. #ASHG18
— Avery Davis Bell PhD (@averydavisbell) October 17, 2018
Given that 52% of #GeneticCounselors are in 10 states, & 60% are in metro areas: We need more genetic counselors, we need GC assistants, we need streamlining and improved efficiency AND let's talk about more genetic training for MDs, NPs, and PAs! @Kelly_M_East #ASHG18
— Sally G Pasion (@sgpombe) October 17, 2018
KE how to educate these providers? Case based, inter professional, and electronic/web based - good opportunitieshere especially as these platforms already heavily used in ongoing medical training #ASHG18
— Avery Davis Bell PhD (@averydavisbell) October 17, 2018
Kelly East: a lot of opportunity for developing web based activities to help train non-genetics colleagues (who are hard to get into a room given the nature of their work/schedules) #ASHG18
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
.@Kelly_M_East developed a toolkit that is hosted on the ASHG website https://t.co/LvcCzpHjn9 for training non-genetics providers.
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
Feedback: good genetic info, but need more info on suggested next steps (which KE didn’t want to have initially in respect of colleagues) #ASHG18
Hmm, can’t say that I’m a fan of the “SouthSeq” project name. Though I don’t have an alternative name on the top of my mind @Kelly_M_East #ASHG18
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
I guess that it’s for US scientists, but I don’t think of the “Deep South” in the US when I hear “SouthSeq”. Anyway, SouthSeq looks like a great project with many ways to train others in genetics.
“We are not going to run genetic providers out of jobs”. Loved this quote!
Chris Gunter
Chris Gunter @girlscientist will close out the discussion with a call to action - doing science is not enough, you have to communicate your research to the public in any way you can #ASHG18
— Avery Davis Bell PhD (@averydavisbell) October 17, 2018
35,000 page views on DNA awareness day3. 23andMe did a survey study in March 2018
Chris Gunter: your paper is a nucleus for a larger #scicomm ecosystem #ASHG18
— Kathryn Vaillancourt (@MoleculeMind) October 17, 2018
Science literacy does NOT equal support for science. New framework: Science ENGAGEMENT -- a two-way street. @girlscientist #ASHG18
— Cincy Kids Genomics (@CincyKidsGenomX) October 17, 2018
@girlscientist We MUST think about the sociopolitical climate we are sharing knowledge in. This stuff isn’t neutral. #ASHG18
— Avery Davis Bell PhD (@averydavisbell) October 17, 2018
Ohh! #medRxiv will be online soon! Looks like it’s related to @biorxivpreprint (from the website design) right @cshperspectives? @girlscientist announced it at #ASHG18
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
Follow @medrxivpreprint!! #ASHG18 https://t.co/sanAbTK1lI
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
@girlscientist just gave an interesting talk about providing scientific education to general public. Don't think it's as simple as a knowledge deficit issue - much more nuanced and complex. (Just like humans?) #ASHG18
— Cathy Long (@yhtacgnol) October 17, 2018
Hmm, I get the point that a republican scientist might have an easier time communicating with a republican audience. But it also felt discouraging to me. Well, I guess that you should always try to be aware of your audience and try your best to connect with them. #ASHG18
— ???????? Leonardo Collado-Torres (@lcolladotor) October 17, 2018
Beth Tuck: @genome_gov would love to have everyone as partners for DNA Day 2019. Check out their site at https://t.co/DQUWzVO5bB, of their Pinterest, or Twitter, or Facebook, or suggest something new! #ASHG18
— Chris Gunter (@girlscientist) October 17, 2018
Other (morning)
BM: Assumptions $45,000 max for sharing by publisher, recipient pays $180 for data, receives reward of $360 for successful detection. Allow 10% FPR, 50% TPR. Prior of 0.05. #ASHG18 https://t.co/1KYmCaexDb
— Michael Hoffman (@michaelhoffman) October 17, 2018
"For non-scientists like lawyer, cryptographic keys are like dark magic. Explain properly those technology is part of the #privacy challenge." @erlichya #ASHG18 #ASHG2018
— ???????????????????????????????????? ???????????????????? ???????????? (@introspection) October 17, 2018
20BC 4:15 pm (4:23)
Semanti Mukherjee
In session #25: Integrated Variant Analysis in Cancer Genomics. #ASHG18 https://t.co/O3p4JElpB5
— Michael Hoffman (@michaelhoffman) October 17, 2018
#ASHG18 SM: MSK-IMPACT tumor/normal sequencing for 468 cancer related genes,2686 unselected lung cancer cohort, enriched cohort of 73 with early onset or multiple primary or family history
— John Thompson (@Single_Molecule) October 17, 2018
Semanti Mukherjee: 8.5% of patients in an unselected lung cancer cohort had germline mutations in known cancer susceptibility genes including BRCA1/2, CHEK2, P53, MUTYH, and others including highly penetrant variants and low penetrance susceptibility variants #ASHG18
— Claudia Gonzaga-Jauregui (@cgonzagaj) October 17, 2018
Chimene Kesserwan:
Now: Chimene Kesserwan: Assessing causality of pathogenic and likely pathogenic germline variants by integrating somatic and germline sequencing in children with cancer enrolled on the “Genomes for Kids” (G4K) sequencing study at St. Jude Children’s Research Hospital #ASHG18
— Michael Hoffman (@michaelhoffman) October 17, 2018
Cynthia Zepeda
Next @CinthyaZepeda presenting Beyond FISH and Karyotype detecting complex rearrangements by mate-pair sequencing in leukemia and lymphoma #ASHG18 @lcgunam
— Claudia Gonzaga-Jauregui (@cgonzagaj) October 17, 2018
CZ: Going beyond karyotype and FISH using MPseq that identifies chromosomal abnormalities at high resolution in leukemia samples. Identified ~110 abnormalitiesper case in a cohort of 16 B-ALL cases MPseq helped refined karyotype calls #ASHG18
— Claudia Gonzaga-Jauregui (@cgonzagaj) October 17, 2018
Xiaowu Gai
#ASHG18 next up, Xiaowu Gai from CHLA will talk about pan cancer analysis of germline and somatic variants in 621 pediatric cancer patients
— John Thompson (@Single_Molecule) October 18, 2018
He thanked others for uploading data and making it publicly available so bioinformaticians like him can download it and re-analyze it. I totally agree with him!
6C 5:15 pm
Julio Barrera
Replaced by Chiba-Falek (lab PI).
Single cell (Neuron/glia)( ATAC-seq + RNA-seq + case-control data studying LOAD. RNA + ATAC matches.
Yungil Kim
PI Panos Roussos. Single cell data.
Other (afternoon)
Kudos @SarahTishkoff for highlighting the -most- informative single measure of a single human genome: # of heterozygous sites. #ashg18
— Nathan Pearson (@GenomeNathan) October 18, 2018
20 BC 6 pm
Christopher Lau
Chris Lau from @genome_gov now presenting on genes of unknown significance in 20BC to kickoff session 34- reanalysis of sequencing data to increase dx yield #ASHG18
— UDN (@UDNconnect) October 18, 2018
CL: Discussing use of the UDN to match patients with variants impacting the same amino acid in a gene that was not a known disease gene at the time; simply prioritised due to nature of the impact. Chao and Davis et al AJHG 100 2017. #ASHG18
— liz worthey (@lizworthey) October 18, 2018
Matt Velinder
Up now Matt Velinder discussing iterative reanalysis provides diagnostic avenue for previously unsolved rare and complex disease cases #ASHG18
— liz worthey (@lizworthey) October 18, 2018
MV: 44 patients have been accepted into their penelope rare and undiagnosed disease program (out of 70 who applied). Trio WES gave 17 diagnoses, 6 probable diagnoses, and 16 no diagnoses #ASHG18
— liz worthey (@lizworthey) October 18, 2018
Matt Velinder presented results processed using: (they are URLs)
— ???????? Leonardo Collado-Torres (@lcolladotor) October 18, 2018
vcf.iobio bam.iobio echo.iobio
Part of the Undiagnosed Network (UDN) @UDNconnect
#ASHG18
20 A 6:42 pm
Ira Hall
Ira Hall: As SV population frequency goes down size goes up. Ultra rare SVs are larger than common SVs. #ASHG18
— ryanlayer (@ryanlayer) October 18, 2018
Controlling for a nearby pLI gene? I’ve seen pLI mentioned a few times. Gotta read more about it!
Sarcasm/fun
Massively parallel biology students.... #ASHG18
— Tricia Hall (@BiochemG_thall) October 17, 2018
There should be a time penalty for #ASHG18 speakers who use fonts below a certain size. #usebiggerfonts #morepicturesfewerwords
— Chloe Reuter (@ChloeReuterCGC) October 17, 2018
#ASHG18 Best exhibitor presentation I saw was “Long reads? You don’t need no stinking long reads.” at the Illumina booth.
— Testing enthusiast (@apicoplast) October 17, 2018
TFW you're in an overflow room, and the speaker says 'thank you for listening, I'll take questions', and you automatically, absentmindedly start clapping, and nobody else in the room does #ASHG18
— Genome Biology (@GenomeBiology) October 18, 2018
plus they have a 50% off discountNeeded a last min bday present for my brother’s bday dinner tonight. Good thing I’m at #ASHG18 where @23andMe is selling these kits. #iforgetbirrhdays #badsibling #geekypresents pic.twitter.com/eifRa4gCMK
— Joyce Kao (@joyceykao) October 18, 2018
Beginning to think I chose my session attendance poorly. I might be in a broom closet. #ASHG18
— Testing enthusiast (@apicoplast) October 18, 2018
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— The Sheriff of ASHG (@genome_sheriff) October 18, 2018
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HOWDY, I'M THE SHERIFF OF REPRODUCIBLE RESEARCH #ASHG18
Diversity
Recording questions at #ASHG18 with @NatalieTelis at https://t.co/tqdWgqSG7F but it's getting a bit depressing. If you're more established in the field, please consider waiting a beat before stepping up to the mic.. Would love to hear questions from a diverse set of voices!
— Nicole Ersaro (@ferraronm) October 17, 2018
@SarahTishkoff now presenting on behalf of a former postdoc who couldn’t get a visa (!!! This is such a problem and not unique) #ASHG18
— Avery Davis Bell PhD (@averydavisbell) October 18, 2018
So lucky to hear @SarahTishkoff speak at #ASHG18 but heartbroken she’s subbing in bc of visa issues. Isolationism and strict immigration policies are not how we keep pursuing scientific progress.
— Natalie Telis (@NatalieTelis) October 18, 2018
Just putting this out there for #ASHG18 :D https://t.co/LuG14mYpbD
— liz worthey (@lizworthey) October 18, 2018
Motivational
When I grow up I want to be as excellent of a speaker as the speakers in this tumor heterogeneity session #goals #ASHG18
— Sarah Garcia (@skerfoot) October 17, 2018
Acknowledgments
This blog post was made possible thanks to:
- BiocStyle (Oleś, Morgan, and Huber, 2020)
- blogdown (Xie, Hill, and Thomas, 2017)
- knitcitations (Boettiger, 2019)
- sessioninfo (Csárdi, core, Wickham, Chang, et al., 2018)
and everyone who wrote tweets with the ASHG18 hashtag!
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) October 14, 2018
References
[1] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.10. 2019. URL: https://CRAN.R-project.org/package=knitcitations.
[2] G. Csárdi, R. core, H. Wickham, W. Chang, et al. sessioninfo: R Session Information. R package version 1.1.1. 2018. URL: https://CRAN.R-project.org/package=sessioninfo.
[3] A. Oleś, M. Morgan, and W. Huber. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.14.4. 2020. URL: https://github.com/Bioconductor/BiocStyle.
[4] Y. Xie, A. P. Hill, and A. Thomas. blogdown: Creating Websites with R Markdown. ISBN 978-0815363729. Boca Raton, Florida: Chapman and Hall/CRC, 2017. URL: https://github.com/rstudio/blogdown.
Reproducibility
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## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/libraryThanks for visiting r-craft.org
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