Category Archives: Astuce de la semaine

dtc_testing

Astuce Vidéo de la semaine: Direct to Consumer Genetic Testing and Genetic Counselling

Au OpenHelix, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, Je sais, it still varies). But outreach really is getting better. There are journals now that are also enforcing more reader-friendly ways to describe the research, with non-jargon summaries and some terrific visual aids.

De plus en plus, there are also videos associated with papers. I just came across this one, and thought it was a nice example of an important issue for non-scientists to access.

So this looks at direct-to-consumer (DTC) services available in Europe, but some of the same ones are available in the US. Bien sûr,, aux États-Unis, as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. Soupir.

Astuce a:

Référence:

Middleton, A., Mendes, Á., Benjamin, C. M., & Howard, H. C. (2017). Direct-to-consumer genetic testing: where and how does genetic counseling fit?. La médecine personnalisée, (14:3) , Pages 249-257 , DOI 10.2217/pme-2017-0001.

 

Astuce Vidéo de la semaine: Neandertal Inheritance and Consequences

Ok, it’s been a while since this was a regular feature. But I am still finding that I want to show some videos of science topics and software tools sometimes. So it may not be a regular feature, but I will be highlighting some videos that seem interesting to me for various reasons.

This video struck me because I recently gave a talk about the information from ancestral genomes and the influence of the DNA on us today (as well as how we visualize that). They use software that we’ve talked about before, PolyPhen et EIPD, in this analysis. And it would have been handy to have this as a resources to give out to the audience members, who were general public folks in a pub. I am impressed that a research team did this additional step of explaining their research in this way.

Référence:

Dannemann, M., Prüfer, K., Wagner, A., & Kelso, J. (2017). Functional implications of Neandertal introgression in modern humans Genome Biology 18:61. DOI: 10.1186/s13059-017-1181-7

support_MODs

Astuce Vidéo de la semaine: FlyBase TV, and a letter of support for model organism communities

This week’s video tip was prompted by a couple of things. Première, il était un tweet de FlyBase, about their video channel. Ça a été un moment depuis que nous avions fait une Airbase Conseil de la semaine, donc ça a été une raison suffisante.

Mais il est également venu juste après que je pensais à l'importance des organismes modèles, sur la base de la campagne par les bases de données d'organismes modèles pour sauver leur financement. Voici un tweet de la base de données du génome de la levure (SGD) avec un plaidoyer:

Mais cette lettre cite la levure, vole, WormBase, Danse, MGI, RGD et Gene Ontology ainsi.

mergeJ'ai un faible pour les organismes modèles, non seulement en raison de la quantité énorme de grande biologie qu'ils ont fourni. J'étais un postdoc au laboratoire Jackson, et je suis parfaitement conscient de l'importance cruciale est d'avoir la profondeur des spécialistes des espèces impliquées dans la création et le maintien des ressources qui sont appropriées pour leur organisme. Mais il est plus que de simples connaissances institutionnelles et les données, bien sûr. Il est également l'importance de la communauté des chercheurs travaillant sur cet organisme, les soutenir et ayant leurs besoins satisfaits à bien des égards avec des ressources spécifiques aux espèces.

Donc, la pointe de cette semaine met en évidence certaines caractéristiques des outils de FlyBase, comme un moyen de rappeler aux gens du grand travail qui est en cours au modèle des bases de données de l'organisme (MODs).

Maintenant, si vous ne l'avez pas déjà fait, s'il vous plaît envisager de signer à la lettre de soutien à ces bases de données. Vous pouvez en savoir plus sur la question plus sur le site, mais brièvement:

NHGRI / NIH a récemment avancé un plan dans lequel les MODs seront intégrées dans une base de données combinée unique, ainsi qu'un 30% réduction du financement pour chaque MOD (voir également Nature et Science reportages). Alors que l'intégration accrue présentera de nombreux avantages, le plan se traduira par une perte d'ensembles de données spécifiques à l'organisme critiques. La coupe de financement sera également paralyser les fonctions de base telles que la littérature de haute qualité curation et annotation du génome, dégrader l'utilité des MODs. Étant donné le grand nombre de scientifiques que ce changement de politique aurait une incidence et l'importance de leur travail, ceci est une question extrêmement préoccupante.

J'ai toujours crié sur l'importance de curation de haute qualité. Il est tellement sous-évalué, mais il est seulement de plus en plus crucial maintenant que nous obtenons des données de séquence tant et nous avons besoin des meilleures connaissances existantes pour nous guider à travers elle. Maintenant, est pas le moment de réduire les curation.

Donc, si vous avez évalué les données MOD et les sites communautaires, s'il vous plaît envisager de signer à la lettre d'appui.

Liens rapides:

FlyBase: http://flybase.org/

Modèle de soutien Organism Bases de données lettre: http://www.genetics-gsa.org/MODSupport/

Références:

Hayden, Erica Check. “Le financement des bases de données modèle-organismes en difficulté.” Nature Nouvelles. () DOI: 10.1038/nature.2016.20134

Kaiser, Jocelyn. “Le financement des ressources de données clés en danger.” Science 351.6268 (2016): 14-14. DOI: 10.1126/science.351.6268.14

Attrill, Helen, et al. “FlyBase: établir une ressource Gene groupe pour Drosophila melanogaster.” Nucleic Acids Research (2015): gkv1046. DOI: 10.1093/grenade / gkv1046

genonets_quickstart

Astuce Vidéo de la semaine: Genonets, exploring genotype-phenotype relationships

Lately I’ve been keeping an eye on a lot of the tools that link individuals with sequence data, leurs phénotypes, and researchers/physicians who may either study or treat the associated medical issues (voir MyGene2 most recently) . But there’s a lot of room upstream of these kinds of patient outcomes to explore genotypes and phenotypes. This week’s Video Tip of the Week is for Genonets, offering “Analysis and Visualization of Genotype Networks”, a tool that can help to explore these relationships for pre-clinical/research scenarios as well.

A recent paper explains the goals behind their tools, and they also have a series of videos on their web site to help you get going with Genonets. I’ll put the intro video here, but be sure to click over to their “Learn Genonets” page for a lot more. There’s also a text-based tutorial you can work through which is helpful.

You can also kick the tires a bit with a sample file that’s available from their search page. Just click the checkbox to load it up and try it out. And then be sure to explore those “deep dives” videos to go further.

Astuce a:

Quick link:

Genonets: http://ieu-genonets.uzh.ch

Référence:

Khalid, F., Aguilar-Rodríguez, J., Wagner, A., & Payne, J. (2016). Genonets server—a web server for the construction, analysis and visualization of genotype networks Nucleic Acids Research DOI: 10.1093/nar/gkw313

UCSC Genome Bioinformatics

Astuce Vidéo de la semaine: UCSC Genome Browser Exon-only Mode

L'équipe UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “multi-region” option. When it was first launched, I did a tip on how to use that, with some of the things that I noticed while I was testing it pre-launch. But now the folks at UCSC have their own video on the exon-only display that you might also find useful.

One of the things that is illustrated here is how the exon-only mode is handy to enhance your exploration of RNA-Seq data. It also uses a great ENCODE data set as an example, and if you haven’t been using that collection it’s a good reminder of the kinds of things you can find in that resource still. And this extensive data set shows how much easier it is to look at different isoforms in the data in this new exon-only mode.

So have a look at this display option if you haven’t before, especially how it can help you to see transcript differences. If you aren’t familiar with the Encoder des données that’s being used, you can also see our training on that which will help you to understand how to use that data and the filtering features that are also used in this video.

Note spéciale: I have updated the UCSC Intro slides to include the new Gateway strategies as well. So download those slides for the latest look.

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Divulgation: UCSC Genome Browser tutorials are freely available because UCSC commanditaires us to do training and outreach on the UCSC Genome Browser.

Liens rapides:

UCSC Genome Browser: http://genome.ucsc.edu

UCSC Genome Browser training materials: http://openhelix.com/ucsc

ENCODE: http://www.openhelix.com/ENCODE2

Références:

Éperon, M., Direction, A., Rosenbloom, K., Raney, B., Sponsors, B., Nejad, P., Lee, B., Apprises, K., Karolchik, D., Hinrichs, A., Heitner, S., Dur, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barber, G., Haussler, D., Kuhn, R., & Kent, Dans. (2016). La base de données UCSC Genome Browser: 2016 mise à jour Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

Le consortium du projet ENCODE (2012). Une encyclopédie intégrée des éléments d'ADN dans le génome humain Nature, 489 (7414), 57-74 DOI: 10.1038/nature11247

Mygene2_vid

Astuce Vidéo de la semaine: MyGene2, connecting families with rare conditions with each other

Last week’s tip encouraged people to think about how their DNA may be used by various stakeholders. This could be researchers, physicians, pharmaceutical companies, et ainsi de suite. But one thing it didn’t really cover–now that I think of it–was connecting with other families who may share variations that impact the health of someone in their household. If there isn’t research, or treatment, this connection alone might be worth it for some families.

So when NPR recently had a story on a database for families with rare genetic conditions, Je suis allé jeter un oeil: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

Le site est MyGene2, and it can help unrelated folks who have the same genome challenges connect with each other. It also can connect folks to researchers interested in the topic. But it does seem to be aimed more specifically at families seeking each other. It was recently awarded a chance to compete for the final prize in the Open Science Prize effort, and they got a funding boost to keep going.

Il ya un “accueil” video that they’ve made, but it’s light on the software details. Toujours, si, I wanted to share the information so families may find it, and researchers may want to know about this resources as well. The video isn’t embeddable, si, so you’ll have to click to view it:

Mygene2_vid

You can learn more about the resources from their FAQ collection. I’ve found a couple of references (ci-dessous) that provide some further information about the project [Remarque: l' Génétique en médecine one goes to a paywalled, pièce–but you can access the pre-print version PDF at bioRxiv]. As more and more families who are seeking answers will have sequencing information available, they’ll need a place to go with that. I hope they find each other, and find answers.

Liens rapides:

MyGene2: http://www.mygene2.org

Suivez-les sur twitter: https://twitter.com/MyGene2

Find them on Facebook: https://www.facebook.com/MyGene2/

(L' Génétique en médecine piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)

Références:

Panko, B. (2016). Six finalists to compete for Open Science Prize Science DOI: 10.1126/science.aaf9980

Chong, J., Yu, J., Lorentzen, P., Parc, K., Jamal, S., Tabor, H., Rauch, A., Saenz, M., Boltshauser, E., Patterson, K., Nickerson, D., & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features Génétique en médecine DOI: 10.1038/gim.2015.161

ga4gh_vid

Astuce Vidéo de la semaine: Your DNA, Your Say. GA4GH wants to hear from you. Et vous.

L' Alliance mondiale pour la génomique et la santé (GA4GH) has come up a few times on our blog. The last time we highlighted them for a tip, it was about their Beacon tool. The idea of the Beacon is that it could interrogate a database but in a very subtle way, without needing access to the entire sequence information of a patient. It would ask a simple yes/no question about a given sequence variant–and if a “oui” came back, then a researcher could go through the process of getting proper access to protected patient data.

So it was a way to keep people from pawing through data that they don’t need. And yet it could still connect people who might benefit from research, with researchers who need information.

But certainly issues of patient or donor privacy are hot topics. More and more data will come in from large projects, or from diagnostic samples, and cancer vs normal tissue comparisons, and we are going to struggle with the access vs. privacy matters for a while. The general public is only now becoming aware of the impacts. But we certainly need people to understand and we’ll want them to contribute to expanding our knowledge about health and disease.

That’s why the folks associated with GA4GH, the Wellcome Trust, and the Wellcome Genome Campus are eager to engage the public on their feelings on use of genomic sequence data. Ils ont launched a project called “Your DNA Your Say”[PDF], in the form of a survey with videos to help understand where people are on this issue. Here’s the intro video to entice you to answer the survey:

I answered the survey because I do have concerns about access to information that will help us drive the science forward, as well as about the potential for misuse of the information. But I would like them to hear from as many people as possible, so that we can understand the barriers to research and donation that are looming. Have your say. Et passer le mot.

You can learn more about their ideas in a variety of publications–I’ll link to one below, but there are other publications and more details about the overall projects and individual tools at the GA4GH web site.

Liens rapides:

Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/

Références:

Lawler, M., Siu, L., Rehm, H., Chanock, S., Alterovitz, G., Burn, J., Chauve, F., Lacombe, D., Ces, B., Du nord, K., Sawyers, C., & , . (2015). All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health Cancer Discovery, 5 (11), 1133-1136 DOI: 10.1158/2159-8290.CD-15-0821

ProSplign

Astuce Vidéo de la semaine: ProSplign in NCBI’s Genome Workbench

ProSplign

There are many tools at NCBI, with a huge range of functions. Littérature, données de séquence, les variations, la structure des protéines, chemicals and bioassays, et plus. It’s hard to keep track of what’s available. Their video tutorials are helping me to be aware of new tools, and new features within existing tools. Pour le Conseil de la semaine cette semaine, we’ll look at their recent video for ProSplign. It’s a tool that will help you align protein information to genomic sequences.

Bien que le Génome Workbench itself has been around for a while (we featured it as a tip it first in 2013), it is constantly underdevelopment, and new features are available regularly. And although this tip focuses on how to use the ProSplign piece, if you haven’t used it much it will help you to understand how a number of tools within the Workbench can be accessed. You can also see that Splign is available in the tool list–which is another NCBI tool for a similar type of process, but with mRNA sequences as the focus.

If you want to have a text-based type of walk-through instead, there is a page that will take you through the features (see the quick links below). And there are other videos that will help you to explore the Genome Workbench features as well–there’s a handy special playlist of just those vidéos. Subscribe to their YouTube channel for notices of their new items.

Quick link:

NCBI Génome Workbench: http://www.ncbi.nlm.nih.gov/tools/gbench/

Text-based tutorial page: https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial13/

Références:

Kapustin, Y., Souvorov, A., Tatusova, T., & Lipman, D. (2008). Splign: algorithms for computing spliced alignments with identification of paralogs Biology Direct, 3 (1) DOI: 10.1186/1745-6150-3-20

NCBI staff (2016). Base de données des ressources du Centre national d'information sur la biotechnologie Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1290

Mason_JGI

Astuce Vidéo de la semaine: JGI user meeting videos, and MetaSUB

Mason JGIThis week’s Video Tip of the Week is actually a whole bunch of videos. Although I’ll highlight one here as our tip, there are many great talks from the recent JGI Genomics of Energy & Environment meeting. Although typically we focus on specific software tools for our tips, I think this is a nice case of also looking at the type of research done with the tools.

This is a nice example of how to make a meeting accessible for a lot of people as well, using multiple strategies. L' video channel, a Storify, dropboxes of slides (ci-dessous), et le agenda details can help you to decide what might be relevant for your work. Par exemple, nous avons parlé Docker, but you can now see how it’s deployed by the folks who are talking about it here. There’s a talk with Phytozome. And much more.

For today I’ll highlight MetaSub as one of the projects from the Mason lab. The Mason lab has participated in projects you probably heard about in the media–including swabbing the NYC subway system. You can see that data at PathoMap. MetaSUB stands for a data collection effort coming up soon, the Metagenomics & Metadesign of Subways and Urban Biomes. A global swabbing festival of the 10 busiest subways in the world (including my own–I wonder if I can do the station in my neighborhood?), to get more geospatial metagenomics maps, find antimicrobial resistance markers, and look for new biosynthetic gene clusters. It will be held on June 21, 2016–the summer solstice. It will tell us way more about our urban environments than we currently know. Maybe too much. But it’s a great idea, sure to reveal things we don’t know about our lived environment right now.

And here are the slides for the talk, as promised in the video. Mason tweets them:

He seriously did get through those 138 slides in 30 minutes. I was skeptical when I downloaded them before watching through them with the talk–but he really managed it. I was kind of out-of-breath just watching it.

He also talked about extreme environment sampling, et MetaPhlan2 et HUMAnN2 analyses, in a later segment. The whole thing is an excellent and breezy discussion of real-world genomics and a lot of appealing stories that the public would connect with. They are also doing educational outreach with a HTGAA course (How To Grow Almost Anything). There some really fun stuff with the Gowanus canal (sérieux), and so much opportunity just hanging around in our cities. Mais aussi–what’s growing in space. They are working on space station mold. And astronauts–the NASA twins. They are also sending up a MinION (which they checked to see would work in microgravity–see paper below).

It was a very engaging talk. From an apparently very busy guy.

Astuce a:

Liens rapides:

PathoMap: http://www.pathomap.org/

MetaSUB: http://www.metasub.org/

Références:

Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E., Zumbo, P., Walsh, M., O’Mullan, G., Tighe, S., Dudley, J., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T., Boone, B., Jones, A., Muth, T., Paolantonio, K., Alter, E., Schadt, E., Garbarino, J., Prill, R., Carlton, J., Levy, S., & Mason, C. (2015). Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Cell Systems, 1 (1), 72-87 DOI: 10.1016/j.cels.2015.01.001

Alexa B.R. McIntyre, Lindsay Rizzardi, Angela M Yu, Gail L. Rosen, Noah Alexander, Douglas J. Botkin, Kristen K. John, Sarah L. Castro-Wallace, Aaron S. Burton, Andrew Feinberg, & Christopher E. Mason (2015). Nanopore Sequencing in Microgravity bioRxiv DOI: 10.1101/032342