Archiv der Kategorie: Tipp der Woche

dtc_testing

Video Tipp der Woche: Direct to Consumer Genetic Testing and Genetic Counselling

Am OpenHelix, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, Ich weiß,, 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.

Zunehmend, 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. Natürlich, in den USA, as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. Seufzer.

Hat tip:

Referenz:

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

 

Video Tipp der Woche: Neandertal Inheritance and Consequences

OK, es ist schon eine Weile her, seit dies ein fester Bestandteil war,,en,Aber ich finde immer noch, dass ich manchmal ein paar Videos von naturwissenschaftlichen Themen und Software-Tool zeigen will,,en. 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 und SIFT, 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.

Referenz:

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

Video Tipp der Woche: Airbase TV, und ein Brief der Unterstützung für Modellorganismus Gemeinden

In dieser Woche Video-Tipp wurde durch ein paar Dinge aufgefordert. Erste, es war ein Tweet von FlyBase, über ihre Videokanal. Es ist schon eine Weile her, seit wir ein getan hatte Airbase Tipp der Woche, so das war Grund genug,.

Aber es kam auch nur, nachdem ich über die Bedeutung der Modellorganismen dachte, auf der Grundlage der Kampagne von den Modellorganismus Datenbanken ihre Finanzierung zu sichern. Hier ist ein Tweet aus dem Hefegenom Datenbank (SGD) mit einem Plädoyer:

Aber dieser Brief zitiert Hefe, Fliegen, WormBase, Tanz, MGI, RGD und Gene Ontology sowie.

mergeIch habe ein Faible für Modellorganismen, nicht nur wegen der enormen Menge von großer Biologie sie zur Verfügung gestellt haben. Ich war ein Postdoc-Aufenthalt am Jackson Lab, und ich bin sehr bewusst, wie wichtig es ist, die Tiefe der Spezies Spezialisten beteiligt zu haben, bei der Schaffung und Erhaltung der Ressourcen, die für ihren Organismus angemessen sind. Aber es ist mehr als nur institutionelle Wissen und Daten, natürlich. Es ist auch die Bedeutung der Gemeinschaft der Forscher auf diesem Organismus arbeiten, sie unterstützen und mit ihren Bedürfnissen in vielerlei Hinsicht mit artspezifischen Ressourcen erfüllt.

So Der Tip der Woche zeigt einige Merkmale der FlyBase Tools, als eine Möglichkeit, Leute von der großen Arbeit zu erinnern, dass bei Modellorganismus Datenbanken los ist (Modifikationen).

Jetzt, wenn Sie nicht bereits getan haben, beachten Sie bitte an die Unterzeichnung auf Schreiben der Unterstützung für diese Datenbanken. Sie können mehr über das Thema über an der Stelle lesen, aber kurz:

NHGRI / NIH fortgeschritten ist vor kurzem einen Plan, in dem die MODs werden in einer einzigen kombinierten Datenbank integriert werden, zusammen mit einem 30% Kürzung der Mittel für jeden MOD (siehe auch diese Nature und Wissenschaft Nachrichten). Während eine verstärkte Integration wird viele Vorteile präsentieren, Der Plan wird in einem Verlust von kritischen Organismus spezifische Datensätze führen. Die Finanzierung Schnitt wird auch Kernfunktionen Krüppel wie hochwertige Literatur Kuration und Genomannotation, Verschlechtern der Nützlichkeit der MODs. Angesichts der großen Zahl von Wissenschaftlern, dass diese Änderung der Politik beeinflussen würde und die Bedeutung ihrer Arbeit, dies ist eine Angelegenheit von äußerster Besorgnis.

Ich habe schrie immer über die Bedeutung von qualitativ hochwertigen curation. Es ist so unterbewertet, aber es ist nur mehr und mehr von entscheidender Bedeutung jetzt, dass wir so viel Sequenzdaten bekommen und wir brauchen die beste vorhandene Wissen uns durch sie zu helfen. Jetzt ist nicht die Zeit, auf Kuration, um wieder.

Also, wenn Sie MOD Daten bewertet und Community-Sites, beachten Sie bitte auf das Schreiben der Unterstützung bei der Unterzeichnung.

Quick-Links:

FlyBase: http://flybase.org/

Unterstützung Modellorganismus Datenbanken Schreiben: http://www.genetics-gsa.org/MODSupport/

Referenzen:

Hayden, Erica überprüfen. “Die Finanzierung für Modellorganismus Datenbanken in Schwierigkeiten.” Nature News. () DOI: 10.1038/nature.2016.20134

Kaiser, Jocelyn. “Die Finanzierung für die wichtigsten Datenressourcen in Gefahr.” Wissenschaft 351.6268 (2016): 14-14. DOI: 10.1126/science.351.6268.14

Attrill, Helen, et al. “FlyBase: eines Gene-Gruppe Ressource für Drosophila melanogaster zu etablieren.” Nucleic Acids Research (2015): gkv1046. DOI: 10.1093/Granatapfel / gkv1046

genonets_quickstart

Video Tipp der Woche: Genonets, erforschen Genotyp-Phänotyp-Beziehungen

In letzter Zeit habe ich auf eine Menge der Werkzeuge im Auge behalten worden, die Personen mit Sequenzdaten verknüpfen, ihre Phänotypen, und Forscher / Ärzte, die entweder studieren kann oder die damit verbundenen medizinischen Fragen behandeln (siehe MyGene2 zuletzt) . Aber es gibt viel Raum vor dieser Art von Patientenergebnissen Genotypen und Phänotypen zu erkunden. In dieser Woche Video Tipp der Woche ist für Genonets, Opfer “Analyse und Visualisierung von Genotype Networks”, ein Werkzeug, das auch diese Beziehungen für die präklinische / Forschung Szenarien erkunden möchte, kann helfen.

Eine aktuelle Papier erläutert die Ziele hinter ihren Werkzeugen, und sie haben auch eine Reihe von Videos auf ihrer Website zu helfen Sie mit Genonets loslegen. Ich werde das Intro-Video setzen hier, aber achten Sie darauf, klicken Sie auf, um ihre “Erfahren Genonets” Seite für viel mehr. Es gibt auch ein textbasiertes Tutorial Sie durch die arbeiten können, ist hilfreich.

Sie können auch die Reifen ein wenig mit einer Beispieldatei treten, die von ihrer Suchseite verfügbar ist. Klicken Sie einfach auf das Kontrollkästchen es zu laden und ausprobieren. Und dann sicher sein, diejenigen zu erkunden “Tieftauchen” Videos, weiter zu gehen.

Hat tip:

Quick-Link:

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

Referenz:

Khalid, F., Aguilar-Rodriguez, J., Wagner, A., & Payne, J. (2016). Genonets server ein Web-Server für den Bau, Analyse und Visualisierung von Genotyp-Netzwerke Nucleic Acids Research DOI: 10.1093/Granatapfel / gkw313

UCSC Genome Bioinformatics

Video Tipp der Woche: UCSC Genome Browser Exon-only-Modus,en

Das Team von 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 ENCODE Daten 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.

Besonderer Hinweis: 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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Bekanntgabe: UCSC Genome Browser tutorials are freely available because UCSC Sponsoren us to do training and outreach on the UCSC Genome Browser.

Quick-Links:

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

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

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

Referenzen:

Sporn, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., RAMspan>, Hinrichs, AS, Hsu, F., Kober, KM, Miller, W., Pedersen, JS, Pohl, A., Raney, BJ , A., Heitner, S., Harte, R., Häußler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Friseur, G., Haussler, D., Kuhn, R., & Kent, In. (2016). Die UCSC Genome Browser Datenbank: 2016 Update Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

Das ENCODE Project Consortium (2012). Eine integrierte Enzyklopädie der DNA-Elemente im menschlichen Genom Nature, 489 (7414), 57-74 DOI: 10.1038/nature11247

Mygene2_vid

Video Tipp der Woche: 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, und so weiter. 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, Ich ging, um einen Blick haben: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

Die Website ist 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.

Es gibt eine “willkommen” video that they’ve made, but it’s light on the software details. Still, obwohl, 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, obwohl, 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 (unten) that provide some further information about the project [Note: der Genetik in der Medizin one goes to a paywalled, Stück–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.

Quick-Links:

MyGene2: http://www.mygene2.org

Folgen Sie ihnen auf twitter: https://twitter.com/MyGene2

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

(Das Genetik in der Medizin piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)

Referenzen:

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

Chong, J., Yu, J., Lorentzen, P., Park, 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 Genetik in der Medizin DOI: 10.1038/gim.2015.161

ga4gh_vid

Video Tipp der Woche: Your DNA, Your Say. GA4GH wants to hear from you. Und Sie.

Das Global Alliance for Genomics und Gesundheit (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 “ja” 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. Sie haben 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. Und das Wort zu verbreiten.

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.

Quick-Links:

Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/

Referenzen:

Lawler, M., Siu, L., Rehm, H., Chanock, S., Alterovitz, G., Burn, J., GLATZKÖPFIG, F., Lacombe, D., Diese, B., Nördlich, 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

Video Tipp der Woche: in NCBI Genome Workbench ProSplign

ProSplign

There are many tools at NCBI, with a huge range of functions. Literatur, Sequenzdaten, Variationen, Protein-Struktur, chemicals and bioassays, und mehr. 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. Für diese Woche Tipp der Woche, we’ll look at their recent video for ProSplign. It’s a tool that will help you align protein information to genomic sequences.

Obwohl die Genome 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 Videos. Subscribe to their YouTube channel for notices of their new items.

Quick-Link:

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

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

Referenzen:

Kapustin, Y., Suworow, 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). Database Ressourcen des National Center for Biotechnology Information Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1290

Mason_JGI

Video Tipp der Woche: 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. Das video channel, a Storify, dropboxes of slides (unten), und die agenda details can help you to decide what might be relevant for your work. Zum Beispiel, Wir haben darüber gesprochen 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 Minuten. 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, und MetaPhlan2 und HUMAnN2 Analysen, 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 (ernst), and so much opportunity just hanging around in our cities. Aber auch–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.

Hat tip:

Quick-Links:

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

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

Referenzen:

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., Platte, S., & Maurer, 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. Maurer (2015). Nanopore Sequencing in Microgravity bioRxiv DOI: 10.1101/032342