Archivo de la categoría: Consejo del la Semana

dtc_testing

Vídeo Consejo de la semana: Direct to Consumer Genetic Testing and Genetic Counselling

En OpenHelix, nos recuerda los días en que la gente ni siquiera apenas tienen documentación con su software cuando se ponen hacia fuera,en (yah, Sé que, 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.

Cada vez más, 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. Por supuesto, en los EE.UU., as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. Suspiro.

Sombrero de punta:

De referencia:

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

 

Vídeo Consejo de la semana: 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 y 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.

De referencia:

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

Vídeo Consejo de la semana: base aérea de TV, y una carta de apoyo a las comunidades organismo modelo

This week’s video tip was prompted by a couple of things. Primero, era un tweet de FlyBase, about their video channel. Ha sido un tiempo desde que habíamos hecho una Base aérea Consejo de la semana, así que fue una razón suficiente.

Pero también se produjo justo después de que yo estaba pensando acerca de la importancia de los organismos modelo, sobre la base de la campaña de las bases de datos organismo modelo para salvar a su financiación. Aquí está un tweet de la base de datos del genoma de la levadura (SGD) con una petición:

Pero esta carta cita la levadura, moscas, WormBase, Danza, MGI, RGD y Gene Ontology también.

mergeTengo una debilidad por los organismos modelo, no sólo debido a la enorme cantidad de gran biología que han proporcionado. Yo era un post-doctorado en el Laboratorio Jackson, y soy muy consciente de lo importante que es tener la profundidad de los especialistas en especies involucradas en la creación y el mantenimiento de los recursos que sean apropiados para su organismo. Pero es más que conocimientos institucional y de datos, por supuesto. Es también la importancia de la comunidad de investigadores que trabajan en ese organismo, apoyándolos y tener sus necesidades cubiertas en muchos aspectos con los recursos específicos de cada especie.

Así que el consejo de esta semana pone de relieve algunas de las características de las herramientas FlyBase, como una manera de recordar a la gente de la gran obra que está pasando en las bases de datos de organismos modelo (MODs).

Ahora, si no lo ha hecho, por que no firmar el carta de apoyo a estas bases de datos. Puede leer más sobre el tema más en el sitio, pero brevemente:

NHGRI / NIH ha avanzado recientemente un plan en el que los mods se integrarán en una única base de datos combinada, junto con una 30% reducción de los fondos para cada MOD (véase también éstos Naturaleza y Ciencia noticias). Aunque el aumento de la integración presentará muchas ventajas, el plan se traducirá en una pérdida de datos críticos organismos específicos. El corte financiación también paralizar funciones básicas tales como curación de la literatura de alta calidad y la anotación del genoma, degradar la utilidad de los MODs. Dado el gran número de científicos que este cambio de política afectaría y la importancia de su trabajo, esto es un motivo de preocupación extrema.

Siempre he gritado sobre la importancia de curación de alta calidad. Es tan infravalorado, but it’s only more and more crucial now that we are getting so much sequence data and we need the best existing knowledge to help guide us through it. Now is not the time to cut back on curation.

So if you have valued MOD data and community sites, please consider signing on to the letter of support.

Enlaces rápidos:

FlyBase: http://flybase.org/

Support Model Organism Databases carta: http://www.genetics-gsa.org/MODSupport/

Referencias:

Hayden, Erica Check. “Funding for model-organism databases in trouble.” Nature News. () DOI: 10.1038/nature.2016.20134

Emperador, Jocelyn. “Funding for key data resources in jeopardy.” Ciencia 351.6268 (2016): 14-14. DOI: 10.1126/science.351.6268.14

Attrill, Helen, et al. “FlyBase: establishing a Gene Group resource for Drosophila melanogaster.” Los ácidos nucleicos de investigación (2015): gkv1046. DOI: 10.1093/nar/gkv1046

genonets_quickstart

Vídeo Consejo de la semana: Genonets, exploring genotype-phenotype relationships

Lately I’ve been keeping an eye on a lot of the tools that link individuals with sequence data, sus fenotipos, and researchers/physicians who may either study or treat the associated medical issues (ver 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.

Sombrero de punta:

Enlace rápido:

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

De referencia:

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

Vídeo Consejo de la semana: UCSC Genome Browser Exon modo de sólo,en

El equipo de 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 CODIFICAR 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. Si usted no está familiarizado con el Codifica los datos 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.

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

+++++++++++++

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

Enlaces rápidos:

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

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

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

Referencias:

Espolón, M., Rama, A., Rosenbloom, K., Raney, B., Patrocinadores, B., Nejad, P., Sotavento, B., Aprendido, K., Karolchik, D., Hinrichs, A., Heitner, S., Duro, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Peluquero, G., Haussler, D., Kuhn, R., & Kent, En. (2016). La UCSC Genome Browser base de datos: 2016 actualización Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

El proyecto ENCODE Consorcio (2012). Una enciclopedia de elementos de ADN integrado en el genoma humano Naturaleza, 489 (7414), 57-74 DOI: 10.1038/nature11247

Mygene2_vid

Vídeo Consejo de la semana: MyGene2, familias que conectan con condiciones poco comunes con los demás

la punta de la semana pasada animó a la gente a pensar acerca de cómo su ADN puede ser utilizado por diversos grupos de interés. Esto podría ser investigadores, médicos, compañías farmacéuticas, etcétera. Pero una cosa que realmente no cubre–ahora que lo pienso de ella–se conecta con otras familias que pueden compartir las variaciones que afectan a la salud de alguien en su hogar. Si no hay investigación, o tratamiento, A este respecto solo podría valer la pena para algunas familias.

Así que cuando NPR recientemente tuvo una historia en una base de datos para las familias con enfermedades genéticas raras, Fui a echar un vistazo: Las familias aisladas por las condiciones genéticas raras encontrar nuevas formas de llegar.

El sitio es MyGene2, y puede ayudar a las personas no relacionadas que tienen los mismos retos del genoma se conectan entre sí. También se puede conectar a la gente a los investigadores interesados ​​en el tema. Pero parece estar dirigida más específicamente a las familias que buscan el uno al otro. Se recibió recientemente una oportunidad de competir por el premio final en el esfuerzo Premio de Ciencia Abierta, y consiguieron un aumento de fondos para seguir adelante.

Hay una “bienvenida” de vídeo que han hecho, pero es luz sobre los detalles de software. Todavía, aunque, Quería compartir la información para que las familias pueden encontrar, y los investigadores pueden querer saber acerca de estos recursos, así. El vídeo no es integrable, aunque, por lo que tendrá que hacer clic para visualizarla:

Mygene2_vid

Usted puede aprender más acerca de los recursos de su colección de FAQ. He encontrado un par de referencias (a continuación) que proporcionan alguna información adicional sobre el proyecto [Nota: la Genética en Medicina uno va a un paywalled, pieza–pero se puede acceder a la previa a la impresión versión PDF en bioRxiv]. A medida que más y más familias que buscan respuestas tendrán la secuenciación de la información disponible, que van a necesitar un lugar para ir con eso. Espero que encuentren uno al otro, y encontrar respuestas.

Enlaces rápidos:

MyGene2: http://www.mygene2.org

Les siguen en twitter: https://twitter.com/MyGene2

Encontrarlos en Facebook: https://www.facebook.com/MyGene2/

(La Genética en Medicina También toma nota de pieza My46.org, “una herramienta basada en la web para la gestión de devolución de resultados de pruebas genéticas”.)

Referencias:

Panko, B. (2016). Seis finalistas para competir por el Premio de Ciencia Abierta Ciencia DOI: 10.1126/science.aaf9980

Chong, J., Yu, J., Lorentzen, P., Parque, K., Jamal, S., Tabor, H., Rauch, A., Sáenz, M., Boltshauser, E., Patterson, K., Nickerson, D., & gráficos, AbT.l. (2015). el descubrimiento de genes para las condiciones mendelianos través de redes sociales: variantes de novo en KDM1A causan retraso en el desarrollo y las características faciales distintivas Genética en Medicina DOI: 10.1038/gim.2015.161

ga4gh_vid

Vídeo Consejo de la semana: Your DNA, Your Say. GA4GH wants to hear from you. Y.

La Alianza Global para la Genómica y Salud (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 “sí” 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. Ellos han 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. Y correr la voz.

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.

Enlaces rápidos:

Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/

Referencias:

Lawler, M., Siu, L., Rehm, H., Chanock, S., Alterovitz, G., Burn, J., Calvo, F., Lacombe, D., Estos, B., Norte, 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

Vídeo Consejo de la semana: ProSplign en la NCBI Genoma Workbench,en

ProSplign

There are many tools at NCBI, with a huge range of functions. Literatura, datos de la secuencia, variaciones, estructura de la proteína, chemicals and bioassays, y más. 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. Para Tip de esta semana de la Semana, we’ll look at their recent video for ProSplign. It’s a tool that will help you align protein information to genomic sequences.

Aunque el Genoma 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 Vídeos. Subscribe to their YouTube channel for notices of their new items.

Enlace rápido:

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

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

Referencias:

Kapustin, Y., Suvorov, 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). Los recursos de base de datos del Centro Nacional de Información Biotecnológica Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1290

Mason_JGI

Vídeo Consejo de la semana: 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. La video channel, a Storify, dropboxes of slides (a continuación), y el agenda details can help you to decide what might be relevant for your work. Por ejemplo, hemos hablado de 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 minutos. 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, y MetaPhlan2 y HUMAnN2 análisis, 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 (en serio), and so much opportunity just hanging around in our cities. Pero también–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.

Sombrero de punta:

Enlaces rápidos:

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

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

Referencias:

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., García, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alejandro, 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., Disco, S., & Albañil, 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. Juan, Sarah L. Castro-Wallace, Aaron S. Burton, Andrew Feinberg, & Christopher E. Albañil (2015). Nanopore Sequencing in Microgravity bioRxiv DOI: 10.1101/032342