카테고리 아카이브: 금주의 팁


주의 비디오 도움말: Direct to Consumer Genetic Testing and Genetic Counselling

OpenHelix시, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, 나도 알아, 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.

점점, 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. 물론 이죠, 미국, as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. 한숨.

모자 팁:


Middleton, 대답 :, Mendes, Á., 베냐민, C 조. 엠, & Howard, H 조. C 조. (2017). Direct-to-consumer genetic testing: where and how does genetic counseling fit?. 맞춤 의학, (14:3) , 페이지 249-257 , 간접 자원부 10.2217/pme-2017-0001.


주의 비디오 도움말: Neandertal Inheritance and Consequences

확인, 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, PolyPhen엄밀히 조사하다, 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.


Dannemann, 엠, Prüfer, 사장님, 와그너, 대답 :, & 켈소의, Kokocinski. (2017). Functional implications of Neandertal introgression in modern humans 게놈 생물학 18:61. 간접 자원부: 10.1186/s13059-017-1181-7


주의 비디오 도움말: 공군 기지 TV, 및 모델 생물 공동체에 대한 지원의 편지

이번 주 비디오 팁 몇 가지 메시지가 표시되었다. 처음으로, 그것은에서 트윗이었다 FlyBase, 자신의 비디오 채널에 대한. 우리가 일을했던 이래로 동안이었다 금주의 공군 기지 팁, 그래서 그 이유의 충분했다.

그러나 그것은 또한 내가 모델 생물의 중요성에 대해 생각했다 직후했다, 자신의 자금을 저장하는 모델 생물 데이터베이스로 캠페인을 기반으로. 여기에 효모 게놈 데이터베이스에서 트윗입니다 (SGD) 항변과:

그러나이 편지는 효모를 인용, 파리, WormBase, 댄스, MGI, RGD유전자 온톨로지 뿐만 아니라.

merge나는 모델 생물에 대한 애착을 가지고, 뿐만 아니라 큰 생물학의 엄청난 양의가 제공했기 때문에. 나는 잭슨 연구소에서 박사 후 연구원이었다, 나는 그들의 유기체에 적합한 리소스를 생성 및 유지에 관련된 종 전문가의 깊이를 가지고하는 것이 얼마나 중요한의 급성 알고. 그러나 그것은 단지 제도적 지식과 데이터보다 더 많은입니다, 물론. 또한, 해당 생물에서 작동 연구자들의 커뮤니티의 중요성, 이를 지원 및 요구 종 특이 자원 여러면에서 만족 구비.

그래서 이번 주 팁은 FlyBase 도구의 일부 기능을 강조, 모델 생물 데이터베이스에서 무슨 큰 일의 사람들을 생각 나게하는 방법으로 (에서 MOD).

지금, 당신은 이미하지 않은 경우, 받는 사람에 서명 고려하시기 바랍니다 이러한 데이터베이스에 대한 지원의 편지. 당신은 사이트에서 문제에 대한 자세한을 통해 읽을 수 있습니다, 하지만 간단히:

NHGRI / NIH 최근 개조가 단일 결합베이스에 통합 될 것이다 계획 고급, 와 함께 30% 각 MOD 자금 감소 (이러한 참조 자연과학 뉴스). 증가 통합은 많은 장점을 제공되지만, 계획은 중요한 생물 특정 데이터 세트의 손실이 발생합니다. 자금 컷은 또한 고품질의 문학 큐 레이션 및 게놈 주석 같은 핵심 기능을 무력화한다, 개조의 유틸리티를 저하. 이 정책의 변화에​​ 영향을 미칠 것이라는 과학자들의 다수 그들의 작업의 중요성을 감안, 이 극단적 인 우려의 문제입니다.

난 항상 높은 품질의 큐 레이션의 중요성에 대해 소리 쳤다했다. 그것은 너무 저평가있어, 하지만 우리가 너무 많은 시퀀스 데이터를 가져 오는 것을 이제 점점 더 중요한을 그리고 우리는 그것을 통해 우리를 안내하기 위해 최선의 기존 지식이 필요. 이제 큐 레이션에 전환 할 수있는 시간이 아니다.

당신은 MOD 데이터와 커뮤니티 사이트를 평가 한 그래서 경우, 지원의 편지에 서명 고려하시기 바랍니다.

빠른 링크:

FlyBase: http://flybase.org/

지원 모델 생물 데이터베이스 편지: http://www.genetics-gsa.org/MODSupport/

참고 문헌:

헤이든, 에리카 확인. “문제의 모델 생물 데이터베이스에 대한 자금.” 자연 뉴스. () 간접 자원부: 10.1038/nature.2016.20134

황제, 조슬린. “위험의 주요 데이터 자원에 대한 자금.” 과학 351.6268 (2016): 14-14. 간접 자원부: 10.1126/science.351.6268.14

Attrill, 헬렌, 외. “FlyBase: 노랑 초파리에 대한 유전자 그룹 자원을 구축.” 핵산 연구 (2015): gkv1046. 간접 자원부: 10.1093/석류 / gkv1046


주의 비디오 도움말: Genonets, exploring genotype-phenotype relationships

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

모자 팁:

빠른 링크:

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


Khalid, F., Aguilar-Rodríguez, 제이, 와그너, 대답 :, & 페인, Kokocinski. (2016). Genonets server—a web server for the construction, analysis and visualization of genotype networks 핵산 연구 간접 자원부: 10.1093/nar/gkw313

UCSC Genome Bioinformatics

주의 비디오 도움말: UCSC Genome Browser Exon-only Mode

팀에서 UCSC 게놈 브라우저 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 인코딩 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. 당신은에 익숙하지 않은 경우 인코딩 데이터 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.

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


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

빠른 링크:

UCSC 게놈 브라우저: http://genome.ucsc.edu

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

인코딩: HTTP를://www.openhelix.com/ENCODE2

참고 문헌:

박차, 엠, 분기, 대답 :, Rosenbloom, 사장님, 래니 소장, B를, 스폰서, B를, Nejad, 추신, 리, B를, 배운, 사장님, Karolchik, 디, 힌릭스, 대답 :, Heitner, 미국, 하트, 기철, Haeussler, 엠, Guruvadoo, 실은, 후지타, 추신, Eisenhart, C., Diekhans, 엠, 클로슨, 반장님, 캐스퍼, 제이, 이발사, 샷, Haussler, 디, Kuhn, 기철, & 켄트, 에. (2016). UCSC의 게놈 브라우저베이스: 2016 업데이트 핵산 연구, 44 (D1) 간접 자원부: 10.1093/nar/gkv1275

인코딩 프로젝트 컨소시엄 (2012). 인간 게놈의 DNA 요​​소의 통합 백과 사전 자연, 489 (7414), 57-74 간접 자원부: 10.1038/nature11247


주의 비디오 도움말: MyGene2, 서로 드문 조건을 연결하는 가족

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, 등. 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, 나는 모습을 가지고 갔다: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

사이트입니다 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.

있다 “환영” video that they’ve made, but it’s light on the software details. 아직, 그래도, 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, 그래도, so you’ll have to click to view it:


You can learn more about the resources from their FAQ collection. I’ve found a couple of references (아래) that provide some further information about the project [참고: the 의학 유전학 one goes to a paywalled, 조각–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.

빠른 링크:

MyGene2: http://www.mygene2.org

트위터에 올려 따라: https://twitter.com/MyGene2

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

(The 의학 유전학 piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)

참고 문헌:

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

Chong, 제이, 유, 제이, Lorentzen, 추신, 공원, 사장님, Jamal, 미국, Tabor, 반장님, Rauch, 대답 :, Saenz, 엠, Boltshauser, 이봐요, E., Patterson, 사장님, Nickerson, 디, & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features 의학 유전학 간접 자원부: 10.1038/gim.2015.161


주의 비디오 도움말: Your DNA, Your Say. GA4GH wants to hear from you. 그리고.

The 유전체학과 건강을위한 글로벌 제휴 (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 “예” 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. 그들이 launched a project called “Your DNA Your Say”[PDF 파일], 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. 그리고 단어를 확산.

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.

빠른 링크:

Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/

참고 문헌:

Lawler, 엠, Siu, 실은, 렘, 반장님, Chanock, 미국, Alterovitz, 샷, Burn, 제이, Calvo, F., Lacombe, 디, Teh, B를, 북, 사장님, 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 간접 자원부: 10.1158/2159-8290.CD-15-0821


주의 비디오 도움말: ProSplign in NCBI’s Genome Workbench


There are many tools at NCBI, with a huge range of functions. 문학, 시퀀스 데이터, 유사, 단백질 구조, chemicals and bioassays, 더. 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. 주의 이번주의 팁, we’ll look at their recent video for ProSplign. It’s a tool that will help you align protein information to genomic sequences.

하지만 게놈 워크벤치 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 동영상. Subscribe to their YouTube channel for notices of their new items.

빠른 링크:

NCBI의 게놈 워크 벤치: http://www.ncbi.nlm.nih.gov/tools/gbench/

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

참고 문헌:

Kapustin, Y를, Souvorov, 대답 :, Tatusova, 토니, & Lipman, 디. (2008). Splign: algorithms for computing spliced alignments with identification of paralogs Biology Direct, 3 (1) 간접 자원부: 10.1186/1745-6150-3-20

NCBI staff (2016). 생명 공학 정보를위한 국립 센터의 데이터베이스 자원 핵산 연구, 44 (D1) 간접 자원부: 10.1093/nar/gkv1290


주의 비디오 도움말: 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. The video channel, a Storify, dropboxes of slides (아래), 그리고 agenda details can help you to decide what might be relevant for your work. 예를 들어, 우리에 대해 얘기 했어요 고정 표시기, 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 분. 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, 및 MetaPhlan2 및 HUMAnN2 분석, 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 (심각), and so much opportunity just hanging around in our cities. 뿐만 아니라–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.

모자 팁:

빠른 링크:

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

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

참고 문헌:

Afshinnekoo, 이봐요, E., Meydan, C., Chowdhury, 미국, Jaroudi, 디, Boyer, C., 번스타인, 북아 일, Maritz, 제이, Reeves, 디, Gandara, 제이, Chhangawala, 미국, Ahsanuddin, 미국, Simmons, 대답 :, Nessel, 토니, Sundaresh, B를, Pereira, 이봐요, E., 조젠슨은, 이봐요, E., Kolokotronis, 미국, Kirchberger, 북아 일, 가르시아, 나, Gandara, 디, Dhanraj, 미국, Nawrin, 토니, Saletore, Y를, 알렉산더, 북아 일, Vijay, 추신, Hénaff, 이봐요, E., Zumbo, 추신, 월시, 엠, O’Mullan, 샷, Tighe, 미국, 더들리, 제이, Dunaif, 대답 :, Ennis, 미국, O’Halloran, 이봐요, E., Magalhaes, 토니, Boone, B를, 존스, 대답 :, Muth, 토니, Paolantonio, 사장님, Alter, 이봐요, E., Schadt, 이봐요, E., Garbarino, 제이, Prill, 기철, Carlton, 제이, 디스크, 미국, & 석공, C 조. (2015). Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Cell Systems, 1 (1), 72-87 간접 자원부: 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. 존, Sarah L. Castro-Wallace, Aaron S. 버튼, Andrew Feinberg, & Christopher E. 석공 (2015). Nanopore Sequencing in Microgravity bioRxiv 간접 자원부: 10.1101/032342