태그 아카이브: 희귀 질환

Mygene2_vid

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:

Mygene2_vid

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

Genomics England is responsible for the 100,000 Genomes Project

주의 비디오 도움말: PanelApp, 부터 100000 Genomes 프로젝트

Genomics England is responsible for the 100,000 Genomes Project

Genomics England is responsible for the 100,000 Genomes 프로젝트

Last week I talked about the 100,000 Genomes 프로젝트 in the UK. That video tip was an introduction and overview of the project. 이번 주, 그래도, we’ll highlight one software piece that is in place now. PanelApp is a collection of gene lists, with information about the evidence associated with variations in these genes. The goal is to inform clinical interpretation based on the best quality evidence.

It’s a straigtforward interface, with a traffic-light based system (녹색, 황색, 빨강) to assist with quick diagnostic assessments. The lists are based on a set of rare disease categories and phenotypes, and the idea is that qualified reviewers will create a definitive list of evidence for certain variations, and rate the genes accordingly. Ultimately they want to create a consensus gene panel collection. They describe the evidence thresholds this way:

  • Green = highest level of confidence; a gene from 3 또는 4 소스.
  • Amber = intermediate; a gene from 2 소스.
  • Red = lowest level of confidence; 1 의 4 sources or from an expert list.

당신은 그들의 발표에서 전략에 대해 자세히 알아볼 수 있습니다: New rare disease gene tool launched – PanelApp. This first video will give you an idea of how this looks. A public interface is available for anyone to look around and download the information. You don’t need to log in, you can click on the “Browse Panels” tab for an idea of the organization and information content.

So crowd-sourcing this evidence is the idea here. And they are interested in having people contribute to these panels. A separate video describes the roles for people who are interested in contributing to the collection and curation of the information. Reviewers will evaluate the existing items and also add new genes. 그들이 detailed instructions and guidelines available to help. 그러나, the first round of review ended already (October 19 2015). The panels will remain available to explore and download. But there will be another review period opening in the future. So if you are considering a contribution to this work, not to worry–your chance will come and it won’t hurt to be prepared. 또한, if you are considering using the panels, I think it’s a good idea to know how the curation and review is done.

The information in the panels now has been seeded by many key sources that you may be familiar with. They have used data from OMIM, OrphaNet, 유전학 홈 참조, the Decipher DDD project, HGNC, ClinVar, UniProt, NCBI Nucleotide, 및 ENSEMBL among others to add phenotype and gene details of many types. So for any gene you can keep digging for addtional information.

There are a long more details over at the announcment post: New rare disease gene tool launched – PanelApp. But I think the structure and color cues are helpful. (잠깐 만요, 색, 오른쪽? UK variation). Check it out yourself, 그래도, with the link below. You can hear more in this podcast as well.

빠른 링크:

PanelApp: 은 https://bioinfo.extge.co.uk/crowdsourcing/PanelApp/

100,000 Genomes 프로젝트: http://www.genomicsengland.co.uk/

참고 문헌:

Siva, 없음. (2015). UK gears up to decode 100 000 genomes from NHS patients 랜싯, 385 (9963), 103-104 간접 자원부: 10.1016/S0140 - 6736(14)62453-3

Caulfield M., Davies J., Dennys M., et al “The 100,000 Genomes Project Protocol” London: Genomics England (2014) Available at: genomicsengland.co.uk/?wpdmdl=5168 (액세스: Oct 8 2015)
SNPpets_2

금요일 SNPpets

이번 주 SNPpets 기존 도구에 대한 업데이트가 포함되어 있습니다, 같은 Reactome그림, 가장 큰 JBrowse 디스플레이 내가 이제까지 본, 단어 구름과 같은 # ASHG15의 다양한 맛있는 가벼운 음식, 유전자 편집, 맞춤 의학 및 희귀 질병을 통해 조각, 그리고 가상 머신 카탈로그. 이번 주 가장 특이한 것은: 최근 진화 유전체학 연구는 빅뱅 이론에 도착. 그리고 더 많은….


SNPpets_2오신 것을 환영 금요일 기능 링크 모음: SNPpets. 일주일 동안 우리는 링크의 많은 가로질러 와서 우리가 흥미있는 것을 읽습니다, 하지만 블로그 게시물에 그것을 만들지 마. 여기에 그들은 당신의 즐거움을위한…


조사는 시간에 의해 폐쇄되어있는 경우이 건너, 답변을 참조 (그리고 트위터 토론 게시글은 재미입니다)

Biostars

무슨 대답이야? (genomics guidance for the general public)

This week’s highlighted discussion at Biostars was one that I opened. I’ve been thinking a lot about this, because I’m seeing it come up in a number of different ways. There are folks who are googling and finding genomics nerds in a variety of places. Some of the communities will be more welcoming than others. But I think it’s in our best interest to be helpful to families with data, and not come off too harsh because it’s not exactly how our forum works….


Biostars 질문에 대한 사이트입니다, 생물 정보학 질문과 문제에 대한 답변 및 토론. 우리의 회원 Biostars_logo 커뮤니티는 매우 유용한 찾아. 종종 질문과 답변은 우리의 독자들에게 밀접한 있습니다 Biostars에서 발생 (게놈 자원의 최종 사용자). Thursdays we will be highlighting one of those items or discussions here in this thread. 당신이이 스레드에 질문을 할 수, 또는 당신은 항상 Biostars에의 가입하실 수 있습니다.


포럼: For the general public seeking advice from this community

안녕하세요 여러분–

Yesterday I saw a thread posted by a member of the general public, looking for advice for their child’s medical issues. This thread has been deleted (내 생각은), but I was able to read some of the commentary before it disappeared.

The community had some concerns about private medical information being revealed. And some concerns about seeking advice from strangers on the internet instead of qualified practitioners in real life. These are valid issues.

그러나, my point is more general. This may become increasingly an issue here as more people have (or hear about) 시퀀스 정보, and want some advice for it. I think it is wise for this community to stay away from diagnosis. But I think we could offer these folks some guidance to appropriate resources.

Please have some compassion for the desperation that the parents of kids with undiagnosed conditions face. And keep in mind that their thresholds for privacy are not the same as everyone else, 가능. And understand that they are hearing stories about how familes connected with researchers who could help them from random internet forums. The most recent one I saw was this: 답변.

But other stories like this are widely read: How Genome Sequencing Creates Communities Around Rare Disorders.

Could we possibly have a place to point these families, like a thread that we can sticky or something? Where we can offer them connections to the Rare Disease sequencing projects, or genetic counseling resources, non-wonky information sources like 유전학 홈 참조, 이나 뭐? The international group here probably could collect a good set of pointers for people around the world.

I guess I’m asking for a constructive place for some guidance for families, and a policy about how to deal with those kinds of threads.

Open for discussion.

Has any of the genomics nerd discussion communities developed a policy on this? Should we reach out to genetic counselors, 아마도? We may also need legal advice. Anyone seen other places take this on? Please add your thoughts over at Biostars.

dna_cutting_with_scissors_hr-150x150

금요일 SNPpets

This week’s SNPpets offered a lot of good stuff, everybody must be out of their summer vacation mode and back to the lab. 가 BLASTX alternative, a helpful tip in workshop teaching, quack DTC tests, handy errors (정말), new variant database DIVAS, exome sequencing patients and outcomes, imputation, 24M novel rare variants, variant caller comparison, the long term evolution experiment hits a milestone, new citrus resources, eQTLs, 더. The best item this week, 그래도, was a story of a family with a rare disease situation that found genomics researchers via Reddit, and that gave them answers and hope.


오신 것을 환영 금요일 기능 링크 모음: SNPpets. 일주일 동안 우리는 링크의 많은 가로질러 와서 우리가 흥미있는 것을 읽습니다, 하지만 블로그 게시물에 그것을 만들지 마. 여기에 그들은 당신의 즐거움을위한…


금주의 팁: 드문 질병 정보 Orphanet

나는 새 OMIM 사이트에서 관련 자료에 대한 링크 중 일부에 주변을 두리번 거 렸지으로, 나는 Orphanet로 연결되는 링크가 있었다 것으로 나타났습니다. 전에 Orphanet의 들었어요–자신의 정보에 의하면 그들은 이후에 둘러싸여있어 1997, 하지만 가까 이서 보았다 않았다. 그래서 주이 주 팁에 대한 우리 Orphanet을 찾아 보죠.

나는 기본 방문 페이지에 탐색하기 시작, http://www.orpha.net/. 방문 페이지에서는 검색 유형 및 데이터 컬렉션의 다양한 액세스할 수 있습니다. 상단 탭 탐색 영역은 여러 관점에서 진입 점을 제공합니다: 희귀 질환, 고아 약품, 전문가 센터, 진단 테스트, 연구 및 실험, 환자 단체, 디렉토리, 더. 그것은 희귀 질병에 대한 정보를 친절하게 조직 포탈입니다.

동영상 팁 필자는 이러한 모든 구성 요소에 갈 시간이 없습니다, 당신이 자신을 둘러 보러 장려. 나는 희귀한 질환에 대한 검색에 초점을 맞추고 있습니다, 그 페이지에서 사용할 수있는 기능을보고. 당시이 글을 작성하는 경우, 거의 없습니다 6000 사이트에 저장된 정보와 함께 기록된 희귀 질환 (5954).

하나는 내가 정말 좋아하는 기능은 최근에 추가되었습니다–임상 유틸리티 유전자 카드 (CUGCs). 우리가 지금의 자신을 찾은 DNA 테스트의 서부에 대한 것들 중 하나는 가끔 테스트 유틸리티는 분명 아니라는 것입니다. 이러한 질병의 경우, 유틸리티 중요, 그리고 그들은이 페이지의 테스트에 대한 지침을 제공합니다. 그리고 그것은이 유틸리티의 여러 측면을 설명–그들은 시험이 얼마나 유용할 수 있습니다 고려에 대한 좋은 일반적인 모델 아르, 내 생각은, 및 테스트가 정말 사람을 제공할 것입니다 무엇 평가. 예를 들어, 이 하나를 체크 아웃 헌팅턴 병 (PDF 파일).

나는 우리가 탐험 자원에 대한 참조를 제공하는 것, 하지만 Orphanet에 대한 하나를 찾을 수 없습니다. 그러나, 당신은 그들을 둘러볼 수 있습니다 섹션 도움말 사이트를 사용하는 방법에 대한 자세한 내용을 보려면, 그들의 사명과 자금 출처에 대한. 그들이 거기를 참조 한 가지과의 관계이다 EuroGenTest, 를 생각나게하는 사이트 자원 GeneTests NCBI에서. EuroGenTest에 시험 연구소에 대한 검색을 수행하는 것은 어쨌든 Orphanet으로 돌아갑니다, 진단 테스트 검색을 사용하여.

빠른 링크:

Orphanet: HTTP를://www.orpha.net

EuroGenTest: http://www.eurogentest.org/

NCBI에서 GeneTests: http://www.ncbi.nlm.nih.gov/sites/GeneTests