Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases.
Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases.
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DOI：
10.1016/j.xgen.2022.100246
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发表时间：
2023-02-08
期刊：
影响因子：
--
通讯作者：
Beltran, Sergi
中科院分区：
文献类型：
--
作者：
Corvo, Alberto;Matalonga, Leslie;Spalding, Dylan;Senf, Alexander;Laurie, Steven;Pico-Amador, Daniel;Fernandez-Callejo, Marcos;Paramonov, Ida;Romero, Anna Foix;Garcia-Rios, Emilio;Ciges, Jorge Izquierdo;Mohan, Anand;Thomas, Coline;Valencia, Andres Felipe Silva;Halmagyi, Csaba;Freeberg, Mallory Ann;Topf, Ana;Horvath, Rita;Saunders, Gary;Gut, Ivo;Keane, Thomas;Piscia, Davide;Beltran, Sergi
Solve-RD项目的目标包括通过对共享基因组-表型组数据集的合作研究来解决未诊断的罕见疾病（RD）。用于数据整理和分析的RD-Connect Genome-Phenome Analysis Platform（GPAP）和用于文件存储的European Genome-Phenome Archive（EGA）是Solve-RD基础设施的两个关键组成部分。临床研究人员可以识别RD-Connect GPAP中的候选遗传变异，并且由于这里作为联合ELIXIR活动的一部分所展示的发展，能够远程可视化存储在EGA中的相应比对。全球基因组学与健康联盟（GA 4GH）htsget流式传输应用程序编程接口（API）用于检索比对切片，比对切片由嵌入GPAP中的集成基因组查看器（IGV）实例呈现。因此，超过11，000个数据集不再需要下载大型对齐文件以在本地对其进行可视化。这项工作从用户和基础设施的角度强调了实施互操作性标准以建立联合基因组数据网络的优势。序列比对的可视化使基因组变异的评估成为可能RD-Connect GPAP用户可以通过GA 4 GH htsget远程可视化在EGA上进行真实的实时比对，避免了经常性的大量数据下载Solve-RD Corvestival等人的项目中已经检查了数百种罕见的致病变异。提出了一个GA 4GH htsget实现，使RD-Connect GPAP用户能够远程可视化基因组比对在EGA在真实的时间，避免了大量下载的需要。事实证明，这对于评价Solve-RD项目中数百名患者的潜在罕见致病遗传变异至关重要。
The Solve-RD project objectives include solving undiagnosed rare diseases (RD) through collaborative research on shared genome-phenome datasets. The RD-Connect Genome-Phenome Analysis Platform (GPAP), for data collation and analysis, and the European Genome-Phenome Archive (EGA), for file storage, are two key components of the Solve-RD infrastructure. Clinical researchers can identify candidate genetic variants within the RD-Connect GPAP and, thanks to the developments presented here as part of joint ELIXIR activities, are able to remotely visualize the corresponding alignments stored at the EGA. The Global Alliance for Genomics and Health (GA4GH) htsget streaming application programming interface (API) is used to retrieve alignment slices, which are rendered by an integrated genome viewer (IGV) instance embedded in the GPAP. As a result, it is no longer necessary for over 11,000 datasets to download large alignment files to visualize them locally. This work highlights the advantages, from both the user and infrastructure perspectives, of implementing interoperability standards for establishing federated genomics data networks. Visualization of sequence alignments enables the evaluation of genomic variants RD-Connect GPAP users can visualize alignments at the EGA through GA4GH htsget Remote visualization in real time avoids recurrent large data downloads Hundreds of rare disease-causing variants have been inspected in project Solve-RD Corvò et al. present a GA4GH htsget implementation enabling RD-Connect GPAP users to remotely visualize genomic alignments at the EGA in real time, avoiding the need for large downloads. This has proven essential to evaluate potentially rare disease-causing genetic variants in hundreds of patients from the Solve-RD project.
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DOI：
10.1038/s41431-021-00901-1
发表时间：
2021-09
期刊：
European journal of human genetics : EJHG
影响因子：
--
作者：
Schüle R;Timmann D;Erasmus CE;Reichbauer J;Wayand M;Solve-RD-DITF-RND;van de Warrenburg B;Schöls L;Wilke C;Bevot A;Zuchner S;Beltran S;Laurie S;Matalonga L;Graessner H;Synofzik M;Solve-RD Consortium
通讯作者：
Solve-RD Consortium
影响因子：
3.9
作者：
Laurie, Steven;Piscia, Davide;Matalonga, Leslie;Corvo, Alberto;Fernandez-Callejo, Marcos;Garcia-Linares, Carles;Hernandez-Ferrer, Carles;Luengo, Cristina;Martinez, Ines;Papakonstantinou, Anastasios;Pico-Amador, Daniel;Protasio, Joan;Thompson, Rachel;Tonda, Raul;Bayes, Monica;Bullich, Gemma;Camps-Puchadas, Jordi;Paramonov, Ida;Trotta, Jean-Remi;Alonso, Angel;Attimonelli, Marcella;Beroud, Christophe;Bros-Facer, Virginie;Buske, Orion J.;Canada-Pallares, Andres;Fernandez, Jose M.;Hansson, Mats G.;Horvath, Rita;Jacobsen, Julius O. B.;Kaliyaperumal, Rajaram;Lair-Preterre, Severine;Licata, Luana;Lopes, Pedro;Lopez-Martin, Estrella;Mascalzoni, Deborah;Monaco, Lucia;Perez-Jurado, Luis A.;Posada de la Paz, Manuel;Rambla, Jordi;Rath, Ana;Riess, Olaf;Robinson, Peter N.;Salgado, David;Smedley, Damian;Spalding, Dylan;'t Hoen, Peter A. C.;Topf, Ana;Zaharieva, Irina;Graessner, Holm;Gut, Ivo G.;Lochmuller, Hanns;Beltran, Sergi
通讯作者：
Beltran, Sergi
DOI：
10.1038/s41431-021-00853-6
发表时间：
2021-09
期刊：
European journal of human genetics : EJHG
影响因子：
--
作者：
Te Paske IBAW;Garcia-Pelaez J;Sommer AK;Matalonga L;Starzynska T;Jakubowska A;Solve-RD-GENTURIS group,;van der Post RS;Lubinski J;Oliveira C;Hoogerbrugge N;de Voer RM
通讯作者：
de Voer RM
影响因子：
3.9
作者：
Laurie, Steve;Fernandez-Callejo, Marcos;Marco-Sola, Santiago;Trotta, Jean-Remi;Camps, Jordi;Chacon, Alejandro;Espinosa, Antonio;Gut, Marta;Gut, Ivo;Heath, Simon;Beltran, Sergi
通讯作者：
Beltran, Sergi
影响因子：
46.9
作者：
Wagner, Justin;Olson, Nathan D.;Harris, Lindsay;McDaniel, Jennifer;Cheng, Haoyu;Fungtammasan, Arkarachai;Hwang, Yih-Chii;Gupta, Richa;Wenger, Aaron M.;Rowell, William J.;Khan, Ziad M.;Farek, Jesse;Zhu, Yiming;Pisupati, Aishwarya;Mahmoud, Medhat;Xiao, Chunlin;Yoo, Byunggil;Sahraeian, Sayed Mohammad Ebrahim;Miller, Danny E.;Jaspez, David;Lorenzo-Salazar, Jose M.;Munoz-Barrera, Adrian;Rubio-Rodriguez, Luis A.;Flores, Carlos;Narzisi, Giuseppe;Evani, Uday Shanker;Clarke, Wayne E.;Lee, Joyce;Mason, Christopher E.;Lincoln, Stephen E.;Miga, Karen H.;Ebbert, Mark T. W.;Shumate, Alaina;Li, Heng;Chin, Chen-Shan;Zook, Justin M.;Sedlazeck, Fritz J.
通讯作者：
Sedlazeck, Fritz J.