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Drori E, Levy D, Smirin-Yosef P, Rahimi O, Salmon-Divon M. CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files. Bioinformatics 2018; 33:1392-1393. [PMID: 28453675 DOI: 10.1093/bioinformatics/btw834] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/29/2016] [Indexed: 02/06/2023] Open
Abstract
Summary Visualization of whole-genomic variations in a meaningful manner assists researchers in gaining new insights into the underlying data, especially when it comes in the context of whole genome comparisons. CircosVCF is a web based visualization tool for genome-wide variant data described in VCF files, using circos plots. The user friendly interface of CircosVCF supports an interactive design of the circles in the plot, and the integration of additional information such as experimental data or annotations. The provided visualization capabilities give a broad overview of the genomic relationships between genomes, and allow identification of specific meaningful SNPs regions. Availability and Implementation CircosVCF was implemented in JavaScript and is available at http://www.ariel.ac.il/research/fbl/software. Contact malisa@ariel.ac.il. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- E Drori
- Agriculture and Oenology Research Department, Eastern R&D Center, 40700 Ariel, Israel
| | - D Levy
- Department of Molecular Biology, Ariel University, 40700 Ariel, Israel
| | - P Smirin-Yosef
- Department of Molecular Biology, Ariel University, 40700 Ariel, Israel
| | - O Rahimi
- Agriculture and Oenology Research Department, Eastern R&D Center, 40700 Ariel, Israel
| | - M Salmon-Divon
- Department of Molecular Biology, Ariel University, 40700 Ariel, Israel
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Weisz Hubshman M, Basel-Vanagaite L, Krauss A, Konen O, Levy Y, Garty BZ, Smirin-Yosef P, Maya I, Lagovsky I, Taub E, Marom D, Gaash D, Shichrur K, Avigad S, Hayman-Manzur L, Villa A, Sobacchi C, Shohat M, Yaniv I, Stein J. Homozygous deletion of RAG1, RAG2 and 5' region TRAF6 causes severe immune suppression and atypical osteopetrosis. Clin Genet 2017; 91:902-907. [PMID: 27808398 DOI: 10.1111/cge.12916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 10/24/2016] [Accepted: 10/30/2016] [Indexed: 01/17/2023]
Abstract
Mutations of several genes have been implicated in autosomal recessive osteopetrosis (OP), a disease caused by impaired function and differentiation of osteoclasts. Severe combined immune deficiencies (SCID) can likewise result from different genetic mutations. We report two siblings with SCID and an atypical phenotype of OP. A biallelic microdeletion encompassing the 5' region of TRAF6, RAG1 and RAG2 genes was identified. TRAF6, a tumor necrosis factor receptor-associated family member, plays an important role in T cell signaling and in RANKL-dependent osteoclast differentiation and activation but its role in human OP has not been previously reported. The RAG proteins are essential for recombination of B and T cell receptors, and for the survival and differentiation of these cells. This is the first study to report a homozygous deletion of TRAF6 as a cause of human disease.
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Affiliation(s)
- M Weisz Hubshman
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L Basel-Vanagaite
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - A Krauss
- Bone Marrow Transplantation Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - O Konen
- Radiology Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Y Levy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Kipper Institute of Immunology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - B Z Garty
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel.,Kipper Institute of Immunology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - P Smirin-Yosef
- Felsenstein Medical Research Center, Petach Tikva, Israel.,Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - I Maya
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - I Lagovsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E Taub
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - D Marom
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - D Gaash
- Hemato-Oncology Department, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - K Shichrur
- Hemato-Oncology Department, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - S Avigad
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel.,Hemato-Oncology Department, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - L Hayman-Manzur
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pathology Department, Rabin Medical Center, Petach Tikva, Israel
| | - A Villa
- CNR/IRGB, UOS Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - C Sobacchi
- CNR/IRGB, UOS Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - M Shohat
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Bioinformatics Unit, Cancer Center, Sheba Medical Center, Tel Aviv, Israel.,Genetic Institute, Maccabi Megalab, Rehovot, Israel
| | - I Yaniv
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Bone Marrow Transplantation Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - J Stein
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Bone Marrow Transplantation Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
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