The pedigree tool: Web‐based visualization of a family tree

Lachmund, Peter; Nebel, Istvan-Tibor; Führer, Dagmar; Paschke, Ralf

doi:10.1002/humu.10301

Cited by 4 publications

(4 citation statements)

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“…Thesystem wasbuiltonaLAMPS (Linux, Apache, MySQL,P erl, SSL)a rchitecture. TheR DE module wasi mplementeda sa n extension to the KPOH medical image clearinghouse, allowing re-useo fi nfrastructure components likeu ser administration,p ermissions andG UI.P edigree input anddisplaywas achievedbyadapting an existing Java-based toolf or the system whichsupports the Newicknotation [13].…”

Section: Methodsmentioning

confidence: 99%

Experiences with an Interoperable Data Acquisition Platform for Multi-centric Research Networks Based on HL7 CDA

Klein

Prokosch²,

Müller³

et al. 2007

Methods Inf Med

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Summary Objectives: Today’s increasing specialization of medicine necessitates the integration oftelematic platforms for cross-institutional cooperation. In orderto leverage the strengths of each cooperating institution a centralized unified storage using shared electronic patient records (EPRs) as well as secured remote data entry capabilities for supporting collaborative clinical research and care is essential. The objective of this project was to develop and introduce into routine use such a shared remote data entry (RDE) platform for the German multicentric Epidermolysis Bullosa (EB) network. Methods: An existing telematic application was extended by a remote data entry (RDE) module enabling thestorage of structured data and pedigrees. HL7 Clinical Document Architecture (CDA) was chosen as a suitable standardized storage format that provides flexibility and future interoperability. Flexible data entry forms adaptable to distinct medical domains were implemented using XML-based technologies. Results: A flexible and comprehensive ePR/RDE platform was successfully implemented in the German EB network. A set of specific data entry forms was created to fully cover the network’s documentation needs. The platform has been in productive use since 2005. Conclusions: Standardized documentation by using HL7 CDA to store the medical research data as an EPR can contribute to high interoperability and an easier integration of heterogeneous health care information systems. Existing XML technologies offer a high degree of flexibility and adaptability to distinct medical domains. The ongoing development of standards (e.g. HL7 CDA R2) and interfaces (CDA/CDISC bridge) could further improve semantic and syntactic interoperability.

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Section: Methodsmentioning

confidence: 99%

Experiences with an Interoperable Data Acquisition Platform for Multi-centric Research Networks Based on HL7 CDA

Klein

Prokosch²,

Müller³

et al. 2007

Methods Inf Med

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“…Dies entspricht den klinischen Charakteristika des autonomen Adenoms. Inzwischen sind mehr als 50 verschiedene, aktivierende Mutationen im TSH-Rezeptor-Gen bekannt (http://www.uni-leipzig.de/ innere/tsh/) [14]. Die Prävalenz dieser Mutationen in heißen Knoten liegt, unabhängig von einem solitären oder multifokalen Auftreten der Autonomie und von der histologischen Diagnose eines Kolloidknotens oder follikulären Adenoms, in verschiedenen Untersuchungen zwischen 55-80 % [15,16].…”

Section: Autonome Adenome (Heiße Knoten)unclassified

Molekulare Mechanismen der Schilddrüsentumorgenese

Krause¹,

Führer²

2008

Nuklearmediziner

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Schilddrüsenknoten liegen in bis zu 30 % der deutschen Bevölkerung vor und zählen damit zu den häufigsten endokrinologischen Erkrankungen. Schilddrüsenknoten sind außerordent-lich heterogen. Die Entstehung von Tumoren mit unterschiedlichen funktionellen und morphologischen Eigenschaften aus einer einzigen Vorläuferzelle ist ein besonderes Charakteristikum der Schilddrüse (SD) und wird durch spezifische genetische Veränderungen verursacht. Bei etwa 60-70 % der differenzierten SD-Karzinome sind Mutationen in bekannten Genen nachweisbar, die über konstitutive Signaltransduktionsaktivierung den Phänotyp des Karzinoms determinieren. In sporadischen papillären SD-Karzinomen (PTCs) liegen BRAF-(oder seltener RAS-)Mutationen vor, während chromosomale Rearrangements (RET, TRK, AKAP9 / BRAF) vorrangig in strahleninduzierten PTCs auftreten. Diese genetischen Veränderungen führen zur MAPKinasen-Aktivierung. In follikulären SDKarzinomen (FTC) liegen RAS-Mutationen oder PAX8 / PPARg-Rearrangements vor, diese sind allerdings auch in einem Teil der follikulären Adenome (FA) nachgewiesen. Des Weiteren zeigen aktuelle Arbeiten, dass eine Aktivierung der PI3K / AKT-Signaltransduktion in follikulären SD-Tumoren besonders häufig ist. Undifferenzierte (anaplastische) Schilddrüsenkarzinome (ATC) weisen genetische Merkmale von FTC oder PTC auf und darüber hinaus eine drastische Aktivierung mehrerer Tyrosinkinasekaskaden (Überexpression oder Mutationen im PI3K und MAPKinase-Pathway). Dies unterstreicht das Konzept einer sequenziellen Entwicklung eines ATC aus einem differenzierten SD-Karzinom, als dessen Triggermechanismus die p53-Inaktivierung angesehen wird. Mit Ausnahme der SD-Autonomie, die durch konstitutive cAMP-Aktivierung (TSHR oder selAbstract ! Thyroid nodules are the most frequent endocrine disorder and occur in approximately 30 % of the German population. Thyroid nodular disease constitutes a very heterogeneous entity. A striking diversity of possible functional and morphological features of a thyroid tumour derived from the same thyroid ancestor cell, is a hallmark of thyroid tumorigenesis and is due to specific genetic alterations. Defects in known candidate genes can be found in up to 70 % of differentiated thyroid carcinomas and determine the respective cancer phenotype. Papillary thyroid cancers (PTC) harbour BRAF (or much less frequently RAS) mutations in sporadically occurring tumours, while radiation-induced PTC display chromosomal rearrangements such as RET, TRK, APR9 / BRAF. These genetic events results in constitutive MAPKinase activation. Follicular thyroid cancers (FTC) harbour RAS mutations or PAX8 / PPARg rearrangements, both of which, however have also been identified in follicular adenoma. In addition, recent studies show, that activation of PI3K / AKT signalling occurs with high frequency in follicular thyroid tumours. Undifferentiated (anaplastic) thyroid cancers (ATC) display genetic features of FTC or PTC, in addition to aberant activation of multiple tyrosinkinase pathways (overexpression or mutations in...

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“…To solve this problem, R packages such as Kinship2 ( Sinnwell et al . 2014 ), software programs like PEDHUNTER ( Agarwala et al 1998 ), Pelican ( Dudbridge et al 2004 ), CraneFoot ( Mäkinen et al 2005 ), HaploPainter ( Thiele and Nürnberg 2005 ), Graphviz ( Zhao 2006 ), PyPedal ( Cole 2007 ), GeneaQuilts ( Bezerianos et al 2010 ), PedVis ( Tuttle et al 2010 ), Pedimap ( Voorrips et al 2012 ), Helium ( Shaw et al 2014 ), and E-Brida ( E-Brida 2018 ), and web-based tools for family trees like The Pedigree Tool ( Lachmund et al 2004 ) or for crops like maize and soybean such as PedigreeNet ( Braun et al 2019 ) and SoyPedi ( Jeong et al 2022 ) have been already developed for visualizing pedigrees. The majority of these visualization tools have been designed for breeding purposes, reason why some of them require attached databases, perform genetic calculations, and permit the upload of marker allele data.…”

Section: Introductionmentioning

confidence: 99%

PERSEUS: an interactive and intuitive web-based tool for pedigree visualization

Pradas,

Jurado-Ruiz,

Onielfa

et al. 2024

Bioinformatics

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Summary Pedigree-based analyses’ prime role is to unravel relationships between individuals in breeding programs and germplasms. This is critical information for decoding the genetics underlying main inherited traits of relevance, and unlocking the genotypic variability of a species to carry out genomic selections and predictions. Despite the great interest, current lineage visualizations become quite limiting in terms of public display, exploration, and tracing of traits up to ancestral donors. PERSEUS is a user-friendly, intuitive, and interactive web-based tool for pedigree visualizations represented as directed graph networks distributed using a force-repulsion method. The visualizations do not only showcase individual relationships among accessions, but also facilitate a seamless search and download of phenotypic traits along the pedigrees. PERSEUS is a promising tool for breeders and scientists, advantageous for evolutionary, genealogy, and diversity analyses among related accessions and species. Availability and implementation PERSEUS is freely accessible at https://bioinformatics.cragenomica.es/perseus and GitHub code is available at https://github.com/aranzana-lab/PERSEUS. Supplementary information Supplementary data is available at Bioinformatics online.

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The pedigree tool: Web‐based visualization of a family tree

Cited by 4 publications

References 1 publication

Experiences with an Interoperable Data Acquisition Platform for Multi-centric Research Networks Based on HL7 CDA

Experiences with an Interoperable Data Acquisition Platform for Multi-centric Research Networks Based on HL7 CDA

Molekulare Mechanismen der Schilddrüsentumorgenese

PERSEUS: an interactive and intuitive web-based tool for pedigree visualization

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