GensearchNGS

GensearchNGS is an integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina, Ion Torrent and Proton. It has been designed and developed in close collaboration with leading accredited diagnostics groups in Europe and with the support of the NMDchip FP7 project.

Screen shots:

GensearchNGS screenshot 1 GensearchNGS screenshot 2 GensearchNGS screenshot 3 GensearchNGS screenshot 4 GensearchNGS screenshot 5

It integrates all the steps from importing and filtering sequence reads, bar code splitting, alignment, variant detection and annotation to the final report of detected variants. Variants can be annotated with various public and private data sources (Ensembl, Alamut, Genome Trax,...) They can be filtered by logical combinations between samples for family studies.

Main features:

  • User friendly software for resequencing NGS projects in a diagnostic setting, running on Windows, Linux and MacOS systems.
  • Connects*) to variant interpretation tools, and databases such as: Ensembl, dbSNP, Alamut, Genome Trax, UMD-HTS, Cafe Variome or LOVD1).
  • Filter variants across samples (e.g. variants common to several samples or exclude variants of one sample from another).
  • Patient centric database system to manage sequence data and validated variants.
  • Customisation possible to export data into your laboratory management system.
  • Possibility to publish your variants on the Cafe Variome*).
  • Developed together with accredited laboratories.
  • For larger projects (WES/WGS): possibility to use multiple PCs in parallel.
  • Plugin technology: alignment with proprietary or public algorithms such as Bowtie, BWA or Stampy.
  • Annotation and filtering with HPO, OMIM and Orphanet descriptors and codes, helpful when fishing for mutations in whole exomes.
  • Tools to analyse coverage and detect CNV*).
  • Sanger validation step: you can attach to patients in the database and visualise amplicons sequenced with a capillary sequencer to validate that the NGS detected variant is indeed not an artefact.

 

You can download a demo version after registration. This will allow you to access the download area in our products section.

Some publications, posters and references:

A Novel de novo Mutation in CEACAM16 Associated with Postlingual Hearing Impairment.
Authors: Michaela A.H. Hofrichter, Indrajit Nanda, Jens Gräf, Jörg Schröder, Wafaa Shehata-Dieler, Barbara Vona, Thomas Haaf
Publication: Molecular syndromology 6(4) · August 2015 | DOI: 10.1159/000439576

Research Article DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation.
Authors: Wolf, B., Kuonen, P., Dandekar, Th., Atlan, D.
Publication: BioMed Research International 2015 · June 2015 | DOI: 10.1155/2015/403497

Nail–Patella Syndrome: clinical and molecular data in 55 families raising the hypothesis of a genetic heterogeneity.
Authors: Ghoumid, J., Petit, F., Holder-Espinasse, M., Jourdain, A. S., Guerra, J., Dieux-Coeslier, A., ... & Escande, F.
Publication: European Journal of Human Genetics , (22 April 2015) | doi:10.1038/ejhg.2015.77

Analysis of circulating cell free DNA (ccfDNA): A promising tool for personalized medicine and cancer therapy
Authors: Keup C., Mardin W., Dworniczak J., Dockhorn B., Rijcken E., Dworniczak B.
Conference: GfH Jahrestagung, 2015

Identification of deep intronic variants in 15 haemophilia A patients by next generation sequencing of the whole factor VIII gene.
Authors: Bach JE, Wolf B, Oldenburg J, Müller CR, Rost S.
Publication: European Journal of Human Genetics , (5 November 2014) | Thromb Haemost. 2015 May 7;114(3). [Epub ahead of print]

Zur genetischen Heterogenität der Muskeldystrophien : alternative genetische Ursachen der Myotonen Dystrophie und FSHD.
Author: Mirjam Larsen
Publication: Doctoral thesis, University of Würzburg · December 2015

Distal hereditary motor neuropathy due to BSCL2 mutation in a two generation family
Authors: Ann-Kathrin Zaum, Simone Rost, Beat Wolf, Clemens R. Müller, Thomas Musacchio, Erdmute Kunstmann, Stephan Klebe
Conference: GfH Jahrestagung, 2015

Hereditary Breast/Ovarian Cancer: A systematic screening of DNA repair genes in 300 consecutive patients
Authors: Andrea Gehrig, Birgit Halliger-Keller, Clemens R. Müller
Conference: GfH Jahrestagung, 2015

Novel compound heterozygous mutations in PLEC1 causing epidermolysis bullosa simplex with muscular dystrophy
Authors: Simone Rost, Ann-Kathrin Zaum, Andrea Gehrig, Birgit Halliger-Keller, Wolfram Kress, Clemens R. Müller, Mathias Buttmann, Erdmute Kunstmann
Conference: GfH Jahrestagung, 2015

Deep intronic variants in the factor VIII gene
Authors: J Elisa Bach, Beat Wolf, Johannes Oldenburg, Clemens R Müller, Simone Rost
Conference: GfH Jahrestagung, 2015

Next-generation DNA sequencing of a Swedish malignant hyperthermia cohort
Authors: M. Broman, I. Kleinschnitz, J.E. Bach, S. Rost, G. Islander and C.R. Müller
 Publication: Clinical Genetics  | doi:10.1111/cge.12508

Analysis of circulating cell free DNA (ccfDNA): A promising tool for personalized medicine and cancer therapy
Authors: Keup C., Mardin W., Dworniczak J., Dockhorn B., Haier J., Rijcken E., Rijcken E., Dworniczak B.
Conference: 13th International Symposium on Mutation in the Genome: detection, genome sequencing & interpretation

Diagnostic approach for FSHD revisited: SMCHD1 mutations cause FSHD2 and act as modifiers of disease severity in FSHD1
Authors: Mirjam Larsen, Simone Rost, Nady El Hajj, Andreas Ferbert, Marcus Deschauer, Maggie C Walter, Benedikt Schoser, Pawel Tacik, Wolfram Kress and Clemens R Müller
Publication: European Journal of Human Genetics , (5 November 2014) | doi:10.1038/ejhg.2014.191

VHL mosaicism can be detected by clinical next-generation sequencing and is not restricted to patients with a mild phenotype.
Authors: Lucie Coppin, Claudine Grutzmacher, Michel Crépin, Evelyne Destailleur, Sophie Giraud, Catherine Cardot-Bauters, Nicole Porchet and Pascal Pigny
Publication: European Journal of Human Genetics, 2014, vol. 22, no 9, p. 1149-1152.

Unusual multisystemic involvement and a novel BAG3 mutation revealed by NGS screening in a large cohort of myofibrillar myopathies
Authors: Anna-Lena Semmler et al.
Publication: Orphanet Journal of Rare Diseases 2014, 9:121 doi:10.1186/s13023-014-0121-9

NGS panel for diagnostics of myofibrillar myopathies
Authors: J Elisa Bach, Simone Rost, Anna-Lena Semmler, Kristl G Claeys, Beat Wolf, Wolfram Kress, Clemens R Müller
Conference: GfH Jahrestagung, 2014

A novel approach for heuristic pairwise DNA sequence alignment
Authors: Beat Wolf, Pierre Kuonen
Conference: BIOCOMP'13 - The 2013 International Conference on Bioinformatics & Computational Biology

Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6
Authors: Simone Rost, Elisa Bach, Cordula Neuner, Indrajit Nanda, Sandra Dysek, Reginald E Bittner,
Alexander Keller, Oliver Bartsch, Robert Mlynski, Thomas Haaf, Clemens R Muller and Erdmute Kunstmann.
European Journal of Human Genetics advance online publication 29 May 2013; doi: 10.1038/ejhg.2013.108

IonTorrent: high throughput sequencing in a diagnostic laboratory
Authors: B. Dworniczak, S. Fleige-Menzen, P. Pennekamp.
Conference: European Human Genetics Conference 2013

Store, align and explore your genome outside the Cloud, at home, on your PC
Authors: P. Kuonen, B. Wolf, JT den Dunnen, D.Atlan, T. Dandekar
Conference: European Human Genetics Conference 2013

Nail-Patella Syndrome: evidence for genetic heterogeneity (Poster 01.021)
Authors: F. Petit, F. Escande, A. Jourdain, C. Baumann, F. Fellmann, D. Lacombe, S. Marlin, S. Odent, N. Porchet, M. Holder-Espinasse, S. Manouvrier-Hanu
Conference: European Human Genetics Conference 2013

Novel form of X-linked nonsyndromic hearing loss caused by a mutation in a type IV collagen gene (Poster P-MonoG-202)
Authors: Rost, Bach, Neuner, Nanda, Dysek, Bittner, Keller, Bartsch O., Mlynski, Haaf, Müller, Kunstmann
Conference: GfH Jahrestagung, 2013

Application of targeted next-generation sequencing for molecular diagnostics of Malignant Hyperthermia and Central Core Disease (Poster P-ClinG-087)
Authors: Kleinschnitz I., Bach J.E., Rost S., Gehrig A., Müller C.R.
Conference: GfH Jahrestagung, 2013

NGS goes diagnostics: Multiplex analysis of genes for limb-girdle muscular dystrophies (Poster P-ClinG-045)
Authors: Bach J.E., Rost S., Gehrig A., Kress W., Müller C.R.
Conference: GfH Jahrestagung, 2013

Screening of muscular disease genes with the Access Array System of Fluidigm and Roche’s GS Junior
Authors: J. E. Bach, S. Rost, A. Gehrig, C. R. Müller
Conference: European Human Genetics Conference 2012

IonTorrent: 2nd generation sequencing in a diagnostic laboratory 
Authors: B. Dworniczak, S. Fleige-Menzen, N. Bogdanova-Markov, P. Pennekamp
Conference: European Human Genetics Conference 2012

1)F okkema IFAC, Den Dunnen JT and Taschner PEM (2005). LOVD: easy creation of a locus-specific sequence variation database using an “LSDB-in-a-Box” approach. Hum. Mutat. 2005 Aug; 26(2):63-8.

*) under development.

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