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varSEAK

varSEAK: The Variant Database for Shared Experience And Knowledge

www.varSEAK.bio

varSEAK Connects SEQUENCE Pilot Users

varSEAK is a fast and reliable tool to manage and interpret sequencing data. Worldwide more than 400 SEQUENCE Pilot installations are used to analyse NGS, Sanger and MLPA data. Over the last decade our customers maintained their local databases containing up to 20 % of variants that are not listed in public available databases and acquired a lot of knowledge and experience. varSEAK automatically aggregates all these valuable information in one central database in real time and offers convenient access to the varSEAK community.

varSEAK is Seamlessly Integrated Into Your Daily Workflow

For an easy and safe workflow all relevant patient and sequencing data can be imported by one click. The complete data set, including quality related parameters, is transferred directly from SEQUENCE Pilot into the local varSEAK database. Thereby, confusion of patients is excluded. For users without a SEQUENCE Pilot installation varSEAK open offers extensive options to import variants via vcf-files, including the possibility to use a file-naming-convention to optimize the import.

Classification of Variants

varSEAK provides clearly organised information from public databases in one place to simplify the characterisation and classification of new variants. A detailed lab internal classification of variants can be added to the local varSEAK database. This includes HPO-conform phenotypes, mode of inheritance, documents, weblinks and PubMed IDs as well as descriptions for internal use and medical reports.

Networking: Connection and Communication

varSEAK enables users and laboratories that have identified the same or similar variants in close genomic proximity to connect via a built-in message system. varSEAK members can subscribe to watchlists for variants, genes, gene panels and phenotypes to be actively notified about new scientific evidence or changes in classification.

Efficient Filtering Strategies

varSEAK offers a sophisticated and highly customizable feature for filtering by phenotype(s), chromosome(s), gene panel(s), classification(s), AF/MAF and various other information provided by public databases and prediction tools like 1000 Genomes, ClinVar, ClinVitae, COSMIC, dbSNP, ESP, ExAC, p53, UK10K and Mutation-Taster, SIFT, etc. Filtering strategies can be defined, applied and shared.

Quality Control

The local varSEAK installation automatically compares various quality criteria like average Phred scores and coverages to the statistics based on all previously analysed samples. It detects significant deviations and provides an overview of those samples that exceed a certain threshold.

Report

Individual variant reports can be created easily according to ESHG and ACMG guidelines, including a predefined subset of the information available in varSEAK and public databases.

Public Access With www.varSEAK.bio

View variants, classifications and summarized information from varSEAK and public databases. Search for a gene and find all variants of a gene in one clearly organised table, including:

  • hg19 and hg38 positions
  • HGVS c. and p. nomenclature
  • classification, allele frequencies and prediction scores
  • direct links to ClinVar, ClinVitae, Cosmic, ExAc, dbSNP and 1000 Genomes Project
  • newly submitted variants and classifications found by varSEAK community members (uploaded in real time)

To join the varSEAK community and profit from the various advantages of Shared Experience And Knowledge visit:

www.varSEAK.bio