GenTalk How To Use GeneTalk - First Steps Whitepaper

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Information about GenTalk How To Use GeneTalk - First Steps Whitepaper

Published on February 28, 2014

Author: AlexejKnaus



A brief introduction into using

Filter your VCF files with easy to use and intuative filtering tools.

4 5 3 2 1 FIRST STEPS IN ANALYZING HUMAN SEQUENCE VARIANTS WITH GENETALK WHAT IS GENETALK: GeneTalk is a web-based tool and platform for filtering and analyzing human sequence variants. Clinicians and scientists that are looking for information about specific sequence variants can find other users with expertise for a particular variant. Reduce your sequence variants with highly effective filtering tools à Save time and money Annotate sequence variants and find out what other GeneTalk users say about specific mutations Discuss with other GeneTalk users about sequence variants and their biological and medical implications HOW TO USE GENETALK: Upload your sequence variants in VCF format of single or multiple samples. Make sure the hg19 or GRCh37 reference is used. Uploaded files are preprocessed and listed in the file manager. Individuals of a multiple VCF are shown after clicking the button. The file can be viewed and shared with other users. By clicking on the pedigree icon one can edit pedigree and phenotype information of the individuals in a multiple VCF file. If exome or genome data was uploaded, the gender of all individuals is automatically determined by polymorphisms on the X chromosome. The information entered in the pedigree editor allows powerful filtering of variants by mode of inheritance such as dominant, recessive homozygous, and recessive compound heterozygous. Open the filter view by clicking on FILTER VCF in the menu. Choose one or multiple VCF files to filter by selecting the checkboxes.

REDUCING SEQUENCE VARIANTS: The filtering menu is displayed in tabs on the top row and provides several options that are adjustable to reduce the number of variants to a manageable amount with only relevant mutations in the variant file. FUNCTIONAL FILTER: Reduce to variants that have an effect on the protein level. LINKAGE FILTER and GENE PANEL FILTER: Restrict the variant list to a certain set of genes or to linkage intervals. FREQUENCY FILTER: Sort out all genotypes that occur more often in the background population than an adjustable cutoff. (Data from the 1000 genomes and 5000 exome sequencing project are used as reference.) INHERITANCE FILTER: Restrict analysis to genotypes that fit to a certain mode of inheritance. ANNOTATION FILTER: Filter out variants based on ratings for medical relevance and scientific evidence. After applying the filter settings, start the filtering process by clicking the F ILTER button. VIEW SEQUECE VARIANTS The filtered VCF file is displayed containing significantly less sequence variants sorted by chromosome and position. Click the A NNOTATE button to provide an annotation for that variant. The MORE button displays a popup with detailed variant information. ANNOTATIONS AND EXPERTS The star rating for the categories MEDICAL RELEVANCE and  S CIENTIFIC EVIDENCE shows that for a certainposition at least one annotation exists. Clickingon the stars opens the annotation and expertview. For position 35091529 at chromosome 9 an expert in GPI anchor deficiency providesa gene panel that includes the gene PIGO. p etkraw is therefore listed as an expert and can be contacted for further discussion. Additionally, the user Alexej has left an annotation for this position in PIGO, rating an insertion as disease causing.

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