New functionalities added to mirVAFC, April 26th, 2016
- Many new functionalities and some changes have been made to mirVAFC:
- (1), hg38 (or GRCH38) genome assembly is supported;
- (2), User could upload pathogenic evidences file for variants classifications;
- (3), Incidental genes list could be supplied to find incidental findings;
- (4), Annotation for specific transcript could be retained by filtering;
- (5), Variants could be filtered based on 3 types of conservation scores;
- (6), Genes could be excluded for analysis by filtering;
- (7), Databases versions for annotation data is presented in result part.
mirVAFC updated on August, 23th, 2015
- Currently, mirVAFC contain 20 public databases for variants annotations, and 15 different parameters for variants filtering. mirVAFC will be updated quarterly to incorporate more data resources and functionality.
Gene enrichment to functional unit test applied in mirVAFC updated on June 11th, 2015
- (1) To find about possible new pathogenic genes and reveal molecular mechanism underlying disease, we annotate each affected gene with the function annotations which include biological pathways (KEGG, BioCarta), GO terms (GO), protein interactions (BioGRID), co-expressions (COXPRESdb), protein complex (CORUM);
- (2) Then for each function unit, that refer to genes from same pathways, GO terms, or with physically or regulatory interactions, we test its enrichment of previously known pathogenic or related genes, which were collected in OMIM, MGI, and DisGenet et al.
Newly released standards and guidelines for sequence variants interpretation by ACMG were actualized in mirVAFC for more effective variants clinical classifications on March 27th, 2015
- Defined terms and detailed criteria, processes for sequence variants clinical classifications were published by ACMG and two other medical associations on the GENETIC in MEDICIN journal.
FTP file transfer functionality were added to support larger sequence variants file uploading on January 20th, 2015
- For variants files with size larger than 80Mb, FTP transfer should be used.
ExAC databases were incorporated in mirVAFC on September 18th, 2014
- The ExAC databases aggregate and harmonize exome sequencing data from a wide variety of large-scale sequencing projects, as the largest human variation database now, which provide genetic variation for more than 60,000 individuals from different ethnic groups.
The mirVAFC webserver was basically constructed and tested to be usable on December 11th, 2014
- (1) mirVAFC was constructed under an Apache/PHP/MySQL environment on the Red Hat Enterprise 5.5 Linux operating system, using Perl/Java/R languages;
- (2) mirVAFC has been successfully tested with different releases of Microsoft Internet Explorer 11.0, Firefox 38, Google Chrome 45, and Safari 5.1 under different versions of MacOS, Microsoft Windows and Linux.
The mirVAFC webserver development was initiated on January 16th, 2014
- To identify pathogenic genetic variants from NGS data during clinical testing is challenging and complicated, so we will develop an easy-to-use webserver: mirVAFC for sequence variants analysis to help with clinical diagnosis based on WGS/WES data. Three main functionalities:
- (1) Comprehensive variants annotation using multiple public data resources that cover multiple nucleotide and gene level function related information;
- (2) Filtering using different criteria from different aspects of population data, functional data, family data et al;
- (3) And classifications as for clinical significance according to the ACMG guidelines will be integrated in mirVAFC, which will greatly facilitate pathogenic sequence variants identifications.