GeneMap

[…] nt of NGS technologies has accelerated disease‐gene discovery such that (as of January 2016) there are now reported to be 5654 phenotypes for which the genetic basis is known (www.omim.org/statistics/geneMap). For the remaining rare genetic disorders in which the underlying molecular mechanisms have not yet been determined, online tools such as GeneMatcher , GenomeConnect and MyGene2 have been d […]

[…] ead-Chip (Illumina, San Diego, CA, USA) with the following quality-control criteria: genotyping call rate >0.95; MAF >0.05; and GenCall score >0.2. The concordance among replicates was >99.9% and the GeneMap software was used to analyze the data and prepare reports.Linkage disequilibrium was analyzed in Haploview Software (Broad Institute of Harvard and Massachusetts Institute of Technology, Cambr […]

[…] Disease genes were parsed from the OMIM database genemap (03/02/2014 update; ) and filtered according to ‘confirmed’ genes (observed in at least two laboratories). Disease genes that had no disease annotation in the “disorder” field of the genemap w […]

[…] as a learning set for the predictive scores (ROC analyses), we used a catalogue of pathogenic mutations from the Online Mendelian Inheritance in Man database. Only genes with a cytogenetic location (genemap2.txt accessed 18/10/2013 at OMIM: ftp.omim.org) and with a gene status of confirmed or provisional were kept. For each gene with an associated OMIM number, all allelic variants with a “live” s […]

[…] For a certain locus, the allele size range (S) was directly obtained from the Genemap® 4.0 software. The number of alleles (A) and their frequency (F), the observed heterozygosity (Ho) and the expected heterozygosity (He) were calculated using the computer program POPGENE 32. T […]

[…] Bank proteins and by viewing of genome-predicted proteins on the genome contigs at UCSC Genome Bioinformatics. In the case of D. rerio, initial identification of gene neighbors was made from the NCBI Genemap Table of the 2004 Zv4 assembly. Gene neighbors were re-confirmed on the contigs of the 2005 scaffold assembly Zv5 at Ensembl (EBI) []. For identification of parologous TSP-encoding regions in […]