GRC reference assembly curation with BioNano maps

Commercial whole genome mapping systems, such as OpGen and BioNano, are playing an increasingly important role in a variety of genomic analyses, including de novo assembly, structural variant detection and assembly curation.Comparison of a reference assembly to a collection of whole genome maps can help curators find potential regions of misassembly and identify genomic variations that are candidates for representation in alternate loci scaffolds. For example, optical maps played a key role in the GRC's resolution of the human 10q11.22 tiling path, as described in this prior GRC blog post.To assist with curation efforts, the Wellcome Trust Sanger Institute, a GRC member, has integrated BioNano data sets for human, mouse and zebrafish assemblies into the gEVAL browser. They have also provided data from OpGen maps and optical maps from David Schwartz (PMID: 20534489). Common curation use cases for these browser data include:Gap sizingConfirmation of assembly componentsIdentification of problems in assembly componentsIdentification of assembly regions missing sequenceDetection of haplotype over-expansionsBelow is an example highlighting the potential usage.The issue (HG-172) reports possible assembly error or missing sequence from reference component AL691432.54 that affects CDC2L1 (GeneID:984) in GRCh37.  Navigating to this region in gEVAL and turning on the tracks for:REFSEQ transcript mappingsBspQI insilico digestJIRA issue entriesBionano genome mapsNA12878 NA24143 ...

Source: GenomeRef - March 9, 2016 Category: Genetics & Stem Cells Source Type: blogs