Today I am traveling to Minnesota to meet with our PALM Vision and Change team. I have an evening flight and will watch another shorter London Calling 2024 session. Eddy de Boer from the University Medical Center Groningen in the Netherlands was the presenter. This one focused on using adaptive sampling for genome sequencing and diagnostics. de Boer spoke about the challenges of sequencing regions of the human genome with short reads. The team designed a panel of genes associated with neurological and epileptic diseases, genes carrying repeats, pseudogenes, and genes affected by methylation. In total, 471 genes were targeted! The team used the Short Read Eliminator and Covaris fragmentation. The team used the Ligation Sequencing Kit (LSK) v14. With an optimized sample, the team had about 18 Gbases and covered all the genes in their panel. The pilot study tested fifteen samples with Fragile X and other diseases. The team developed a pipeline for pre-processing and variant calling, as well as cataloging variants. The pipeline is called Molgenis VIP. The pilot study results indicated that variants were identified, but in some cases, expansion numbers were different than those determined with current methods. Methylation helped identify pathogenicity, according to the presenter. I was impressed by the coverage of targets and the throughput the team obtained! This emphasized the importance of short-read elimination and starting with more input.
