Characterization of structural variations and chromothripsis in nanopore sequencing data of human genomes
Wigard Kloosterman, Center for Molecular Medicine, UMC Utrecht, gives a plenary talk at Nanopore Community Meeting 2016.
Large capital investments are needed for second-generation sequencing equipment, which has led to the concentration of human genome sequencing efforts in specialized sequencing centers. We demonstrate feasibility to sequence the entire genome of a patient with congenital abnormalities using the MinION sequencer. By combining data from R7 and R9 sequencing chemistries, we reached 14x mean coverage of the genome. We developed a novel bioinformatic pipeline — nanoSV — to efficiently map genomic structural variants (SVs) from the nanopore data. We systematically compared SVs identified from nanopore data with those detected from Illumina short-read sequencing. We show that nanopore reads enable efficient phasing of genetic variations and we used this feature to reconstruct the long-range structure of chromothripsis rearrangements in the patient’s genome. The valuable data output combined with the small-size and low-cost investment makes nanopore sequencing a prominent platform for human genome sequencing in future life sciences research and diagnostics.