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Cancer researchers routinely use High Throughput Sequencing (HTS), but its uptake into the clinical environment has been slow, mainly because of sequencing costs and the complexity of data analysis. The former issue is being addressed by rapid technology improvements in HTS equipment but data complexity and problems associated with data analysis remain a serious impediment to the wider use of genomics in clinical pathology.
The Peter MacCallum Cancer Centre is the largest cancer hospital in Australia and has implemented HTS services as a routine assay for tumour and germline samples. To resolve the clinical sequencing analysis bottleneck we have developed PathOS, a web application that streamlines the clinical curation of HTS generated cancer variants. The integration of all aspects of the molecular pathology pipeline from sequencer through to clinical report facilitates a ‘curation workbench’ to structure workflows needed for managing HTS data. PathOS is now implemented as the internal curation system for the hospital’s Molecular Pathology laboratory. The lab performs routine sequencing analysis of blood and tumour samples from both in-patient and external customers using Illumina HiSeq and MiSeq instruments. Raw sequence data is automatically processed by an in-house developed bioinformatics pipeline to identify variants. Raw variants are loaded into the system where they are normalised, filtered and matched with previously curated variants and external databases. Stringent filtering is applied to raw variants based on the assay method. The system allows filters to be described in a flexible domain specific language (DSL) by the scientist creating the HTS assay. The sequencing QC data for runs, samples and variants are stored, and displayed as interactive charts. Integration of the IGV browser through
a web server allows the user to directly visualise reads giving rise to a variant. Designed with accreditation for clinical testing in mind, a full audit trail of source data and external evidence used to classify variants allows the pedigree of any clinical data to be ascertained. After curation, variants can be exported to a file to support external curation systems such as LOVD. PathOS generates clinical reports as PDF or Word documents using MS-Word templates giving the reporting scientist maximum presentation flexibility. Reclassification of previously reported variants causes PathOS to flag reports that need to be amended.
To validate PathOS, the Cancer 2015 study was used: a large-scale, prospective, longitudinal, multi-site cohort study of cancer in the Victorian population. As at January 2014, 769 patients were sampled and generated 141,657 unfiltered variants. PathOS has provided the pipeline framework, repository and curation for this data. Of these variants 1,618 were automatically flagged as inferred deleterious mutations.