Clinically Responsive Genomic Analysis Pipelines
| Autor: | Sarah Lang, Anna E. Richards, Lisa Ewans, David Mowat, Janice M. Fletcher, Maie Walsh, Michael Buckley, Cheng-Yee Nixon, Corrina Cliffe, Arthavan Selvanathan, Ying Zhu, Guus M. Teunisse, Carey-Anne Evans, Michelle A. Farrar, Edwin P. Kirk, Meredith Wilson, Rani Sachdev, Nila Quayum, Sarah A. Sandaradura, Rebecca Walsh, Deborah Schofield, Tony Roscioli, Kerith-Rae Dias, Shuxiang Goh, Marina Berbic, George Elakis, Suzanna E. L. Temple, Samantha Leigh Sundercombe |
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| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Massive parallel sequencing Computer science Computational biology Genome Pipeline (software) Pathology and Forensic Medicine Pipeline transport 03 medical and health sciences Consistency (database systems) symbols.namesake ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology 0302 clinical medicine 030220 oncology & carcinogenesis Mendelian inheritance symbols Molecular Medicine Gene Symbol Exome |
| Zdroj: | The Journal of Molecular Diagnostics. 23:894-905 |
| ISSN: | 1525-1578 |
| Popis: | Massively parallel sequencing has markedly improved mendelian diagnostic rates. This study assessed the effects of custom alterations to a diagnostic genomic bioinformatic pipeline in response to clinical need and derived practice recommendations relative to diagnostic rates and efficiency. The Genomic Annotation and Interpretation Application (GAIA) bioinformatics pipeline was designed to detect panel, exome, and genome sample integrity and prioritize gene variants in mendelian disorders. Reanalysis of selected negative cases was performed after improvements to the pipeline. GAIA improvements and their effect on sensitivity are described, including addition of a PubMed search for gene-disease associations not in the Online Mendelian Inheritance of Man database, inclusion of a process for calling low-quality variants (known as QPatch), and gene symbol nomenclature consistency checking. The new pipeline increased the diagnostic rate and reduced staff costs, resulting in a saving of US$844.34 per additional diagnosis. Recommendations for genomic analysis pipeline requirements are summarized. Clinically responsive bioinformatics pipeline improvements increase diagnostic sensitivity and increase cost-effectiveness. |
| Databáze: | OpenAIRE |
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