Identifying large indels in targeted next generation sequencing assays for myeloid neoplasms: a cautionary tale of the ZRSR1 pseudogene
| Autor: | Chin Hin Ng, Jia Jin Low, Christopher Ng, Isaac Ks Ng, Benedict Yan, Wee Joo Chng, Lily Chiu, Elaine Seah, Kenneth Hon Kim Ban |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Genetics medicine.medical_specialty Myeloid Molecular pathology Pseudogene General Medicine Biology DNA sequencing Pathology and Forensic Medicine 03 medical and health sciences 030104 developmental biology medicine.anatomical_structure Open source hemic and lymphatic diseases Molecular genetics medicine In patient Indel |
| Zdroj: | Journal of Clinical Pathology. 70:1069-1073 |
| ISSN: | 1472-4146 0021-9746 |
| Popis: | Targeted next generation sequencing platforms have been increasingly utilised for identification of novel mutations in myeloid neoplasms, such as acute myeloid leukaemia (AML), and hold great promise for use in routine clinical diagnostics. In this study, we evaluated the utility of an open source variant caller in detecting large indels in a targeted sequencing of AML samples. While we found that this bioinformatics pipeline has the potential to accurately capture large indels (>20 bp) in patient samples, we highlighted the pitfall of a confounding ZRSR1 pseudogene that led to an erroneous ZRSR2 variant call. We further discuss possible clinical implications of the ZRSR1 pseudogene in myeloid neoplasms based on its molecular features. Knowledge of the confounding ZRSR1 pseudogene in ZRSR2 sequencing assays could be particularly important in AML diagnostics because the detection of ZRSR2 in AML patients is highly specific for an s-AML diagnosis. |
| Databáze: | OpenAIRE |
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