Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms
| Autor: | Ai Kaiho-Soma, Chizuko Hirama, Hironori Harada, Daichi Sadato, Mina Ogawa, Noriko Doki, Kazuteru Ohashi, Keisuke Oboki, Sonomi Takakuwa, Hiroko Kogure, Yuka Harada, Ayaka Yamaguchi |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Myeloid Molecular biology Biopsy Gene Identification and Analysis Gene mutation Biochemistry Hematologic Cancers and Related Disorders chemistry.chemical_compound Sequencing techniques 0302 clinical medicine Gene Frequency Animal Cells Bone Marrow Nucleic Acids Fusion Genes Medicine and Health Sciences DNA sequencing Leukemia Multidisciplinary High-Throughput Nucleotide Sequencing RNA sequencing Hematology Genomics Myeloid Leukemia medicine.anatomical_structure Oncology Leukemia Myeloid 030220 oncology & carcinogenesis Medicine Tissue Preservation Cellular Types Transcriptome Analysis Research Article Acute Myeloid Leukemia Next-Generation Sequencing Science Bone Marrow Cells Biology Sensitivity and Specificity 03 medical and health sciences Gene Types Diagnostic Medicine Genetics Cancer Detection and Diagnosis medicine Humans Genetic Testing Mutation Detection Gene Allele frequency Biology and life sciences Cancers and Neoplasms Computational Biology RNA DNA Cell Biology Genome Analysis Research and analysis methods Molecular biology techniques 030104 developmental biology chemistry Mutation Cancer research Bone marrow |
| Zdroj: | PLoS ONE, Vol 16, Iss 7, p e0255257 (2021) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | Gene abnormalities, including mutations and fusions, are important determinants in the molecular diagnosis of myeloid neoplasms. The use of bone marrow (BM) smears as a source of DNA and RNA for next-generation sequencing (NGS) enables molecular diagnosis to be done with small amounts of bone marrow and is especially useful for patients without stocked cells, DNA or RNA. The present study aimed to analyze the quality of DNA and RNA derived from smear samples and the utility of NGS for diagnosing myeloid neoplasms. Targeted DNA sequencing using paired BM cells and smears yielded sequencing data of adequate quality for variant calling. The detected variants were analyzed using the bioinformatics approach to detect mutations reliably and increase sensitivity. Noise deriving from variants with extremely low variant allele frequency (VAF) was detected in smear sample data and removed by filtering. Consequently, various driver gene mutations were detected across a wide range of allele frequencies in patients with myeloid neoplasms. Moreover, targeted RNA sequencing successfully detected fusion genes using smear-derived, very low-quality RNA, even in a patient with a normal karyotype. These findings demonstrated that smear samples can be used for clinical molecular diagnosis with adequate noise-reduction methods even if the DNA and RNA quality is inferior. |
| Databáze: | OpenAIRE |
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