Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms.
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...
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2021
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oai:doaj.org-article:3173f9b171914b53b197c507cbe2a6722021-12-02T20:06:29ZArchival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms.1932-620310.1371/journal.pone.0255257https://doaj.org/article/3173f9b171914b53b197c507cbe2a6722021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0255257https://doaj.org/toc/1932-6203Gene 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.Daichi SadatoChizuko HiramaAi Kaiho-SomaAyaka YamaguchiHiroko KogureSonomi TakakuwaMina OgawaNoriko DokiKazuteru OhashiHironori HaradaKeisuke ObokiYuka HaradaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0255257 (2021) |
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Medicine R Science Q |
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Medicine R Science Q Daichi Sadato Chizuko Hirama Ai Kaiho-Soma Ayaka Yamaguchi Hiroko Kogure Sonomi Takakuwa Mina Ogawa Noriko Doki Kazuteru Ohashi Hironori Harada Keisuke Oboki Yuka Harada Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. |
| description |
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. |
| format |
article |
| author |
Daichi Sadato Chizuko Hirama Ai Kaiho-Soma Ayaka Yamaguchi Hiroko Kogure Sonomi Takakuwa Mina Ogawa Noriko Doki Kazuteru Ohashi Hironori Harada Keisuke Oboki Yuka Harada |
| author_facet |
Daichi Sadato Chizuko Hirama Ai Kaiho-Soma Ayaka Yamaguchi Hiroko Kogure Sonomi Takakuwa Mina Ogawa Noriko Doki Kazuteru Ohashi Hironori Harada Keisuke Oboki Yuka Harada |
| author_sort |
Daichi Sadato |
| title |
Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. |
| title_short |
Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. |
| title_full |
Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. |
| title_fullStr |
Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. |
| title_full_unstemmed |
Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. |
| title_sort |
archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/3173f9b171914b53b197c507cbe2a672 |
| work_keys_str_mv |
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