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Deep targeted sequencing of cytological tumor cells using whole genome amplification.
Amemiya, Kenji; Hirotsu, Yosuke; Mochizuki, Hitoshi; Higuchi, Rumi; Nakagomi, Takahiro; Goto, Taichiro; Oyama, Toshio; Kondo, Tetsuo; Omata, Masao.
Afiliación
  • Amemiya K; Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.
  • Hirotsu Y; Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.
  • Mochizuki H; Department of Pathology, School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan.
  • Higuchi R; Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.
  • Nakagomi T; Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.
  • Goto T; Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.
  • Oyama T; Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.
  • Kondo T; Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.
  • Omata M; Pathology Division, Laboratory Department, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan.
Cancer Cytopathol ; 131(1): 58-68, 2023 01.
Article en En | MEDLINE | ID: mdl-36219530
BACKGROUND: Genomic profiling in lung cancer is essential for precision medicine. Cytological specimens provide an alternative to formalin-fixed paraffin-embedded (FFPE) samples for comprehensive genomic analysis. However, this approach remains challenging when a limited number of tumor cells are available. We applied whole genome amplification (WGA) to cytology specimens to overcome this limitation. METHODS: Using a lung cancer panel targeting 58 genes, we performed next-generation sequencing of whole genome-amplified DNA extracted from cytological specimens containing 10-20 tumor cells (cyto-WGA) and DNA from corresponding FFPE tumor tissue. We compared sequencing data from cyto-WGA and FFPE samples to examine the detection accuracy of copy number variations and oncogenic and drug-matched variants. RESULTS: The DNA quality and quantity from cyto-WGA were higher than those from FFPE samples (p < .0005 and p < .05, respectively). Sequencing metrics of cyto-WGA and FFPE tissues showed no difference in the number of mapped reads and mean coverage depth, but there were significant differences in the on-target rate (p < .05) and uniformity (p < .0005). Copy number variations in cyto-WGA samples (n = 211) were higher than in FFPE samples (n = 9) (p < .0001). Fourty nine oncogenic variants were detected in cyto-WGA and 39 in FFPE. Of these variants, 34 (63%) were present in both samples. In addition, all 16 drug-matched variants were detected in FFPE and cyto-WGA samples with 100% concordance. CONCLUSION: Cyto-WGA can be a feasible and alternative method to detect oncogenic and drug-matched variants.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Variaciones en el Número de Copia de ADN / Neoplasias Pulmonares Límite: Humans Idioma: En Revista: Cancer Cytopathol Año: 2023 Tipo del documento: Article País de afiliación: Japón Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Variaciones en el Número de Copia de ADN / Neoplasias Pulmonares Límite: Humans Idioma: En Revista: Cancer Cytopathol Año: 2023 Tipo del documento: Article País de afiliación: Japón Pais de publicación: Estados Unidos