Detection of actionable mutations in archived cytological bile specimens

Ohyama, Hiroshi; Hirotsu, Yosuke; Amemiya, Kenji; Oyama, Toshio; Iimuro, Yuji; Kojima, Yuichiro; Mikata, Rintaro; Mochizuki, Hitoshi; Kato, Naoya; Omata, Masao

doi:10.1002/jhbp.994

Cited by 8 publications

(11 citation statements)

References 34 publications

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“…Ascites fluid was collected at the same time as the surgically resected specimens. The preparation of DNA from cytology specimens was done as previously described 9 . Briefly, a glass slide was soaked in xylene for 1 to 7 days, then the coverglass was removed.…”

Section: Methodsmentioning

confidence: 99%

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Molecular analysis of ascitic fluid cytology reflects genetic changes of malignancies of the ovary equivalent to surgically resected specimens

Nozaki

Sakamoto

Kagami

et al. 2022

Cancer Cytopathology

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BACKGROUND The objective of this study was to identify the clinical utility of genomic analysis of ascitic fluid cytology (AC) in patients with epithelial ovarian cancer. METHODS Targeted next‐generation sequencing was used to analyze 66 samples from 33 patients who had ovarian (n = 23), fallopian tube (n = 2), and peritoneal (n = 8) carcinoma, and the concordance rate of molecular profiles was compared between surgically resected, formalin‐fixed, paraffin‐embedded (FFPE) tissues and AC samples. RESULTS In total, 159 mutations were identified (54 oncogenic mutations and 105 nononcogenic mutations) in 66 DNA samples (33 FFPE tissues and 33 AC samples) from 33 patients. Of the 159 mutations, 57 (35.8%) were shared between surgically resected FFPE tissues and AC samples. However, the concordance rate of the molecular profiles between the 2 was significantly higher for oncogenic mutations compared with nononcogenic mutations (85.1% vs 10.5%; P < .01). Indeed, the AC samples covered all oncogenic mutations (n = 46) that were detected in surgically resected specimens and identified additional mutations (n = 8). CONCLUSIONS The current results indicated that genomic analysis of AC can identify all of the genetic changes associated with epithelial ovarian cancer to understand tumor characteristics without interventional surgery or biopsy and may play an important role in developing personalized precision medicine.

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Section: Methodsmentioning

confidence: 99%

“…The preparation of DNA from cytology specimens was done as previously described. 9 Briefly, a glass slide was soaked in xylene for 1 to 7 days, then the coverglass was removed. The tumor-rich clusters were peeled off from the glass slides with a razor blade and processed (Fig.…”

Section: Preparation Of Formalin-fixed Paraffin-embedded Tissues and ...mentioning

confidence: 99%

Molecular analysis of ascitic fluid cytology reflects genetic changes of malignancies of the ovary equivalent to surgically resected specimens

Nozaki

Sakamoto

Kagami

et al. 2022

Cancer Cytopathology

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“…FFPE tumor tissue was microdissected by LCM using Arcturus CapSure Macro LCM Caps (Thermo Fisher Scientific) on an Arcturus XT system (Thermo Fisher Scientific). FFPE DNA was extracted using the GeneRead DNA FFPE Kit (Qiagen) according to the manufacturer's instructions 31 …”

Section: Methodsmentioning

confidence: 99%

“…FFPE DNA was extracted using the GeneRead DNA FFPE Kit (Qiagen) according to the manufacturer's instructions. 31…”

Section: Extraction Of Ffpe Dnamentioning

confidence: 99%

Deep targeted sequencing of cytological tumor cells using whole genome amplification

Amemiya

Hirotsu

Mochizuki

et al. 2022

Cancer Cytopathology

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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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“…Han et al 49 reported bile-derived miR-30d-5p and miR-92a-3p as biomarkers for CCA; however, 81.1% SN and 60.5% SP were insufficient due to the diversity of mutations in biliary genes. A study by Ohyama et al 50 suggested that genomic profiling of archived bile cytological specimens with NGS-based targeted sequencing could discriminate between malignant and benign disorders with 93% accuracy, 91% SN, and 100% SP, including six cases (6/44 = 13.6%) with stage I BTC using a 60-gene panel. All six patients had ≥1 gene mutations (KRAS 1/6; TP53, 3/6; ERBB2, 2/6; ERBB3, 2/6; and SMAD4, 3/6 cases).…”

Section: Genomicsmentioning

confidence: 99%

Pathological and molecular diagnoses of early cancer with bile and pancreatic juice

Kuwatani

Sakamoto

2022

Digestive Endoscopy

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The dismal prognosis of pancreaticobiliary malignancies is mainly attributed to the extremely difficult detection of earlystage lesions, including intraepithelial neoplasia. To improve prognosis, several studies on the early detection of cancer have been conducted using bile and pancreatic juices for pathological or molecular analyses. One approach is liquid biopsy that includes information about the tumor, such as circulating tumor cells, circulating tumor DNA, microRNAs, and exosomes released by the tumor. Another approach is proteomics/metabolomics that reflects specific conditions in the tumor. These two approaches lead to artificial intelligencebased multiomics analyses that comprises genomics, proteomics/metabolomics, and transcriptomics. Based on the findings of molecular analysis, pathological analysis using immunohistochemical staining/fluorescence in situ hybridization has also been developed. Moreover, there have been reports of new methods/ingenuities for obtaining appropriate samples for the diagnosis of early-stage cancer. Here we review the knowledge on cutting-edge pathological and molecular analyses of bile and pancreatic juices, introduce some ingenuities in sampling and sample processing to promote effective clinical practice, and provide a basis for future studies.

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Detection of actionable mutations in archived cytological bile specimens

Cited by 8 publications

References 34 publications

Molecular analysis of ascitic fluid cytology reflects genetic changes of malignancies of the ovary equivalent to surgically resected specimens

Molecular analysis of ascitic fluid cytology reflects genetic changes of malignancies of the ovary equivalent to surgically resected specimens

Deep targeted sequencing of cytological tumor cells using whole genome amplification

Pathological and molecular diagnoses of early cancer with bile and pancreatic juice

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