Search

Background: Fusion genes are important biomarkers in cancer research because their expression can produce abnormal proteins with oncogenic properties. Long-read RNA sequencing (long-read RNA-seq), which can sequence full-length mRNA transcripts, facilitates the detection of such fusion genes. Several tools have been proposed for detecting fusion genes in long-read RNA-seq datasets derived from cancer cells. However, the high sequencing error rate in long-read RNA-seq makes fusion gene detection challenging. Methods: To address this issue, additional steps were incorporated into the fusion detection tool to improve detection accuracy. These steps include anchoring breakpoints to exon boundaries, realigning unaligned regions, and clustering breakpoints. To evaluate the accuracy of our tool in detecting fusion genes, we compared its detection accuracy with two representative existing tools, JAFFAL and FusionSeeker. Results: Our tool outperformed the two existing tools in detecting fusion genes, as demonstrated in long-read RNA-seq datasets. We also identified potentially novel fusion genes consistently detected across multiple tools or datasets. Conclusions: The application of our tool to the detection of fusion genes in long-read RNA-seq datasets from two different cancer cell lines demonstrated the detection effectiveness of this tool.

Abstract Background Since humoral hypercalcemia of malignancy (HHM) in breast cancer patients without bone metastasis is rare, the clinical features of this condition are not fully understood. Case presentation During the recent 12 years, 3602 patients were diagnosed with breast cancer in our institution, and only three patients developed HHM without bone metastasis. They were all recurrent breast cancer patients with visceral metastases including the lung and the liver. It took no more than 2 months since symptomatic onset to hospitalization because of hypercalcemia. The maximum serum calcium concentrations were 15.0 mg/dL or higher. All patients had symptoms related to hypercalcemia. Treatment of hypercalcemia including hydration, calcitonin, bisphosphonate, and diuretics was initially effective in the three patients. However, two of three cases were eventually fatal because of unsuccessful treatment of breast cancer. Conclusions The common features of HHM without bone metastasis in breast cancer patients include acute onset, severe symptomatic hypercalcemia, and presence of visceral metastasis. Treatment of hypercalcemia decreased serum calcium level in a short period, while successful treatment of breast cancer was essential for a long-term management of HHM. This report provides a consideration to help elucidate the pathophysiology and medical care of breast cancer patients with HHM without bone metastasis.

The restriction enzyme-based digital methylation-specific polymerase chain reaction (RE-dMSP) assay is useful for diagnosing sentinel lymph node (SN) metastasis in patients with breast cancer, by detecting tumor-derived methylated Ras association domain-containing protein 1 (RASSF1A). In addition, this assay has high concordance (95.0%) with one-step nucleic acid amplification (OSNA). The present study aimed to perform RE-dMSP using OSNA lysate from more patients and to re-evaluate its clinical usage. Overall, 418 SNs from 347 patients were evaluated using both OSNA and RE-dMSP. The concordance rate was 83.3% (348/418). RASSF1A methylation of the primary tumors was negative in 36 patients. When these patients were excluded, the concordance rate improved to 88.2% (330/374). Of the 79 OSNA-negative cases, 19 were RE-dMSP-positive, although all were positive for cytokeratin 19 expression in the primary tumor, suggesting that RE-dMSP can detect tumor-derived DNA with a higher sensitivity. The percent of methylated reference of the breast tumors showed a wide variety in the 16 OSNA-positive/RE-dMSP-negative cases, and such variability of methylation could have affected the results in these patients. In conclusion, although RE-dMSP can diagnose SN metastasis with high sensitivity and accuracy, and can be a supplementary tool to OSNA in breast cancer, RE-dMSP showed certain discordance with OSNA and critically depended on the absence or heterogeneity of DNA methylation in breast tumors. Further research is expected to develop an assay targeting other DNA alterations, such as mutations. [ABSTRACT FROM AUTHOR]