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Updated: May 5, 2026
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
Exploratory analysis of the molecular and genomic landscape of upper tract urothelial carcinoma using long-read
Zhi Shang1,2,3, Xiuxin Ling4, Shengming Jin5,6,7
1Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China.
Background:
Upper tract urothelial carcinoma (UTUC), including renal pelvic urothelial carcinoma and ureter urothelial carcinoma, accounts for 10% of urothelial carcinoma (UC). Poorer outcomes and different genetic characteristics of UTUC were reported compared to urothelial carcinoma of the bladder (UCB), which accounts for most cases of UC. Therefore, there is an urgent need for the development of molecular characterization and precision therapies tailored specifically for UTUC.
Methods:
To elucidate the genetic landscape of UTUC, we included 4 UTUC samples in this study and also perform next-generation sequencing (NGS) of whole exome sequencing. After that, long-read sequencing (LRS) was employed to conduct Whole genome sequencing (WGS) analyses on tumor samples obtained from the four UTUC patients, utilizing the Pacific Biosciences (PacBio) REVIO platform.
Results:
The clinical phenotypes of four UTUC patients including tumor stage, location and response to treatment, etc. were collected. NGS of four patients yielded negative results. The WGS mapped the mutation landscape in the tumor tissues of four UTUC patients, and screened the sequencing results according to UTUC and solid tumor related genes. Seven pathogenic or likely pathogenic single nucleotide variant (SNV) were obtained. Among the detected structural variations (SVs), four patients shared multiple segments of SVs with close positions. The 12q24.31-p11.1 inversion was shared by four patients. In the detection of STR and DNA methylation, comparing the results of patients and normal controls, many different fragments were obtained. It shows that LRS has important advantages over NGS for accurate tumor detection and treatment.
Conclusion:
The analysis revealed multiple genetic variants potentially associated with UTUC carcinogenesis or development, and indicated advantages of TGS over next-generation sequencing (NGS) in cancer genetic variant detection, especially in SV and Short Tandem Repeats (STRs). This study may lay the groundwork for molecular classification and offer valuable insights into the development of precision therapies for UTUC.
