Evaluation of whole genome sequencing utility in identifying driver alterations in cancer genome
In cancer genome analysis, identifying pathogenic alterations and assessing their effects on oncogenic processes is important. Although whole exome sequencing (WES) can effectively detect such changes, driver alterations could not be identified in 27.8% of the cases, according to a previous study. The objectives of the present study were to evaluate the utility of whole genome sequencing (WGS) and clarify its differences with WES in terms of driver alteration detection. For this purpose, WGS analysis was conducted on 177 driverless WES samples, selected from 5,480 fresh frozen samples derived from 5,140 Japanese patients with cancer. These samples were selected as primary tumor, both WES and transcriptome profiling were performed, estimated tumor content of ≥ 30%, and no driver alterations were identified by WES. WGS identified driver and likely driver alterations in 68.4 and 22.6% of the samples, respectively. The most frequent alteration type was oncogene amplification, followed by tumor suppressor gene deletion and small variants located outside the coding region. In the remaining 9.0% of samples, no such signals were identified; therefore, further investigations are required. The current study clearly demonstrated the role and utility of WGS in identifying genomic alterations that contribute to tumorigenesis.
Authors
- Takashi Mukaigawa (ORCID: https://orcid.org/0000-0001-9804-7154)
- Yasuyuki Hirashima (ORCID: https://orcid.org/0000-0003-0269-9313)
- Hirohisa Katagiri
- Sumiko Ohnami (ORCID: https://orcid.org/0000-0002-5776-8104)
- Yuji Shimoda (ORCID: https://orcid.org/0009-0002-5613-0886)
- Kenichi Urakami (ORCID: https://orcid.org/0000-0002-4751-0978)
- Yasuhisa Ohde (ORCID: https://orcid.org/0000-0002-1664-2628)
- Katsuhiko Uesaka
- Hirotsugu Kenmotsu (ORCID: https://orcid.org/0000-0003-0590-9259)
- Koichi Mitsuya (ORCID: https://orcid.org/0000-0001-8956-5427)
- Masanori Terashima (ORCID: https://orcid.org/0000-0002-2967-8267)
- Etsuro Bando (ORCID: https://orcid.org/0000-0002-3072-4910)
- Koji Maruyama (ORCID: https://orcid.org/0000-0003-4830-1323)
- Akane Naruoka (ORCID: https://orcid.org/0000-0002-6401-0318)
- Yoshio Kiyohara (ORCID: https://orcid.org/0000-0001-7335-4617)
- Fukumi Kamada
- Teiichi Sugiura (ORCID: https://orcid.org/0000-0001-7163-4084)
- Yuji Ishida (ORCID: https://orcid.org/0000-0003-1855-6325)
- Yoshichika Yasunaga (ORCID: https://orcid.org/0000-0002-4858-6739)
- Maki Mizuguchi
- Akio Shiomi (ORCID: https://orcid.org/0000-0001-5657-8686)
- Masashi Niwakawa
- Takashi Sugino (ORCID: https://orcid.org/0000-0002-0205-0525)
- Takeshi Nagashima (ORCID: https://orcid.org/0000-0002-7261-9908)
- Keiichi Hatakeyama (ORCID: https://orcid.org/0000-0001-6000-5899)
- Tomoe TANABE
- Masakuni Serizawa (ORCID: https://orcid.org/0009-0009-6383-8402)
- Yasuto Akiyama (ORCID: https://orcid.org/0000-0003-3813-7726)
- Ken Yamaguchi (ORCID: https://orcid.org/0000-0002-9893-7218)
- Keiichi Ohshima (ORCID: https://orcid.org/0000-0002-2882-7566)
- Yasuhiro Tsubosa
- Shumpei Ohnami (ORCID: https://orcid.org/0000-0001-7840-3537)
- Seiichiro Nishimura
- Tohru Mochizuki
- Mitsuru Takahashi
- Hiroya Kashiwagi
- Shusuke Yoshikawa (ORCID: https://orcid.org/0009-0002-6082-4696)
- Kaoru Takahashi
Institutions
- Shizuoka Cancer Center (JP)
- SRL (Japan) (JP)
Publication Details
- Journal
- Scientific Reports
- Published
- 2024-10-12
- DOI
- https://doi.org/10.1038/s41598-024-74272-0
- Citations
- 4
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 1.14