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Research: Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
- Akihiro Fujimoto,
- Masashi Fujita,
- Takanori Hasegawa,
- Jing Hao Wong,
- Kazuhiro Maejima,
- Aya Oku-Sasaki,
- Kaoru Nakano,
- Yuichi Shiraishi,
- Satoru Miyano,
- Go Yamamoto,
- Kiwamu Akagi,
- Seiya Imoto,
- and Hidewaki Nakagawa
Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
...mutations and present many mutation-associated neoantigens, which might be recognized by the immune system. Currently, MSI can also be used as a marker to predict the effect of immune therapy (Le et al. 2017). The MSI phenotype is most common in colorectal (CR) cancers, stomach (ST) cancers, and uterine (UT...
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Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...induction in hGOiA3A and TP53KO-hGOiA3A lines.Further, in line with previous reports from cancer (DeWeerd et al. 2022), indels attributable to the COSMIC ID9 signature (Sondka et al. 2024) showed a suggestive positive correlation with the number of A3A-associated base substitutions in hGOiA3A clones, one...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...in the three cancer cell lines (Fig. 2C; Supplemental Fig. S3E,F; Harris et al. 2009; Wylie et al. 2016; Tiwari et al. 2020; McDonald et al. 2021; Zhou et al. 2021). Chromatin accessibility at the promoter regions of DETs was positively correlated with their expression in both control and doxorubicin...
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