CAN-Scan: A multi-omic phenotype-driven precision oncology platform identifies prognostic biomarkers of therapy response for colorectal cancer

Authors: Chia, Shumei ^{1, ∗}, Wen Seow, Justine Jia ¹, Peres da Silva, Rafael ¹, Suphavilai, Chayaporn ¹, Shirgaonkar, Niranjan ¹, Murata-Hori, Maki ¹, Zhang, Xiaoqian ¹, Yong, Elena Yaqing ¹, Pan, Jiajia ², Thangavelu, Matan Thangavelu ^{1, 3}, Periyasamy, Giridharan ^{1, 3}, Yap, Aixin ¹, Anand, Padmaja ¹, Muliaditan, Daniel ¹, Chan, Yun Shen ^{1, 4}, Siyu, Wang ¹, Yong, Chua Wei ¹, Hong, Nguyen ¹, Ran, Gao ¹, Sim, Ngak Leng ¹, Guo, Yu Amanda ¹, Yi Teh, Andrea Xin ², Wei Ling, Clarinda Chua ², Wei Tan, Emile Kwong ⁵, Pei Cherylin, Fu Wan ⁵, Chang, Meihuan ⁵, Han, Shuting ², Seow-En, Isaac ⁵, Chen Hui, Lionel Raphael ⁵, Hsia Gan, Anna Hwee ¹, Yap, Choon Kong ¹, Ng, Huck Hui ^{1, 11}, Skanderup, Anders Jacobsen ¹, Chinswangwatanakul, Vitoon ^{6, 7}, Riansuwan, Woramin ⁶, Trakarnsanga, Atthaphorn ⁶, Pithukpakorn, Manop ^{8, 9}, Tanjak, Pariyada ^{6, 7}, Chaiboonchoe, Amphun ¹⁰, Park, Daye ¹⁶, Kim, Dong Keon ¹⁶, Iyer, Narayanan Gopalakrishna ², Tsantoulis, Petros ¹², Tejpar, Sabine ¹³, Kim, Jung Eun ¹⁵, Kim, Tae Il ^{15, 16}, Sampattavanich, Somponnat ¹⁰, Tan, Iain Beehuat ^{1, 2, 14, ∗∗}, Nagarajan, Niranjan ^{1, 11, ∗∗∗}, DasGupta, Ramanuj ^{1, 17, 18, ∗∗∗∗}

Source: In Cell Reports Medicine 15 April 2025 6(4)

A multimodal atlas of hepatocellular carcinoma reveals convergent evolutionary paths and ‘bad apple’ effect on clinical trajectory

Authors: Chen, Jianbin, Kaya, Neslihan Arife, Zhang, Ying, Kendarsari, Raden Indah, Sekar, Karthik, Lee Chong, Shay, Seshachalam, Veerabrahma Pratap, Ling, Wen Huan, Jin Phua, Cheryl Zi, Lai, Hannah, Yang, Hechuan, Lu, Bingxin, Lim, Jia Qi, Ma, Siming, Chew, Sin Chi, Chua, Khi Pin, Santiago Alvarez, Jacob Josiah, Wu, Lingyan, Ooi, London, Yaw-Fui Chung, Alexander, Cheow, Peng Chung, Kam, Juinn Huar, Wei-Chieh Kow, Alfred, Ganpathi, Iyer Shridhar, Bunchaliew, Chairat, Thammasiri, Jidapa, Koh, Peng Soon, Bee-Lan Ong, Diana, Lim, Jasmine, de Villa, Vanessa H., Dela Cruz, Rouchelle D., Loh, Tracy Jiezhen, Wan, Wei Keat, Leow, Wei Qiang, Yang, Yi, Liu, Jin, Skanderup, Anders Jacobsen, Pang, Yin Huei, Ting Soon, Gwyneth Shook, Madhavan, Krishnakumar, Kiat-Hon Lim, Tony, Bonney, Glenn, Goh, Brian K.P., Chew, Valerie, Dan, Yock Young, Toh, Han Chong, Sik-Yin Foo, Roger, Tam, Wai Leong, Zhai, Weiwei, Kah-Hoe Chow, Pierce

Source: In Journal of Hepatology October 2024 81(4):667-678

PD-L1 score as a prognostic biomarker in asian early-stage epidermal growth factor receptor-mutated lung cancer

Authors: Saw, Stephanie P.L., Ng, Win Pin, Zhou, Siqin, Lai, Gillianne G.Y., Tan, Aaron C., Ang, Mei-Kim, Lim, Wan-Teck, Kanesvaran, Ravindran, Ng, Quan Sing, Jain, Amit, Tan, Wan Ling, Rajasekaran, Tanujaa, Chan, Johan W.K., Teh, Yi Lin, Pang, Mengyuan, Yeo, Jia-Chi, Takano, Angela, Ong, Boon-Hean, Tan, Eng-Huat, Tan, Sze Huey, Skanderup, Anders J., Tan, Daniel S.W.

Source: European journal of cancer. 178:139-149

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100177957903.0x000001&indx=1&recIds=ETOCvdc_100177957903.0x000001

A Randomized Phase 2 Trial of Nivolumab Versus Nivolumab-Ipilimumab Combination in EGFR-Mutant NSCLC

Authors: Lai, Gillianne G.Y., Yeo, Jia Chi, Jain, Amit, Zhou, Siqin, Pang, Mengyuan, Alvarez, Jacob J.S., Sim, Ngak Leng, Tan, Aaron C., Suteja, Lisda, Lim, Tze Wei, Guo, Yu Amanda, Shen, Meixin, Saw, Stephanie P.L., Rohatgi, Neha, Yeong, Joe P.S., Takano, Angela, Lim, Kiat Hon, Gogna, Apoorva, Too, Chow Wei, Da Zhuang, Kun, Tan, Wan Ling, Kanesvaran, Ravindran, Ng, Quan Sing, Ang, Mei Kim, Rajasekaran, Tanujaa, Wang, Lanying, Toh, Chee Keong, Lim, Wan-Teck, Tam, Wai Leong, Tan, Sze Huey, Skanderup, Anders M.J., Tan, Eng-Huat, Tan, Daniel S.W.

Source: In JTO Clinical and Research Reports December 2022 3(12)

A pan-cancer metabolic atlas of the tumor microenvironment

Authors: Rohatgi, Neha, Ghoshdastider, Umesh, Baruah, Probhonjon, Kulshrestha, Tanmay, Skanderup, Anders Jacobsen

Source: In Cell Reports 10 May 2022 39(6)

Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study

Authors: Oner, Mustafa Umit, Chen, Jianbin, Revkov, Egor, James, Anne, Heng, Seow Ye, Kaya, Arife Neslihan, Alvarez, Jacob Josiah Santiago, Takano, Angela, Cheng, Xin Min, Lim, Tony Kiat Hon, Tan, Daniel Shao Weng, Zhai, Weiwei, Skanderup, Anders Jacobsen, Sung, Wing-Kin, Lee, Hwee Kuan

Source: In Patterns 11 February 2022 3(2)

A phase 1b study of OXIRI in pancreatic adenocarcinoma patients and its immunomodulatory effects

Authors: Ng, Matthew, Chen, Sylvia, Ong, Whee Sze, Balachander, Akhila, Seet, Amanda, Yeong, Joe, Sutiman, Natalia, Lim, Tony Kiat Hon, Lee, Bernett, Guo, Yu Amanda, Leong, Wai Fook, Lee, Sze Sing, Lam, Justina, Choo, Su Pin, Skanderup, Anders Jacobsen, Biswas, Subhra Kumar, Tai, David, Chowbay, Balram

Source: International journal of cancer. 151(3):435-449

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100153796755.0x000001&indx=1&recIds=ETOCvdc_100153796755.0x000001

Accurate Ensemble Prediction of Somatic Mutations with SMuRF2

Authors: Huang, Weitai, Sim, Ngak Leng, Skanderup, Anders J.

Source: Methods in molecular biology. 2493:53-66

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN629742487&indx=1&recIds=ETOCRN629742487

A chemical genetic screen identifies Aurora kinases as a therapeutic target in EGFR T790M negative, gefitinib-resistant head and neck squamous cell carcinoma (HNSCC)

Authors: Low, Joo-Leng, Lau, Dawn Pingxi, Zhang, Xiaoqian, Kwang, Xue-Lin, Rohatgi, Neha, Chan, Jane Vin, Chong, Fui-Teen, Wong, Stephen Qi Rong, Leong, Hui-Sun, Thangavelu, Matan Thangavelu, Rikka, Shivaji, Skanderup, Anders Martin Jacobsen, Tan, Daniel Shao Weng, Periyasamy, Giridharan, Koh, Judice Lie Yong, Iyer, N Gopalakrishna, DasGupta, Ramanuj

Source: In EBioMedicine February 2021 64

Ensemble-Based Somatic Mutation Calling in Cancer Genomes

Authors: Huang, Weitai, Guo, Yu Amanda, Chang, Mei Mei, Skanderup, Anders Jacobsen

Source: Methods in molecular biology. 2120:37-46

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN623489405&indx=1&recIds=ETOCRN623489405

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

Authors: Vedanayagam, Jeffrey, Chatila, Walid, Aksoy, Bülent, Majumdar, Sonali, Skanderup, Anders, Demir, Emek, Schultz, Nikolaus, Sander, Chris, Lai, Eric

Source: Nature communications. 10(1):1-14

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100189848913.0x000001&indx=1&recIds=ETOCvdc_100189848913.0x000001

ΔNp63 Inhibits Oxidative Stress-Induced Cell Death, Including Ferroptosis, and Cooperates with the BCL-2 Family to Promote Clonogenic Survival

Authors: Wang, Gary X., Tu, Ho-Chou, Dong, Yiyu, Skanderup, Anders Jacobsen, Wang, Yufeng, Takeda, Shugaku, Ganesan, Yogesh Tengarai, Han, Song, Liu, Han, Hsieh, James J., Cheng, Emily H.

Source: In Cell Reports 5 December 2017 21(10):2926-2939

PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression.

Authors: Lee, Yi Fei, Phua, Cheryl Zi Jin, Yuan, Ju, Zhang, Bin, Lee, May Yin, Kannan, Srinivasaraghavan, Chiu, Yui Hei Jasper, Koh, Casslynn Wei Qian, Yap, Choon Kong, Lim, Edwin Kok Hao, Chen, Jianbin, Lim, Yuhua, Lee, Jane Jia Hui, Skanderup, Anders Jacobsen, Wang, Zhenxun, Zhai, Weiwei, Tan, Nguan Soon, Verma, Chandra S., Tay, Yvonne, Tan, Daniel Shao Weng

Source: Genome Medicine; 7/22/2024, Vol. 16 Issue 1, p1-21, 21p

Subject Terms: LUNG cancer, RNA splicing, CANCER invasiveness, CANCER genes, NON-small-cell lung carcinoma, CELL lines

Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

Authors: Guo, Yu, Chang, Mei, Huang, Weitai, Ooi, Wen, Xing, Manjie, Tan, Patrick, Skanderup, Anders

Source: Nature communications. 9(1):1-14

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132430842.0x000001&indx=1&recIds=ETOCvdc_100132430842.0x000001

Brief Report: Droplet Digital Polymerase Chain Reaction Versus Plasma Next-Generation Sequencing in Detecting Clearance of Plasma EGFR Mutations and Carcinoembryonic Antigen Levels as a Surrogate Measure

Authors: Saw, Stephanie P.L., Tan, Gek San, Tan, Wei Chong, Tan, Aaron C., Lai, Gillianne G.Y., Lim, Darren W.T., Kanesvaran, Ravindran, Tan, Wan Ling, Tan, Sze Huey, Lim, Kiat Hon, Skanderup, Anders J., Tan, Daniel S.W.

Source: In JTO Clinical and Research Reports December 2023 4(12)

MutSpot: detection of non-coding mutation hotspots in cancer genomes

Authors: Guo, Yu Amanda, Chang, Mei Mei, Skanderup, Anders Jacobsen

Source: Npj genomic medicine. 5(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174452901.0x000001&indx=1&recIds=ETOCvdc_100174452901.0x000001

Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

Authors: Razavi-Mohseni, Milad, Huang, Weitai, Guo, Yu A., Shigaki, Dustin, Ho, Shamaine Wei Ting, Tan, Patrick, Skanderup, Anders J., Beer, Michael A.

Source: Genome Research; 2024, Vol. 34 Issue: 5 p680-695, 16p

Landscape of germline pathogenic variants in patients with dual primary breast and lung cancer.

Authors: Lee, Ning-Yuan, Hum, Melissa, Zihara, Sabna, Wang, Lanying, Myint, Matthew K., Lim, Darren Wan-Teck, Toh, Chee-Keong, Skanderup, Anders, Samol, Jens, Tan, Min-Han, Ang, Peter, Lee, Soo-Chin, Tan, Eng-Huat, Lai, Gillianne G. Y., Tan, Daniel S. W., Yap, Yoon-Sim, Lee, Ann S. G.

Source: Human Genomics; 7/17/2023, Vol. 17 Issue 1, p1-15, 15p

PUREE: accurate pan-cancer tumor purity estimation from gene expression data.

Authors: Revkov, Egor, Kulshrestha, Tanmay, Sung, Ken Wing-Kin, Skanderup, Anders Jacobsen

Source: Communications Biology; 4/11/2023, Vol. 6 Issue 1, p1-10, 10p

Subject Terms: SUPERVISED learning, GENE expression, MACHINE learning, GENE expression profiling

Corrigendum to ‘A chemical genetic screen identifies Aurora kinases as a therapeutic target in EGFR T790M negative, gefitinib-resistant head and neck squamous cell carcinoma (HNSCC)’

Authors: Low, Joo-Leng, Lau, Dawn Pingxi, Zhang, Xiaoqian, Kwang, Xue-Lin, Rohatgi, Neha, Chan, Jane Vin, Chong, Fui-Teen, Wong, Stephen Qi Rong, Leong, Hui-Sun, Thangavelu, Matan Thangavelu, Rikka, Shivaji, Skanderup, Anders Martin Jacobsen, Tan, Daniel Shao Weng, Periyasamy, Giridharan, Koh, Judice Lie Yong, Iyer, N Gopalakrishna, DasGupta, Ramanuj

Source: In eBioMedicine April 2021 66