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1. SNP2Vec: Scalable Self-Supervised Pre-Training for Genome-Wide Association Study

Author

Cahyawijaya, Samuel, Yu, Tiezheng, Liu, Zihan, Mak, Tiffany T. W., Zhou, Xiaopu, Ip, Nancy Y., and Fung, Pascale

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence
Abstract

Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they focus only on understanding haploid sequences, which hinders their applicability towards understanding genetic variations, also known as single nucleotide polymorphisms (SNPs), which is crucial for genome-wide association study. In this paper, we introduce SNP2Vec, a scalable self-supervised pre-training approach for understanding SNP. We apply SNP2Vec to perform long-sequence genomics modeling, and we evaluate the effectiveness of our approach on predicting Alzheimer's disease risk in a Chinese cohort. Our approach significantly outperforms existing polygenic risk score methods and all other baselines, including the model that is trained entirely with haploid sequences. We release our code and dataset on https://github.com/HLTCHKUST/snp2vec.

Published
2022

5. Using blood transcriptome analysis for Alzheimer's disease diagnosis and patient stratification

Author

Zhong, Huan, Zhou, Xiaopu, Uhm, Hyebin, Jiang, Yuanbing, Cao, Han, Chen, Yu, Mak, Tiffany T. W., Lo, Ronnie Ming Nok, Wong, Bonnie Wing Yan, Cheng, Elaine Yee Ling, Mok, Kin Ying Boniface, Chan, Andrew Lung Tat, Kwok, Timothy C. Y., Mok, Vincent C. T., Ip, Fanny Chui Fun, Hardy, John, Fu, Amy Kit Yu, Ip, Nancy Yuk-yu, Zhong, Huan, Zhou, Xiaopu, Uhm, Hyebin, Jiang, Yuanbing, Cao, Han, Chen, Yu, Mak, Tiffany T. W., Lo, Ronnie Ming Nok, Wong, Bonnie Wing Yan, Cheng, Elaine Yee Ling, Mok, Kin Ying Boniface, Chan, Andrew Lung Tat, Kwok, Timothy C. Y., Mok, Vincent C. T., Ip, Fanny Chui Fun, Hardy, John, Fu, Amy Kit Yu, and Ip, Nancy Yuk-yu

Abstract

INTRODUCTION Blood protein biomarkers demonstrate potential for Alzheimer's disease (AD) diagnosis. Limited studies examine the molecular changes in AD blood cells. METHODS Bulk RNA-sequencing of blood cells was performed on AD patients of Chinese descent (n = 214 and 26 in the discovery and validation cohorts, respectively) with normal controls (n = 208 and 38 in the discovery and validation cohorts, respectively). Weighted gene co-expression network analysis (WGCNA) and deconvolution analysis identified AD-associated gene modules and blood cell types. Regression and unsupervised clustering analysis identified AD-associated genes, gene modules, cell types, and established AD classification models. RESULTS WGCNA on differentially expressed genes revealed 15 gene modules, with 6 accurately classifying AD (areas under the receiver operating characteristics curve [auROCs] > 0.90). These modules stratified AD patients into subgroups with distinct disease states. Cell-type deconvolution analysis identified specific blood cell types potentially associated with AD pathogenesis. DISCUSSION This study highlights the potential of blood transcriptome for AD diagnosis, patient stratification, and mechanistic studies. Highlights We comprehensively analyze the blood transcriptomes of a well-characterized Alzheimer's disease cohort to identify genes, gene modules, pathways, and specific blood cells associated with the disease. Blood transcriptome analysis accurately classifies and stratifies patients with Alzheimer's disease, with some gene modules achieving classification accuracy comparable to that of the plasma ATN biomarkers. Immune-associated pathways and immune cells, such as neutrophils, have potential roles in the pathogenesis and progression of Alzheimer's disease.

Published
2024

7. Food Fermentation in Space Is Possible, Distinctive, and Beneficial

Author

Coblentz, Maggie, primary, Evans, Joshua D., additional, Kothe, Caroline Isabel, additional, Mak, Tiffany, additional, Valeron, Nabila Rodriguez, additional, Chwalek, Patrick, additional, Wejendorp, Kim, additional, Garg, Shilpa, additional, Pless, Louisa, additional, Mak, Sarah, additional, Sörensen, Pia M., additional, Jahn, Leonie Johanna, additional, and Ekblaw, Ariel, additional

Published
2024
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8. Using blood transcriptome analysis for Alzheimer's disease diagnosis and patient stratification

Author

Zhong, Huan, primary, Zhou, Xiaopu, additional, Uhm, Hyebin, additional, Jiang, Yuanbing, additional, Cao, Han, additional, Chen, Yu, additional, Mak, Tiffany T. W., additional, Lo, Ronnie Ming Nok, additional, Wong, Bonnie Wing Yan, additional, Cheng, Elaine Yee Ling, additional, Mok, Kin Y., additional, Chan, Andrew Lung Tat, additional, Kwok, Timothy C. Y., additional, Mok, Vincent C. T., additional, Ip, Fanny C. F., additional, Hardy, John, additional, Fu, Amy K. Y., additional, and Ip, Nancy Y., additional

Published
2024
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15. Contributors

Author

Abad, Rabia, primary, Abusafa, Abdelrahim, additional, Aghbashlo, Mortaza, additional, Ahmed, Asam, additional, Al-Jabari, Maher, additional, Alexandri, Maria, additional, Aurnob, A.K.M. Kazi, additional, Banerjee, Ayan, additional, Behera, Shishir Kumar, additional, Belard, Laurent, additional, Bezergianni, Stella, additional, Bhaskar, Thallada, additional, Bhuyan, Nilutpal, additional, Choudhury, Hanif A., additional, Chrysikou, Loukia P., additional, Coll Lozano, Caterina, additional, Das, Sutapa, additional, David-Moreno, Antonio, additional, Demichelis, Francesca, additional, Du, Chenyu, additional, Dupont, Capucine, additional, Elhamouz, Amer, additional, Fiore, Silvia, additional, García Torreiro, María, additional, Ghosh, Debashish, additional, González Granados, Inmaculada, additional, Goud, Vaibhav V., additional, Grewal, Jasneet, additional, Herrero García, Natalia, additional, Hosseinzadeh-Bandbafha, Homa, additional, Hsu, Shu-Chien, additional, Kabir, Kazi Bayzid, additional, Kataki, Rupam, additional, Kaur, Ravneet, additional, Khare, S.K., additional, Kirtania, Kawnish, additional, Lam, Chor-Man, additional, Latorre-Sánchez, Marcos, additional, Lebrero, Raquel, additional, Li, Yize, additional, Lu, Diannan, additional, Lübeck, Mette, additional, Mak, Tiffany M.W., additional, Malani, Ritesh S., additional, Manikandan, N. Arul, additional, Moholkar, Vijayanand S., additional, Mojab, Hamidreza, additional, Molto Marin, Jose L., additional, Munir, Sidra, additional, Muñoz, Raul, additional, Musinovic, Hana, additional, Nahid, Ahaduzzaman, additional, Namboodiri, M. M. Tejas, additional, Nizami, Abdul-Sattar, additional, Oliva-Dominguez, Jose Miguel, additional, Ovejero-Roncero, David, additional, Pacheco-Ruiz, Santiago, additional, Pakshirajan, Kannan, additional, Park, Hung-Suck, additional, Pascual, Celia, additional, Pascual, Andrés, additional, Pérez, Víctor, additional, Perkins, Greg, additional, Pleissner, Daniel, additional, Pugazhenthi, G., additional, Raingué, Amélie, additional, Raj, Eldon, additional, Rehan, Mohammad, additional, Rene, Eldon R., additional, Reshad, Ali S., additional, Rodrigo, Alfredo, additional, Roldan-Aguayo, Rocio, additional, Sadaf, Ayesha, additional, Sailwal, Megha, additional, Sawalha, Hassan, additional, Serna-Maza, Alba, additional, Shah, Izhar Hussain, additional, Shukla, Shailendra Kumar, additional, Singh Rathore, Pushpendra Kumar, additional, Smith, Mark, additional, Sut, Debashis, additional, Tabatabaei, Meisam, additional, Tiwari, Pankaj, additional, Tran, Khanh-Quang, additional, Tsang, Daniel C.W., additional, Van de Vossenberg, Jack, additional, van Hullebusch, Eric D., additional, Wambugu, Carol W., additional, Wang, Lei, additional, Watson, Ian, additional, Yadav, Neerja, additional, You, Siming, additional, and Yu, Iris K.M., additional

Published
2020
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20. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp14 RNA cap methyltransferase

Author

Basu, Souradeep, primary, Mak, Tiffany, additional, Ulferts, Rachel, additional, Wu, Mary, additional, Deegan, Tom, additional, Fujisawa, Ryo, additional, Tan, Kang Wei, additional, Lim, Chew Theng, additional, Basier, Clovis, additional, Canal, Berta, additional, Curran, Joseph F., additional, Drury, Lucy S., additional, McClure, Allison W., additional, Roberts, Emma L., additional, Weissmann, Florian, additional, Zeisner, Theresa U., additional, Beale, Rupert, additional, Cowling, Victoria H., additional, Howell, Michael, additional, Labib, Karim, additional, and Diffley, John F.X., additional

Published
2021
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23. Identification of SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of the nsp14 RNA Cap Methyltransferase

Author

Basu, Souradeep, primary, Mak, Tiffany, additional, Ulferts, Rachel, additional, Wu, Mary, additional, Deegan, Tom, additional, Fujisawa, Ryo, additional, Tan, Kang Wei, additional, Lim, Chew Theng, additional, Basier, Clovis, additional, Canal, Berta, additional, Curran, Joseph F., additional, Drury, Lucy, additional, McClure, Allison W., additional, Roberts, Emma L., additional, Weissmann, Florian, additional, Zeisner, Theresa U., additional, Beale, Rupert, additional, Cowling, Victoria H., additional, Howell, Michael, additional, Labib, Karim, additional, and Diffley, John F.X., additional

Published
2021
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