DrABC: deep learning accurately predicts germline pathogenic mutation status in breast cancer patients based on phenotype data.

Journal: Genome medicine
PMID:

Abstract

BACKGROUND: Identifying breast cancer patients with DNA repair pathway-related germline pathogenic variants (GPVs) is important for effectively employing systemic treatment strategies and risk-reducing interventions. However, current criteria and risk prediction models for prioritizing genetic testing among breast cancer patients do not meet the demands of clinical practice due to insufficient accuracy.

Authors

  • Jiaqi Liu
  • Hengqiang Zhao
    Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; DISCO (Deciphering disorders Involving Scoliosis and COmobidities) study group.
  • Yu Zheng
    Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu 610041, China.
  • Lin Dong
    Environmental Exposures Vascular Disease Institute, Shanxi Medical University, Taiyuan, Shanxi, China.
  • Sen Zhao
    College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China.
  • Yukuan Huang
    Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, China.
  • Shengkai Huang
    Department of Laboratory Medicine, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  • Tianyi Qian
  • Jiali Zou
    Department of Breast Surgery, Guiyang Maternal and Child Healthcare Hospital, Guiyang, 550001, China.
  • Shu Liu
    Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: liushuhit@outlook.com.
  • Jun Li
    Department of Emergency, Zhuhai Integrated Traditional Chinese and Western Medicine Hospital, Zhuhai, 519020, Guangdong Province, China. quanshabai43@163.com.
  • Zihui Yan
    Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
  • Yalun Li
    Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ.
  • Shuo Zhang
    Ph.D. Program in Computer Science, The City University of New York, New York, NY, United States.
  • Xin Huang
    Department of ophthalmology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China.
  • Wenyan Wang
    School of Electrical and Information Engineering, Anhui University of Technology, Ma'anshan 243032, China.
  • Yiqun Li
    Department of Oncology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  • Jie Wang
  • Yue Ming
    Beijing Key Laboratory of Work Safety and Intelligent Monitoring, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, China.
  • Xiaoxin Li
    Basic Experimental Center of Natural Science, University of Science and Technology Beijing, Beijing 100083, P. R. China.
  • Zeyu Xing
    Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  • Ling Qin
    Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China.
  • Zhengye Zhao
    Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; DISCO (Deciphering disorders Involving Scoliosis and COmobidities) study group.
  • Ziqi Jia
    Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
  • Jiaxin Li
    Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China.
  • Gang Liu
    Department of Interventional Radiology, Qinghai Red Cross Hospital, Xining, Qinghai, China.
  • Menglu Zhang
    Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  • Kexin Feng
    Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  • Jiang Wu
    College of Energy and Mechanical Engineering, Shanghai University of Electric Power, Shanghai 200090, China. Electronic address: wjcfd2002@163.com.
  • Jianguo Zhang
    College of Automation, Harbin Engineering University, No. 145, Nantong street, Harbin, China.
  • Yongxin Yang
    Beijing Ekitech Co. Ltd., Beijing 100043, China; University of Edinburgh, 10 Crichton Street, Edinburgh, EH8 9AB, United Kindom.
  • Zhihong Wu
    College of Computer Science, Sichuan University, Chengdu, China.
  • Zhihua Liu
    Department of Gynecology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China.
  • Jianming Ying
    Department of Pathology, National Cancer Center /National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  • Xin Wang
    Key Laboratory of Bio-based Material Science & Technology (Northeast Forestry University), Ministry of Education, Harbin 150040, China.
  • Jianzhong Su
    Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019-0408, USA.
  • Xiang Wang
    Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
  • Nan Wu
    Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.