Polygenic risk score for breast cancer risk prediction in Asian BRCA1 and BRCA2 pathogenic variants carriers

Publication: npj Breast Cancer

 

30 September 2025

 

Mei-Chee Tai, Joe Dennis, Sue K. Park, Sung-Won Kim, Jong Won Lee, Nur Tiara Hassan, Ava Kwong, Mikael Hartman, Sook-Yee Yoon, Joanne Ngeow, Yin-Ling Woo, Boyoung Park, Zhi-Lei Wong, Goska Leslie, Manjeet K. Bolla, Daniel R. Barnes, Michael T. Parsons, Penny Soucy, Jacques Simard, Nur Aishah Mohd Taib, Cheng-Har Yip, Douglas F. Easton, Georgia Chenevix-Trench, Antonis C. Antoniou, Soo-Hwang Teo & Weang-Kee Ho

 

Abstract

Polygenic risk scores (PRS) have been shown to be predictive of breast cancer (BC) risk in European BRCA1 and BRCA2 pathogenic variant (PV) carriers, but their utility in Asian populations has not been evaluated. In this study, we evaluated the association of two breast cancer PRS developed for the East Asian general population and three versions of a PRS developed for the European general population in 604 BRCA1 (390 affected by breast cancer) and 785 BRCA2 (552 affected by breast cancer) PV female carriers of Asian ancestry. Only the Asian-based PRS, constructed using approximately 1 million single-nucleotide variations (SNVs), showed a significant association with breast cancer risk (Hazard Ratio per standard deviation (95% Confidence Interval) is 1.47 (1.10–1.95) for BRCA1 and 1.43 (1.04–1.95) for BRCA2). Incorporating this PRS into risk prediction models may improve cancer risk assessment among PV carriers of Asian ancestry.

 

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Humoral responses to SARS-CoV-2 vaccine in vasculitis-related immune suppression


Publication
: Science Advances


Kimia Kamelian, Benjamin Sievers, Michael Chen-Xu, Sam Turner, Mark Tsz, Kin Cheng, Mazharul Altaf, Steven A. Kemp, Adam Abdullahi, Kata Csiba, Dami A. Collier, Petra Mlcochova, Bo Meng, Rachel B. Jones, The CITIID-NIHR BioResource COVID-19 Collaboration, Derek Smith, John Bradley, Kenneth G. C. Smith, Rainer Doffinger, Rona M. Smith and Ravindra K. Gupta.

12 February 2025


Immune suppression poses a challenge to vaccine immunogenicity. We show that serum antibody neutralization against SARS-CoV-2 Omicron descendants was largely absent post-doses 1 and 2 in individuals with vasculitis treated with rituximab. Detectable and increasing neutralizing titers were observed post-doses 3 and 4, except for XBB. Rituximab in vasculitis exacerbates neutralization deficits over standard immunosuppressive therapy, although impairment resolves over time since dosing. We observed discordance between detectable IgG binding and neutralizing activity specifically in the context of rituximab use, with high proportions of individuals showing reasonable IgG titer but no neutralization. ADCC response was more frequently detectable compared to neutralization in the context of rituximab, indicating that a notable proportion of binding antibodies are non-neutralizing. Therefore, use of rituximab is associated with severe impairment in neutralization against Omicron descendants despite repeated vaccinations, with better preservation of non-neutralizing antibody activity.

 

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Misexpression of inactive genes in whole blood is associated with nearby rare structural variants

Publication: American Journal of Human Genetics

Thomas Vanderstichele, Katie L. Burnham, Niek de Klein, Michael Inouye, Dirk S. Paul, Emma E. Davenport et al

24 July 2024

Gene misexpression is the aberrant transcription of a gene in a context where it is usually inactive. Despite its known pathological consequences in specific rare diseases, we have a limited understanding of its wider prevalence and mechanisms in humans. To address this, we analyzed gene misexpression in 4,568 whole-blood bulk RNA sequencing samples from INTERVAL study blood donors.

We found that while individual misexpression events occur rarely, in aggregate they were found in almost all samples and a third of inactive protein-coding genes. Using 2,821 paired whole-genome and RNA sequencing samples, we identified that misexpression events are enriched in cis for rare structural variants. We established putative mechanisms through which a subset of SVs lead to gene misexpression, including transcriptional readthrough, transcript fusions, and gene inversion. Overall, we develop misexpression as a type of transcriptomic outlier analysis and extend our understanding of the variety of mechanisms by which genetic variants can influence gene expression.

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Using machine learning to model older adult inpatient trajectories from electronic health records data

Publication: ScienceDirect

Maria Herrero-Zazo, Tomas Fitzgerald, Vince Taylor, Helen Street, Afzal N. Chaudhry, John R. Bradley, Ewan Birney, Victoria L. Keevil

20 January 2023


  • Time-series blood test & vital sign data from older inpatients were presented to HMM (Hidden Markov Models)
  • Hidden clinically interpretable states were extracted, linked with diagnoses and death
  • States modeled inpatient trajectories, differentiating risk from admission-discharge
  • The clinical interpretation of HMM states helped explain how ML models organise data

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