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PAGEANT: personal access to genome and analysis of natural traits.
Huang, Jie; Liang, Zhi-Sheng; Pallotti, Stefano; Ranson, Janice M; Llewellyn, David J; Zheng, Zhi-Jie; King, Daniel A; Zhou, Qiang; Zheng, Houfeng; Napolioni, Valerio.
  • Huang J; Department of Global Health, Peking University School of Public Health, Beijing, China.
  • Liang ZS; Institute for Global Health and Development, Peking University, Beijing, China.
  • Pallotti S; National Institute of Health Data Science at Peking University, Beijing, China.
  • Ranson JM; Department of Global Health, Peking University School of Public Health, Beijing, China.
  • Llewellyn DJ; Genetics and Animal Breeding Group, School of Pharmacy, University of Camerino, Camerino, Italy.
  • Zheng ZJ; College of Medicine and Health, University of Exeter, Exeter, UK.
  • King DA; College of Medicine and Health, University of Exeter, Exeter, UK.
  • Zhou Q; Alan Turing Institute, London, UK.
  • Zheng H; Department of Global Health, Peking University School of Public Health, Beijing, China.
  • Napolioni V; Northwell Health Cancer Institute and Feinstein Institutes for Research, Lake Success, NY, USA.
Nucleic Acids Res ; 50(7): e39, 2022 04 22.
Article in English | MEDLINE | ID: covidwho-1594198
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ABSTRACT
GWASs have identified numerous genetic variants associated with a wide variety of diseases, yet despite the wide availability of genetic testing the insights that would enhance the interpretability of these results are not widely available to members of the public. As a proof of concept and demonstration of technological feasibility, we developed PAGEANT (Personal Access to Genome & Analysis of Natural Traits), usable through Graphical User Interface or command line-based version, aiming to serve as a protocol and prototype that guides the overarching design of genetic reporting tools. PAGEANT is structured across five core modules, summarized by five Qs (i) quality assurance of the genetic data; (ii) qualitative assessment of genetic characteristics; (iii) quantitative assessment of health risk susceptibility based on polygenic risk scores and population reference; (iv) query of third-party variant databases (e.g. ClinVAR and PharmGKB) and (v) quick Response code of genetic variants of interest. Literature review was conducted to compare PAGEANT with academic and industry tools. For 2504 genomes made publicly available through the 1000 Genomes Project, we derived their genomic characteristics for a suite of qualitative and quantitative traits. One exemplary trait is susceptibility to COVID-19, based on the most up-to-date scientific findings reported.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Genome, Human Type of study: Observational study / Prognostic study / Qualitative research / Reviews Topics: Variants Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2022 Document Type: Article Affiliation country: Nar

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Genome, Human Type of study: Observational study / Prognostic study / Qualitative research / Reviews Topics: Variants Limits: Humans Language: English Journal: Nucleic Acids Res Year: 2022 Document Type: Article Affiliation country: Nar