Ehsan Ullah1, Michaël Aupetit1, Arun Das1, Abhishek Patil1, Noora Al Muftah2, Reda Rawi1,3, Mohamad Saad1, Halima Bensmail1. 1. Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar. 2. Department of Computational Biology and Quantitative Genetics, Harvard School of Public Health, Boston, MA, USA. 3. Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Abstract
MOTIVATION: It is important to characterize individual relatedness in terms of familial relationships and underlying population structure in genome-wide association studies for correct downstream analysis. The characterization of individual relatedness becomes vital if the cohort is to be used as reference panel in other studies for association tests and for identifying ethnic diversities. In this paper, we propose a kinship visualization tool to detect cryptic relatedness between subjects. We utilize multi-dimensional scaling, bar charts, heat maps and node-link visualizations to enable analysis of relatedness information. AVAILABILITY AND IMPLEMENTATION: Available online as well as can be downloaded at http://shiny-vis.qcri.org/public/kinvis/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: It is important to characterize individual relatedness in terms of familial relationships and underlying population structure in genome-wide association studies for correct downstream analysis. The characterization of individual relatedness becomes vital if the cohort is to be used as reference panel in other studies for association tests and for identifying ethnic diversities. In this paper, we propose a kinship visualization tool to detect cryptic relatedness between subjects. We utilize multi-dimensional scaling, bar charts, heat maps and node-link visualizations to enable analysis of relatedness information. AVAILABILITY AND IMPLEMENTATION: Available online as well as can be downloaded at http://shiny-vis.qcri.org/public/kinvis/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich Journal: Nat Genet Date: 2006-07-23 Impact factor: 38.330
Authors: Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham Journal: Am J Hum Genet Date: 2007-07-25 Impact factor: 11.025
Authors: Hyun Min Kang; Jae Hoon Sul; Susan K Service; Noah A Zaitlen; Sit-Yee Kong; Nelson B Freimer; Chiara Sabatti; Eleazar Eskin Journal: Nat Genet Date: 2010-03-07 Impact factor: 38.330
Authors: Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis Journal: Nature Date: 2015-10-01 Impact factor: 49.962