Welcome to the QChip Browser!

This site is under development, pardon our simplicity. Current version 1.0

Introduction

The QChip Browswer is an online resource hub for sharing of documentation, data, and code related to the QChip genomics knowledgebase and genotyping microarray for precision medicine in Qatar. If there is a resource not currently shared that you are interested in obtaining for academic purposes, please contact geneticmedicine@med.cornell.edu.

Documentation

Primary documentation for the resources provided here are our peer-reviewed publications and presentations at academic meetings.

  1. Rodriguez-Flores JL, Messai-Badji R, Robay A, Temanni R, Syed N, Markovic M, Al-khayat E, Qafoud F, Nawaz Z, Badii R, Al-Sarraj Y, Mbarek H, Al-Muftah W, Alvi M, Rostami MR, Martinez Cruzado JC, Mezey JG, Al Shakaki A, Malek JA, Greenblatt MB, Fakhro K, Machaca K, Al-Nabet A, Afifi N, Brooks A, Ismail S, Althani A, Crystal RG. The QChip1 Knowledgebase and Microarray for Precision Medicine in Qatar. (in press, NPJ Genomic Medicine).

Data

Data shared includes (1) data used in the design of QChip, (2) data produced using QChip, and (3) data describing variants included in QChip

  1. Data used in the design of QChip includes data downloaded by the authors from external studies and data produced by the authors. Data produced by the authors came from three sources, including (1) Qatari genomic data produced by Weill Cornell and shared through NCBI SRA, including previously published WGS data shared under BioProject PRJNA288297 and WES data shared under BioProject PRJNA290484 and BioProject PRJNA288292. Previously unpublished data is in preparation for sharing through NCBI DbGaP, currently listed under NCBI BioProject PRJNA774497. (2) Genomic data used for design of QChip also include data produced by Qatar Genome Project from DNA samples collected by Qatar BioBank, accessible through written application to Qatar BioBank. (3) The third source of genomic data was a database of pathogenic variants identified in Qataris by Hamad Medical Corporation, available from our FigShare project repository.
  2. Data produced using QChip includes public access aggregate data and controlled access individual-level data produced using QChip. Aggregate data is available for download from our FigShare project repository, and individual-level data is in preparation for sharing through NCBI DbGaP under BioProject PRJNA774497. Both datasets are also avaiable from the authors upon request.
  3. Data describing variants included in QChip includes annotation produced by the authors and by the genotyping microarray manufacturer (Thermo Fisher Scientific, formerly Affymetrix), available for download from our FigShare repository. In addition, the list of variants of highest value for screening in Qatar was shared through DbGaP Batch 1063269.

Code

Code used in this project will be available for download from Github

Acknowledgements

This server is hosted by the Cornell BioHPC infrastructure and is maintained by the Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA. Further acknowledgements described in the manuscript.