The QChip1 knowledgebase and microarray for precision medicine in Qatar

Juan L. Rodriguez-Flores, Radja Messai-Badji, Amal Robay, Ramzi Temanni, Najeeb Syed, Monika Markovic, Eiman Al-khayat, Fatima Qafoud, Zafar Nawaz, Ramin Badii, Yasser Al-Sarraj, Hamdi Mbarek, Wadha Al-Muftah, Muhammad Alvi, Mahboubeh R. Rostami, Juan Carlos Martinez Cruzado, Jason G. Mezey, Alya Al Shakaki, Joel A. Malek, Matthew B. GreenblattKhalid A. Fakhro, Khaled Machaca, Ajayeb Al-Nabet, Nahla Afifi, Andrew Brooks, Said I. Ismail, Asmaa Althani, Ronald G. Crystal

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop “QChip1,” an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.

Original languageEnglish (US)
Article number3
Journalnpj Genomic Medicine
Issue number1
StatePublished - Dec 2022
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics
  • Genetics(clinical)


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