Table 2 Step 2: Design of QChip1 based on the predicted pathogenic variants in the Qatari Genome.

From: The QChip1 knowledgebase and microarray for precision medicine in Qatar

Microarraya

Probes (n)

Variant sites (n)

Genes (n)

QChip0

184,713

91,942

3540

SNV

179,257

89,696

3529

Indels

5456

2246

10,665

QChip1

70,715

61,592

3438

SNV

69,745

60,858

3472

Indels

970

734

491

  1. aBased on the comprehensive list of Qatari variants and genes of interest for SGD research and screening (Table 1), QChip0, the precursor of QChip1, was designed on the Axion platform with 184,713 probes representing 91,942 variants and 3540 genes (see Methods for a description of prioritization of variants/genes and choice of probes). QChip0 was tested with n = 26 Qatari DNA samples for which whole-genome sequencing was available. The poorly performing probes with low-quality genotype sites were eliminated, resulting in the final design of QChip1 with 70,715 probes representing 61,592 variants and 3438 genes.
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