Table 6 QChip1 pathogenic variants in genomics knowledgebasesa.

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

Knowledgebase

Sample size for allele frequency

QChip1 pathogenic variants

n

%

QChip1

2708

140

100

ClinVar

 

140

100

Hamad Medical Corporation (HMC)

 

25

18

Center for Arab Genetic Studies (CAGS)

 

27

19

Dasman Diabetes Institute (DDI, Kuwait)

540

28

20

GME Variome

886

37

26

Iranome (Iran)

800

32

23

New York City (NYC)

226

16

11

Puerto Ricans (PR)

51

8

6

Anywhere

 

87

62

Middle East (CAGS, Kuwait, GME, Iran)

 

70

50

  1. aIn order to quantify the utility of QChip1 for single gene (Mendelian) disorder screening outside of Qatar, the presence and (when available) allele frequency of each variant in Table 5 was checked in seven datasets, including three produced by this research team (HMC, NYC, PR) and four externally obtained [CAGS (http://cags.org.ae/), Dasman Diabetes Institute, GME Variome (http://igm.ucsd.edu/gme/data-browser.php), Iranome (http://www.iranome.ir/)]. Only the DDI, GME, and Iranome datasets had allele frequency data. Shown is the name of the knowledgebase, the sample size when available, and the QChip1 pathogenic variants found in the knowledgebase, including number and percentage of 140 total on QChip1 (Table 5).
  2. 2For datasets where allele frequency is available, the variant is counted as “present” if the frequency was great than zero. For datasets where allele frequency is not available, the variant is counted as “present” if a query of the dataset found the variant. The bottom two rows show aggregate data, where the “anywhere” row indicates variants present in any of the seven datasets (HMC, CAGS, Kuwait, GME, Iran, NYC, PR), and the “Middle East” row indicates variants present in the Middle Eastern datasets (CAGS, DDI, GME, Iran).
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