The QChip1 knowledgebase and microarray for precision medicine in Qatar

Abstract

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.

Fig. 1. Population distribution of QChip1 variants observed in Qatar.

In order to demonstrate the population-specific value of QChip1, the risk alleles that were discovered by genome/exome sequencing, prioritized in the knowledgebase, included in the array design, successfully genotyped, and observed in array data for at least one of n = 2,708 Qataris are provided for download in Supplementary Table 1 and online at the Qatar Genome Browser (http://qchip.biohpc.cornell.edu). Shown is a summary of the population enrichment of these variants. A Enrichment of potentially pathogenic variants on QChip1 in Qatari subpopulations. In order to determine if Mendelian disease risk alleles were enriched in single Qatari subpopulations, a cross-population allele frequency comparison was conducted for five ancestries observed in Qatar (k1, QGP_PAR, Peninsular Arabs; k2, QGP_GAR, General Arabs; k4, QGP_WEP, Arabs of Western Eurasia and Persia; k5, QGP_SAS, South Asian Arabs, and k3, QGP_AFR, African Arabs). Not shown, QGP_ADM, Admixed Arabs. For each subpopulation, the risk allele frequency was compared to the maximum of the other four subpopulations. Shown is the proportion that was highest in the subpopulation for (left-to-right) QGP_PAR, QGP_GAR, QGP_WEP, QGP_SAS, and QGP_AFR. B Enrichment of potentially pathogenic variants on QChip1 in the Qatari genome relative to non-Qatari. The non-Qatari genomes were residents of New York City (total n = 226) and Puerto Rico (n = 51). The ancestry proportions of these 226 non-Qatari genomes in 5 clusters (k1 to k5) were calculated as described in Fig. 2 (combined analysis of non-Qataris and Qataris using ADMIXTURE), the lowest cross-validation error was for k = 5, with the non-Qataris falling in 3 clusters (African-Americans from NYC, n = 60, k3; European-Americans from NYC, n = 153, k4; South Asian-Americans from NYC, n = 13, k5; Puerto Ricans of European Ancestry, k4; and Puerto Ricans of Afro-Caribbean Ancestry, k3). More details of the population structure were made available in Fig. 2 (Qataris) and Supplementary Fig. 1 (non-Qataris). Shown is the percentage of n = 32,674 potentially pathogenic variants in Mendelian (single gene) disorder genes that were observed in at least one Qatari and have a risk (minor) allele frequency in Qatar higher than in non-Qatari populations. The proportion of variants was calculated that were at elevated minor allele frequency (enriched) in the Qatari genome relative to the genomes of the 5 non-Qatari population clusters tested: USA African-American (k3), USA European-American (k4), USA South-Asian American (k5), PR Afro-Caribbean (k3), PR European (k4). Shown from left-to-right is the proportion that are enriched in Qatar relative to the maximum of all 5 populations, followed the proportion enriched relative to each individual population.

Fig. 2. Strategy to design and assess QChip1.

Step 1. Qatari Genome Knowledgebase. Identification of the single gene (Mendelian) pathogenic variants and genes in protein coding regions of the Qatari genome was generated using whole-genome sequencing, exome sequencing and clinical reports (see Table 1). After cataloging all variants and respective genes, the pathogenic variants and genes were identified using ClinVar and SnpEff. Step 2. Using this list, Qchip0 (the precursor of QChip1) was designed on the Axiom platform which was then tested with 25 Qatari DNA samples for which whole-genome sequencing was available. Step 3. Elimination of poor performance probes and variants led to the final design of QChip1, which was tested for concordance with genome sequencing using DNA samples from Qataris. Step 4. Use of QChip1 to assess the prevalence of pathogenic variants and genes among Qataris, New York City residents and Puerto Ricans.

Fig. 3. Population structure and principal component analysis of ancestry assessed by QChip1.

Sites and samples that failed QC based on variant batch effects or PC outliers were excluded. After QC, ADMIXTURE analysis was conducted on the remaining n = 37,674 variants and n = 2985 samples of Qataris (n = 2708) and non-Qataris (n = 277) for a range of K from 3 to 12. The lowest cross-validation error was observed for k = 5 for the full dataset. After analysis, the Qatari and non-Qatari samples were plotted separately, the panels here show the Qatari samples from the joint analysis. A Admixture (k = 5) proportions. Shown is a plot of the admixture proportions (% k from 0 to 100%, y axis), with each column representing one genome, sorted from left-to-right by dominant (highest %) k, and decreasing % k1 to k5. Genomes are color-coded by the dominant (largest %) ancestry (QGP_PAR, Peninsular Arabs, red; QGP_GAR, General Arabs, orange; QGP_WEP, Arabs of West Eurasia and Persia, bright green; QGP_SAS, South Asian Arabs, olive green; and QGP_AFR, African Arabs, light blue). Samples from prior studies of Qatar population structure (Qatar Genome public samples from Fakhro et al. and Rodriguez-Flores et al. genotyped on QChip1 were included in the clustering analysis and were used to assign the clusters. B Principal components analysis of Qataris. Shown is a PC1 × PC2 plot of Qatari genomes in squares color-coded by cluster of largest proportion of inferred ancestry. Not shown, QGP_ADM, Admixed Arabs.