These authors contributed equally to this work.
Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar
Article first published online: 10 NOV 2013
© 2013 WILEY PERIODICALS, INC.
Volume 35, Issue 1, pages 105–116, January 2014
How to Cite
Rodriguez-Flores, J. L., Fakhro, K., Hackett, N. R., Salit, J., Fuller, J., Agosto-Perez, F., Gharbiah, M., Malek, J. A., Zirie, M., Jayyousi, A., Badii, R., Al-Nabet Al-Marri, A., Chouchane, L., Stadler, D. J., Mezey, J. G. and Crystal, R. G. (2014), Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar. Hum. Mutat., 35: 105–116. doi: 10.1002/humu.22460
Contract grant sponsors: Qatar Foundation and Weill Cornell Medical College – Qatar; National Science Foundation (#0922432); NIH T32 HL09428.
Communicated by David S. Rosenblatt
- Issue published online: 18 DEC 2013
- Article first published online: 10 NOV 2013
- Accepted manuscript online: 10 OCT 2013 11:56AM EST
- Manuscript Accepted: 25 SEP 2013
- Manuscript Received: 21 FEB 2013
- Qatar Foundation and Weill Cornell Medical College – Qatar
- National Science Foundation. Grant Numbers: #0922432, NIH T32 HL09428
Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.
Supp. Figure S1. Site frequency spectrums for the total Qatari population. Shown in log10 scale is the number of variants in the Qatari population on the Y-axis, and the minor allele frequency in Qatari on the X-axis.
Supp. Figure S2. Comparison of the allele frequencies among the Qatari Q1, Q2 and Q3 genetic groups. To identify variants that differentiate Q1, Q2 and Q3 Qatari subpopulations, the allele frequency was compared for 95,840 coding variants using two methods. A-C. Fst; and D-F. allele frequency difference. A-C. Fst was calculated for comparison of Q1 vs Q2, Q1 vs Q3, and Q2 vs Q3. A. is the Fst of Q1 compared to Q2 (x axis) and Q3 (y axis); B. Fst of Q2 compared to Q1 (x axis) and Q3 (y axis); and C. Fst of Q3 compared to Q1 (x axis) and Q2 (y axis). D-F. The standard deviation in absolute value of allele frequency calculated for each pair of populations. D. Q1 vs Q2; E. Q1 vs Q3; and F. Q2 vs Q3. The variants were classified into 4 bins based on standard deviations; variants with allele frequency difference <4 (blue), 4-6 (green), 6-8 (yellow) and >8 (red) standard deviations.
Supp. Figure S3. The Qatari exome. In order to provide a major-allele reference exome for future studies of each Qatari subpopulation, variants were identified where the major allele in a Qatari subpopulation is the non-reference allele. Genome-wide distribution of 11,043 variants where the major allele in Q1 is the non-reference allele (red), 11,033 variants where the major allele in Q2 is the non-reference allele (green), and 11,183 variants where the major allele in Q3 is the nonreference allele (blue). The x axis is chromosome position and the y axis is the chromosome.
Supp. Table S1. SNP Mendelian disease variants directly genotyped in the panel of genetic tests conducted in the Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar 1
Supp. Table S3. Review of Literature for Variants in Table 3
Supp. Table S4. OMIM + HGMD Variants Excluded1
Supp. Table S2 is available as a separate Excel file under the Supporting Information for this article.
Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.