Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations

T. H. Beaty, J. B. Hetmanski, M. D. Fallin, J. W. Park, J. W. Sull, I. McIntosh, K. Y. Liang, C. A. VanderKolk, R. J. Redett, S. A. Boyadjiev, E. W. Jabs, S. S. Chong, F. S.H. Cheah, Y. H. Wu-Chou, P. K. Chen, Y. F. Chiu, V. Yeow, I. S.L. Ng, J. Cheng, S. HuangX. Ye, H. Wang, R. Ingersoll, A. F. Scott

Research output: Contribution to journalArticle

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Abstract

Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.

Original languageEnglish
Pages (from-to)501-518
Number of pages18
JournalHuman Genetics
Volume120
Issue number4
DOIs
Publication statusPublished - Nov 1 2006
Externally publishedYes

Fingerprint

Chromosomes, Human, Pair 2
Genetic Association Studies
Cleft Palate
Linkage Disequilibrium
Population
Single Nucleotide Polymorphism
Haplotypes
Genes
Singapore
Taiwan
Cleft Lip
Nucleotides
Odds Ratio

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Beaty, T. H., Hetmanski, J. B., Fallin, M. D., Park, J. W., Sull, J. W., McIntosh, I., ... Scott, A. F. (2006). Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. Human Genetics, 120(4), 501-518. https://doi.org/10.1007/s00439-006-0235-9

Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. / Beaty, T. H.; Hetmanski, J. B.; Fallin, M. D.; Park, J. W.; Sull, J. W.; McIntosh, I.; Liang, K. Y.; VanderKolk, C. A.; Redett, R. J.; Boyadjiev, S. A.; Jabs, E. W.; Chong, S. S.; Cheah, F. S.H.; Wu-Chou, Y. H.; Chen, P. K.; Chiu, Y. F.; Yeow, V.; Ng, I. S.L.; Cheng, J.; Huang, S.; Ye, X.; Wang, H.; Ingersoll, R.; Scott, A. F.

In: Human Genetics, Vol. 120, No. 4, 01.11.2006, p. 501-518.

Research output: Contribution to journalArticle

Beaty, TH, Hetmanski, JB, Fallin, MD, Park, JW, Sull, JW, McIntosh, I, Liang, KY, VanderKolk, CA, Redett, RJ, Boyadjiev, SA, Jabs, EW, Chong, SS, Cheah, FSH, Wu-Chou, YH, Chen, PK, Chiu, YF, Yeow, V, Ng, ISL, Cheng, J, Huang, S, Ye, X, Wang, H, Ingersoll, R & Scott, AF 2006, 'Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations', Human Genetics, vol. 120, no. 4, pp. 501-518. https://doi.org/10.1007/s00439-006-0235-9
Beaty TH, Hetmanski JB, Fallin MD, Park JW, Sull JW, McIntosh I et al. Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. Human Genetics. 2006 Nov 1;120(4):501-518. https://doi.org/10.1007/s00439-006-0235-9
Beaty, T. H. ; Hetmanski, J. B. ; Fallin, M. D. ; Park, J. W. ; Sull, J. W. ; McIntosh, I. ; Liang, K. Y. ; VanderKolk, C. A. ; Redett, R. J. ; Boyadjiev, S. A. ; Jabs, E. W. ; Chong, S. S. ; Cheah, F. S.H. ; Wu-Chou, Y. H. ; Chen, P. K. ; Chiu, Y. F. ; Yeow, V. ; Ng, I. S.L. ; Cheng, J. ; Huang, S. ; Ye, X. ; Wang, H. ; Ingersoll, R. ; Scott, A. F. / Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. In: Human Genetics. 2006 ; Vol. 120, No. 4. pp. 501-518.
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abstract = "Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.",
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AU - Hetmanski, J. B.

AU - Fallin, M. D.

AU - Park, J. W.

AU - Sull, J. W.

AU - McIntosh, I.

AU - Liang, K. Y.

AU - VanderKolk, C. A.

AU - Redett, R. J.

AU - Boyadjiev, S. A.

AU - Jabs, E. W.

AU - Chong, S. S.

AU - Cheah, F. S.H.

AU - Wu-Chou, Y. H.

AU - Chen, P. K.

AU - Chiu, Y. F.

AU - Yeow, V.

AU - Ng, I. S.L.

AU - Cheng, J.

AU - Huang, S.

AU - Ye, X.

AU - Wang, H.

AU - Ingersoll, R.

AU - Scott, A. F.

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N2 - Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.

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