| Literature DB >> 30411541 |
Bing Li1,2, Lan Ma3, Chi Zhang4, Zhixuan Zhou5, Hua Yuan2,3, Hongbing Jiang2,3, Yongchu Pan3,4,6, Qian Tan1,7.
Abstract
BACKGROUND: The genetic etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) has not been fully clarified to date. Epidermal growth factor receptor (EGFR) was reportedly involved in its biological establishment and regulation of cell migration during the embryonic stage.Entities:
Keywords: endocytosis; epidermal growth factor receptor; genome-wide association study; nonsyndromic cleft lip with or without cleft palate; pathway; single-nucleotide polymorphism
Mesh:
Substances:
Year: 2018 PMID: 30411541 PMCID: PMC6305670 DOI: 10.1002/mgg3.497
Source DB: PubMed Journal: Mol Genet Genomic Med ISSN: 2324-9269 Impact factor: 2.183
Figure 1Manhattan plot of the associations of the SNPs of the super pathway genes with risk of nonsyndromic cleft lip with or without cleft palate. The X‐axis presented different chromosome loci, and the Y‐axis presented −log10 p values of SNPs. Eighty‐two SNPs attained a statistical association with the risk of NSCL/P after an adjustment for multiple testing (Benjamini–Hochberg FDR procedure, p ≤ 0.05)
Figure 2Regional plots of associations of three susceptibility loci with risk of NSCL/p. Figures showed association results of SNPs and recombination rates in three susceptibility loci (10q25.3, 17q12, and 1q23.1), and four lead SNPs were identified shown in a–d. For each plot, the −log10P values of the SNPs were presented according to the chromosomal positions of the SNPs. Estimated recombination rates were shown as light‐blue lines. The lead SNPs were presented in purple, and each of them was more significant than SNPs in moderate to high LD with it (r 2 ≥ 0.5). Other SNPs were colored according to their LD (r 2) with the lead SNP. The genes within or near the susceptibility region were annotated at the bottom, and their transcript direction was shown by arrows
Four lead SNPs showing statistical associations (FDR p ≤ 0.05) with the risk of nonsyndromic cleft lip with or without cleft palate
| SNP | Chr Loci | OR (95% CI) |
|
| Gene |
|---|---|---|---|---|---|
|
g.116979803T>C | 10q25.3 | 1.652 (1.353–2.018) | 8.40E−07 | 3.544E−3 |
|
|
g.117037960A>G | 10q25.3 | 0.5125 (0.3843–0.6834) | 5.30E−06 | 5.081E−3 |
|
|
g.35720163G>C | 17q12 | 0.4574 (0.3013–0.6944) | 2.40E−04 | 2.334E−2 |
|
|
g.156864512G>A | 1q23.1 | 1.969 (1.340–2.892) | 5.53E−04 | 4.823E−2 |
|
CI: Confidence interval; Chr: Chromosome.
NC_000010.11 (Homo sapiens chromosome 10, GRCh38.p12).
NC_000017.11 (Homo sapiens chromosome 17, GRCh38.p12).
NC_000001.11 (Homo sapiens chromosome 1, GRCh38.p12).
Primary p value before multiple testing corrections.
p Value after the false discovery rate (FDR) control.
Figure 3Information of four lead SNPs in 127 reference human epigenomes. (a) Two lead SNPs at 10q25.3 (b) One lead SNP at17q12 (c) one lead SNP at 1q23.1. Four lead SNPs were presented in 127 consolidated human epigenomes based on uniformly processed data sets of Roadmap Epigenomics Project. Annotation for configuring colors was listed in the bottom (d)
Figure 4Three genes expressions in proximal and distal positions of the maxilla and mandible in mouse embryonic stage. Man.Dis: Mandibular distal location; Man.Pro: Mandibular proximal location; Max.Dis: Maxillary distal location; Max.Pro: Maxillary proximal location. Figures showed median levels of SHTN1, AP2B1, and NTRK1 expressions in proximal and distal locations of maxilla and mandible during the 10.5th day to 14.5th day of mouse embryonic stage based on Geo data (GSE67985)