sj-docx-3-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-docx-3-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

sj-docx-5-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-docx-5-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

sj-docx-4-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-docx-4-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

sj-tif-2-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-tif-2-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

sj-tif-1-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-tif-1-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

Genome-wide association study results of NSDTRs with CP.

<p>A. Manhattan plot of −log₁₀ of raw p-values by chromosome. The p_genome value is the p-value after 100000 permutations. The lowest p_genome is found across 8 SNPs on cfa14: 25822897, 25832747, 25847915, 25854827, 25868609, 25995782, 26023199, and 26082330. B. Plot of the raw p-values by Mb on cfa14 depicting the associated region. C. Observed haplotypes in 12 CP NSDTRs. Horizontal bars represent haplotypes from the 12 CP NSDTRs with associated haplotype, with runs of homozygosity in grey. The critical interval is defined by the shared homozygous haplotype denoted by the black bars (cfa14. 24189817-29319290). The 2 CP NSDTRs without the associated haplotype are not included in this figure. D. Quantile-Quantile plot of genome-wide association results. Black dots represent the observed versus expected p-values of all SNPs (λ = 1.05). Grey dots represent the observed versus expected p-values after removal of all SNPs on cfa14. (λ = 1.02). The solid grey line represents the null hypothesis: observed p-values equal expected p-values.</p

A LINE-1 Insertion in DLX6 Is Responsible for Cleft Palate and Mandibular Abnormalities in a Canine Model of Pierre Robin Sequence

<div><p>Cleft palate (CP) is one of the most commonly occurring craniofacial birth defects in humans. In order to study cleft palate in a naturally occurring model system, we utilized the Nova Scotia Duck Tolling Retriever (NSDTR) dog breed. Micro-computed tomography analysis of CP NSDTR craniofacial structures revealed that these dogs exhibit defects similar to those observed in a recognizable subgroup of humans with CP: Pierre Robin Sequence (PRS). We refer to this phenotype in NSDTRs as CP1. Individuals with PRS have a triad of birth defects: shortened mandible, posteriorly placed tongue, and cleft palate. A genome-wide association study in 14 CP NSDTRs and 72 unaffected NSDTRs identified a significantly associated region on canine chromosome 14 (24.2 Mb–29.3 Mb; p_raw = 4.64×10⁻¹⁵). Sequencing of two regional candidate homeobox genes in NSDTRs, distal-less homeobox 5 (DLX5) and distal-less homeobox 6 (DLX6), identified a 2.1 kb LINE-1 insertion within DLX6 in CP1 NSDTRs. The LINE-1 insertion is predicted to insert a premature stop codon within the homeodomain of DLX6. This prompted the sequencing of DLX5 and DLX6 in a human cohort with CP, where a missense mutation within the highly conserved DLX5 homeobox of a patient with PRS was identified. This suggests the involvement of DLX5 in the development of PRS. These results demonstrate the power of the canine animal model as a genetically tractable approach to understanding naturally occurring craniofacial birth defects in humans.</p></div

Schematic illustration of genomic and cDNA DLX6 gene structure in unaffected (WT) and CP1 NSDTRs (CP1).

<p>Nucleotides boxed and in bold are the 13 base pair target site duplication identified as part of the DLX6 LINE-1 insertion. Conservation represents the UCSC genome browser comparative genomics conservation track of human, dog, mouse, and rat sequence conservation. The region of conservation represented in red is the region disrupted by the LINE-1 insertion. Image is not drawn to scale.</p

Pedigree of 7 CP1 NSDTR families depicting segregation of the mutant allele with the LINE-1 element insertion.

<p>Filled symbols represent NSDTRs with the CP1 phenotype. Diagonal lines indicate that the NSDTR is deceased. “+” represents wildtype allele. “m” represents the mutant allele. [ ] genotypes were inferred if DNA was not available.</p

Phenotype of neonatal CP1 NSDTRs.

<p>A. Neonatal CP1 NSDTR with an extensive cleft of the hard and soft palate. B. Neonatal NSDTR with a normal palate (WT). C. Lateral view of CP1 head exhibiting relative mandibular brachygnathia. D. Lateral view of WT head with a normal jaw relationship. E. Coronal CT image depicting the failure of the palatine processes and nasal septum to fuse in CP1 NSDTRs. F. Coronal CT image depicting midline fusion of palatal process and nasal septum in WT. P – Palatine process, NS – Nasal septum G. 3D reconstruction of microCT imaging of CP1 and WT skulls with mandibles removed. CP1 skull shows abnormally shaped palatine process and palatine bones. Bones colored blue are the palatine processes and palatine bones. WT skull shows anatomical location of normal palatine sutures and shape of palatine processes and palatine bones. H. 3D reconstruction of mandibles depicting abnormal angulation of the condylar process (*) in CP1 mandibles compared to WT mandibles.</p