Copy Number Changes Identified Using Whole Exome Sequencing in Nonsyndromic Cleft Lip and Palate in a Honduran Population

Abstract

BACKGROUND The majority of cleft lip with or without cleft palate (CL/P) cases appear as an isolated, non-syndromic entity (NSCLP). With the advent of next generation sequencing, whole exome sequencing (WES) has been used to identify single nucleotide variants and insertion/deletions which cause or increase risk of NSCLP. However, to our knowledge, there are no published studies using WES in NSCLP to investigate copy number changes (CNCs), which are a major component of human genetic variation. Our study aimed to identify CNCs associated with NSCLP in a Honduran population using WES. METHODS WES was performed on two to four members of 27 multiplex Honduran families. CNCs were identified using two algorithms, CoNIFER and XHMM. Priority was given to CNCs that were identified in more than one patient and had variant frequencies of less than 5% in reference data sets. RESULTS WES completion was defined as >90% of the WES target at >8× coverage and >80% of the WES target at >20× coverage. 24 CNCs that met our inclusion criteria were identified by both CoNIFER and XHMM. These CNCs were confirmed using qPCR. Pedigree analysis produced three CNCs corresponding to ADH7, AHR, and CRYZ segregating with NSCLP. Two of the three CNCs implicate genes, AHR and ADH7, whose known biological functions could plausibly play a role in NSCLP. CONCLUSIONS WES can be used to detect candidate CNCs that may be involved in the pathophysiology of NSCLP.

9p24 triplication in syndromic hydrocephalus with diffuse villous hyperplasia of the choroid plexus

“…Fluorescent in situ hybridization (FISH; using dual color probes for the CDKN2A gene at 9p21 and the D9Z3 locus at 9q12; Cytocell Inc.) showed an abnormal pattern of four signals for the CDKN2A probe and three signals for the D9Z3 probe in 94.5% of the peripheral blood leukocytes examined, confirming the mosaic pattern of tetrasomy 9 in this patient. The proband's parents declined cytogenetic studies, hence the nature of the alteration (de novo vs. transmitted) could not be assessed, although one certainly could use WES data and genetic analysis tools like CONIFER and xHMM to determine the triplication ( Cai et al 2017 ).…”

An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate

“…For example, a genome-wide linkage study in the Malay population identified several CL/P candidate genes, including LPHN2, PVRL3, and SATB2 [9]. Whole exome sequencing revealed a change in copy number of ADH7 and AHR in nonsyndromic CL/P [10]. Genome-wide association studies (GWAS) of CL/P have made major advances in the identification of candidate genes and loci in CL/P.…”

Two novel genes TOX3 and COL21A1 in large extended Malay families with nonsyndromic cleft lip and/or palate

“…Recent genomic study carried out among the cleft palate (CPO) of African population found two novel loci on chromosome 2 near CTNNA2 and on chromosome 19 in SULT2A1 (Butali et al, ). In addition, the emergence of next generation sequencing accelerates the finding of new loci associated with orofacial cleft (Cai et al, ). Copy number changes (CNC) analysis in exome sequencing has identified two CNC in ADH7 and AHR in two multiplex families from Honduran population, whereas these two genes play role in craniofacial development (Cai et al, ).…”

“…In addition, the emergence of next generation sequencing accelerates the finding of new loci associated with orofacial cleft (Cai et al, ). Copy number changes (CNC) analysis in exome sequencing has identified two CNC in ADH7 and AHR in two multiplex families from Honduran population, whereas these two genes play role in craniofacial development (Cai et al, ).…”