Fine-mapping of 18q21.1 locus identifies single nucleotide polymorphisms associated with nonsyndromic cleft lip with or without cleft palate

Amit K. Mitra, Holly Stessman, Robert J. Schaefer, Wen Wang, Chad L. Myers, Brian G. Van Ness, Soraya Beiraghi

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital birth defects. NSCL/P is a complex multifactorial disease caused by interactions between multiple environmental and genetic factors. However, the causal single nucleotide polymorphism (SNP) signature profile underlying the risk of familial NSCL/P still remains unknown. We previously reported a 5.7-Mb genomic region on chromosome 18q21.1 locus that potentially contributes to autosomal dominant, low-penetrance inheritance of NSCL/P. In the current study, we performed exome sequencing on 12 familial genomes (six affected individuals, two obligate carriers, and four seemingly unaffected individuals) of a six-generation family to identify candidate SNPs associated with NSCL/P risk. Subsequently, targeted bidirectional DNA re-sequencing of polymerase chain reaction (PCR)-amplified high-risk regions of MYO5B gene and sequenom iPLEX genotpying of 29 candidate SNPs were performed on a larger set of 33 members of this NSCL/P family (10 affected + 4 obligate carriers + 19 unaffected relatives) to find SNPs significantly associated with NSCL/P trait. SNP vs. NSCL/P association analysis showed the MYO5B SNP rs183559995 GA genotype had an odds ratio of 18.09 (95% Confidence Interval = 1.86-176.34; gender-adjusted P = 0.0019) compared to the reference GG genotype. Additionally, the following SNPs were also found significantly associated with NSCL/P risk: rs1450425 (LOXHD1), rs6507992 (SKA1), rs78950893 (SMAD7), rs8097060, rs17713847 (SCARNA17), rs6507872 (CTIF), rs8091995 (CTIF), and rs17715416 (MYO5B). We could thus identify mutations in several genes as key candidate SNPs associated with the risk of NSCL/P in this large multi-generation family.

Original languageEnglish (US)
Article number88
JournalFrontiers in Genetics
Volume7
Issue numberMAY
DOIs
StatePublished - May 23 2016
Externally publishedYes

Fingerprint

Cleft Lip
Cleft Palate
Single Nucleotide Polymorphism
Genotype
Exome
Penetrance
DNA Sequence Analysis
Genes
Chromosomes
Odds Ratio
Genome
Confidence Intervals
Polymerase Chain Reaction
Mutation

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Genetics
  • Genetics(clinical)

Cite this

Fine-mapping of 18q21.1 locus identifies single nucleotide polymorphisms associated with nonsyndromic cleft lip with or without cleft palate. / Mitra, Amit K.; Stessman, Holly; Schaefer, Robert J.; Wang, Wen; Myers, Chad L.; Van Ness, Brian G.; Beiraghi, Soraya.

In: Frontiers in Genetics, Vol. 7, No. MAY, 88, 23.05.2016.

Research output: Contribution to journalArticle

Mitra, Amit K. ; Stessman, Holly ; Schaefer, Robert J. ; Wang, Wen ; Myers, Chad L. ; Van Ness, Brian G. ; Beiraghi, Soraya. / Fine-mapping of 18q21.1 locus identifies single nucleotide polymorphisms associated with nonsyndromic cleft lip with or without cleft palate. In: Frontiers in Genetics. 2016 ; Vol. 7, No. MAY.
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abstract = "Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital birth defects. NSCL/P is a complex multifactorial disease caused by interactions between multiple environmental and genetic factors. However, the causal single nucleotide polymorphism (SNP) signature profile underlying the risk of familial NSCL/P still remains unknown. We previously reported a 5.7-Mb genomic region on chromosome 18q21.1 locus that potentially contributes to autosomal dominant, low-penetrance inheritance of NSCL/P. In the current study, we performed exome sequencing on 12 familial genomes (six affected individuals, two obligate carriers, and four seemingly unaffected individuals) of a six-generation family to identify candidate SNPs associated with NSCL/P risk. Subsequently, targeted bidirectional DNA re-sequencing of polymerase chain reaction (PCR)-amplified high-risk regions of MYO5B gene and sequenom iPLEX genotpying of 29 candidate SNPs were performed on a larger set of 33 members of this NSCL/P family (10 affected + 4 obligate carriers + 19 unaffected relatives) to find SNPs significantly associated with NSCL/P trait. SNP vs. NSCL/P association analysis showed the MYO5B SNP rs183559995 GA genotype had an odds ratio of 18.09 (95{\%} Confidence Interval = 1.86-176.34; gender-adjusted P = 0.0019) compared to the reference GG genotype. Additionally, the following SNPs were also found significantly associated with NSCL/P risk: rs1450425 (LOXHD1), rs6507992 (SKA1), rs78950893 (SMAD7), rs8097060, rs17713847 (SCARNA17), rs6507872 (CTIF), rs8091995 (CTIF), and rs17715416 (MYO5B). We could thus identify mutations in several genes as key candidate SNPs associated with the risk of NSCL/P in this large multi-generation family.",
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