Identification of putative regulatory single-nucleotide variants in NTN1 gene associated with NSCL/P

Tanaka SA, Mahabir RC, Jupiter DC, Menezes JM. Updating the epidemiology of cleft lip with or without cleft palate. Plast Reconstr Surg. 2012;129:511e–8e.

Article  PubMed  Google Scholar 

Fan D, Wu S, Liu L, Xia Q, Tian G, Wang W, et al. Prevalence of non-syndromic orofacial clefts: based on 15,094,978 Chinese perinatal infants. Oncotarget. 2018;9:13981–90.

Article  PubMed  PubMed Central  Google Scholar 

Sivertsen A, Wilcox A, Skjaerven R, Vindenes H, Abyholm F, Harville E, et al. Familial risk of oral clefts by morphological type and severity: population based cohort study of first degree relatives. BMJ. 2008;336:432–4.

Article  PubMed  PubMed Central  Google Scholar 

Marazita ML. The evolution of human genetic studies of cleft lip and cleft palate. Annu Rev Genomics Hum Genet. 2012;13:263–83.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mossey P, Little J, Munger R, Dixon M, Shaw W. Cleft lip and palate. Lancet 2009;374:1773–85.

Article  PubMed  Google Scholar 

Harville E, Wilcox A, Lie R, Vindenes H, Abyholm F. Cleft lip and palate versus cleft lip only: are they distinct defects? Am J Epidemiol. 2005;162:448–53.

Article  PubMed  Google Scholar 

Grosen D, Chevrier C, Skytthe A, Bille C, Mølsted K, Sivertsen A, et al. A cohort study of recurrence patterns among more than 54,000 relatives of oral cleft cases in Denmark: support for the multifactorial threshold model of inheritance. J Med Genet. 2010;47:162–8.

Article  PubMed  Google Scholar 

Beaty TH, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, et al. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet. 2010;42:525–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ludwig KU, Mangold E, Herms S, Nowak S, Reutter H, Paul A, et al. Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. Nat Genet. 2012;44:968–71.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beaty TH, Taub MA, Scott AF, Murray JC, Marazita ML, Schwender H, et al. Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study. Hum Genet. 2013;132:771–81.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Leslie EJ, Carlson JC, Shaffer JR, Feingold E, Wehby G, Laurie CA, et al. A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13. Hum Mol Genet 2016;25:2862–72.

CAS  PubMed  PubMed Central  Google Scholar 

Sun Y, Huang Y, Yin A, Pan Y, Wang Y, Wang C, et al. Genome-wide association study identifies a new susceptibility locus for cleft lip with or without a cleft palate. Nat Commun. 2015;6:6414.

Article  PubMed  Google Scholar 

Mukhopadhyay N, Feingold E, Moreno-Uribe L, Wehby G, Valencia-Ramirez LC, Muneton CPR, et al. Genome-wide association study of non-syndromic orofacial clefts in a multiethnic sample of families and controls identifies novel regions. Front Cell Dev Biol. 2021;9:621482.

Article  PubMed  PubMed Central  Google Scholar 

Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, et al. Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet. 2015;96:397–411.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li D, Zhu G, Lou S, Ma L, Zhang C, Pan Y, et al. The functional variant of NTN1 contributes to the risk of nonsyndromic cleft lip with or without cleft palate. Eur J Hum Genet. 2020;28:453–60.

Article  CAS  PubMed  Google Scholar 

Tam V, Patel N, Turcotte M, Bosse Y, Pare G, Meyre D. Benefits and limitations of genome-wide association studies. Nat Rev Genet. 2019;20:467–84.

Article  CAS  PubMed  Google Scholar 

Bonnefond A, Froguel P. Rare and common genetic events in type 2 diabetes: what should biologists know? Cell Metab. 2015;21:357–68.

Article  CAS  PubMed  Google Scholar 

Sazonovs A, Barrett JC. Rare-variant studies to complement genome-wide association studies. Annu Rev Genomics Hum Genet. 2018;19:97–112.

Article  CAS  PubMed  Google Scholar 

International HapMap C. A haplotype map of the human genome. Nature. 2005;437:1299–320.

Article  Google Scholar 

Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science. 2008;322:881–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012;337:1190–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thieme F, Ludwig KU. The role of noncoding genetic variation in isolated orofacial clefts. J Dent Res. 2017;96:1238–47.

Article  CAS  PubMed  Google Scholar 

Huang L, Jia Z, Shi Y, Du Q, Shi J, Wang Z, et al. Genetic factors define CPO and CLO subtypes of nonsyndromicorofacial cleft. PLOS Genet. 2019;15:e1008357.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25:1754–60.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics.2009;25:2078–9.

Article  PubMed  PubMed Central  Google Scholar 

Yang J, Bakshi A, Zhu Z, Hemani G, Vinkhuyzen A, Lee S, et al. Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index. Nat Genet. 2015;47:1114–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013;Chapter 7:Unit7 20. https://doi.org/10.1002/0471142905.hg0720s76.

Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812–4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7:575–6.

Article  CAS  PubMed  Google Scholar 

Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019;47:D886–D94.

Article  CAS  PubMed  Google Scholar 

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012;22:1790–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Quan C, Ping J, Lu H, Zhou G, Lu Y. 3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database. Nucleic Acids Res. 2022;50:D950–D5.

Article  CAS  PubMed  Google Scholar 

Ward L, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012;40:D930–4.

Article  CAS  PubMed  Google Scholar 

Kou I, Otomo N, Takeda K, Momozawa Y, Lu HF, Kubo M, et al. Genome-wide association study identifies 14 previously unreported susceptibility loci for adolescent idiopathic scoliosis in Japanese. Nat Commun. 2019;10:3685.

Article  PubMed  PubMed Central  Google Scholar 

Barbeira AN, Bonazzola R, Gamazon ER, Liang Y, Park Y, Kim-Hellmuth S, et al. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol. 2021;22:49.

Article  PubMed  PubMed Central  Google Scholar 

Chen S, Jia Z, Cai M, Ye M, Wu D, Wan T, et al. viaSP1-mediated upregulation of long noncoding RNA ZFAS1 involved in non-syndromic cleft lip and palate inactivating WNT/β-catenin signaling pathway. Front Cell Dev Biol. 2021;9:662780.

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