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    A hypofunctional PAX1 mutation causes autosomal recessively inherited otofaciocervical syndrome
    (Springer, 2013) Pohl, Esther; Aykut, Ayca; Beleggia, Filippo; Karaca, Emin; Durmaz, Burak; Keupp, Katharina; Arslan, Esra; Onay, Melis Palamar; Yigit, Goekhan; Özkınay, Ferda; Wollnik, Bernd
    Otofaciocervical syndrome (OFCS) is an autosomal recessively inherited disorder characterized by facial dysmorphism, external ear anomalies with preauricular pits and hearing impairment, branchial cysts or fistulas, anomalies of the vertebrae and the shoulder girdle, and mild intellectual disability. In a large consanguineous family with OFCS from Turkey, we performed whole-exome sequencing (WES) of a single pooled DNA sample of four affected individuals. Filtering for variants with a percentage of alternate reads a parts per thousand yen90 % and a coverage of at least five reads identified only a single novel homozygous variant, c.497G > T, located in PAX1 that co-segregated with the disease in the family. PAX1 encodes a transcription factor with a critical role in pattern formation during embryogenesis in vertebrates. The mutation is predicted to substitute the glycine at position 166 to valine (p.G166V) within the highly conserved paired-box domain of the PAX1 protein. We performed a dual luciferase reporter assay to examine the transactivation of a regulatory sequence in the Nkx3-2 promoter region, which is a direct target of mouse Pax1 transcriptional regulation. We observed a significantly reduced transactivation in HEK293T cells overexpressing Pax1(G157V) in comparison to Pax1(WT) expressing cells, indicating a reduced DNA-binding affinity of the mutant protein. Taken together, our results show that the strategy of pooling DNA is a powerful, cost-effective application for WES in consanguineous families and establish PAX1 as a new disease-causing gene for OFCS and as part of the EYA-DACH-SIX-PAX network, important in early embryogenesis.
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    A hypofunctional PAX1 mutation causes autosomal recessively inherited otofaciocervical syndrome (vol 132, pg 1311, 2013)
    (Springer, 2013) Pohl, Esther; Aykut, Ayca; Beleggia, Filippo; Karaca, Emin; Durmaz, Burak; Keupp, Katharina; Arslan, Esra; Palamar, Melis; Yigit, Goekhan; Özkınay, Ferda; Wollnik, Bernd
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    Molecular Basis of beta-Thalassemia in the Population of the Aegean Region of Turkey: Identification of A Novel Deletion Mutation
    (Taylor & Francis Ltd, 2015) Özkınay, Ferda; Onay, Huseyin; Karaca, Emin; Arslan, Esra; Erturk, Biray; Solmaz, Asli Ece; Tekin, Ismihan Merve; Cogulu, Ozgur; Aydinok, Yesim; Vergin, Canan
    beta-Thalassemia (beta-thal) is the most common monogenic disorder in Turkey. The aim of this study was to investigate the spectrum of beta-thal mutations in the Aegean region of Turkey. The data was derived from 1171 unrelated beta-thal subjects, detected in a regional reference hospital between November 2004 and December 2013. Screening for the 22 common mutations was performed using the polymerase chain reaction (PCR)-reverse dot-blot method, and direct automated DNA sequencing for the unknown samples. Thirty-one different beta-thal alleles were identified. Seven mutations, namely IVS-I-110 (G>A) (41.7%), IVS-I-1 (G>A) (8.9%), IVS-II-745 (C>G) (8.6%), codon 8 (-AA) (7.7%), IVS-II-1 (G>A) (7.2%), IVS-I-6 (T>C) (6.6%), codon 39 (C>T) (4.6%) accounted for 85.3% of the mutated alleles. Frequencies of the remaining 24 beta-thal mutations were less than 2.2%; these included one novel mutation [HBB: c. 206_ 212del (p. Leu69Profs* 19)], and four others [-56 (G>C), codon 16 (-C), IVS-I (-3) (C>T) (codon 29), codon 76 (-C)] found in Turkey for the first time. The results will help to prevent severe beta-thal through genetic counseling and prenatal diagnosis (PND) in the Aegean region of Turkey.
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    Relationship Between IL1 beta-511C > T and ILRN VNTR Polymorphisms and Keratoconus
    (Lippincott Williams & Wilkins, 2014) Palamar, Melis; Onay, Huseyin; Ozdemir, Taha Resid; Arslan, Esra; Egrilmez, Sait; Özkınay, Ferda; Yagci, Ayse
    Purpose:The aim of this study was to evaluate the relationship between keratoconus (KC) and interleukin-1 (IL1 ) (-511C>T) and interleukin-1 receptor antagonist (IL1RN) variable number of tandem repeat (VNTR) polymorphisms that are potentially associated in their genetic susceptibility to KC.Methods:A total of 121 patients with KC and 121 healthy individuals were enrolled. Blood samples with ethylenediamine tetraacetic acid were obtained, and IL1 (-511C>T) (rs16944) (polymerase chain reaction-restriction fragment length polymorphism method) and IL1RN VNTR polymorphisms (rs2234663) (polymerase chain reaction and agarose gel imaging) were investigated.Results:Genotype and allele distribution for IL1 (-511C>T) and IL1RN VNTR polymorphisms among the KC and healthy groups showed no difference (for all; P > 0.05).Conclusions:Because the genotype and allele frequency of both polymorphisms are identical, it is most likely that IL1-511C>T and IL1RN VNTR polymorphisms do not play a role in the development of KC in the Turkish population.