Guney Bademci - Academia.edu (original) (raw)

Papers by Guney Bademci

Research paper thumbnail of Comprehensive Analysis of Deafness Genes in Families with Autosomal Recessive Nonsyndromic Hearing Loss

PLOS ONE, 2015

Comprehensive genetic testing has the potential to become the standard of care for individuals wi... more Comprehensive genetic testing has the potential to become the standard of care for individuals with hearing loss. In this study, we investigated the genetic etiology of autosomal recessive nonsyndromic hearing loss (ARNSHL) in a Turkish cohort including individuals with cochlear implant, who had a pedigree suggestive of an autosomal recessive inheritance. A workflow including prescreening of GJB2 and a targeted next generation sequencing panel (Illumına TruSightTM Exome) covering 2761 genes that we briefly called as mendelian exome sequencing was used. This panel includes 102 deafness genes and a number of genes causing Mendelian disorders. Using this approach, we identified causative variants in 21 of 29 families. Three different GJB2 variants were present in seven families. Remaining 14 families had 15 different variants in other known NSHL genes (MYO7A, MYO15A, MARVELD2, TMIE, DFNB31, LOXHD1, GPSM2, TMC1, USH1G, CDH23). Of these variants, eight are novel. Mutation detection rate of our workflow is 72.4%, confirming the usefulness of targeted sequencing approach in NSHL.

Research paper thumbnail of Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome

Orphanet Journal of Rare Diseases, 2015

Background: 3MC1 syndrome is a rare autosomal recessive disorder characterized by intellectual di... more Background: 3MC1 syndrome is a rare autosomal recessive disorder characterized by intellectual disability, short stature and distinct craniofacial, umbilical, and sacral anomalies. Five mutations in MASP1, encoding lectin complement pathway enzymes MASP-1 and MASP-3, have thus far been reported to cause 3MC1 syndrome. Only one previously reported mutation affects both MASP-1 and MASP-3, while the other mutations affect only MASP-3. Methods: We evaluated six unrelated individuals with 3MC1 syndrome and performed Sanger sequencing for all coding exons of MASP1. We also measured complement lectin and alternative pathway activities in an affected individual's serum. Results: We found two novel splice site mutations, c.1012-2A > G in one and c.891 + 1G > T in two probands, and three novel missense mutations, c.1451G > A (p.G484E), c.1657G > A (p.D553N), and c.1987G > T (p.D663Y). Missense mutations affect only MASP-3, while splice site mutations affect both MASP-1 and MASP-3. In a proband who is homozygous for c.891 + 1G > T, we detected a total lack of lectin complement pathway activity and a 2.5-fold lower alternative pathway activity. The phenotype observed in patients whose both MASP-1 and MASP-3 are affected and in those whose only MASP-3 is affected does not appear to be different. We observed structural brain abnormalities, neonatal tooth, a vascular anomaly and a solid lesion in liver as novel phenotypic features of 3MC1 syndrome. Conclusion: Novel mutations and additional phenotypic features expand the genotypic and phenotypic spectrum of 3MC1 syndrome. Although patients with MASP-1 dysfunction in addition to disrupted MASP-3 have an altered complement system, their disease phenotype is not different from those having only MASP-3 dysfunction.

Research paper thumbnail of A mayan founder mutation is a common cause of deafness in guatemala

Clinical Genetics, 2015

Over 5% of the world population have varying degrees of hearing loss. Mutations in GJB2 are the m... more Over 5% of the world population have varying degrees of hearing loss. Mutations in GJB2 are the most common cause of autosomal recessive non-syndromic hearing loss (NSHL) in many populations. The frequency and type of mutations are influenced by ethnicity. Guatemala is a multi-ethnic country with four major populations: Maya, Ladino, Xinca, and Garifuna. To determine the mutation profile of GJB2 in a NSHL population from Guatemala, we sequenced both exons of GJB2 in 133 unrelated families. A total of six pathogenic variants were detected. The most frequent pathogenic variant is c.131G>A (p.Trp44*) detected in 21 of 266 alleles. We show that c.131G>A is associated with a conserved haplotype in Guatemala suggesting a single founder. The majority of Mayan population lives in the west region of the country from where all c.131G>A carriers originated. Further analysis of genome-wide variation of individuals carrying the c.131G>A mutation compared to those of Native American, European, and African populations shows a close match with the Mayan population.

Research paper thumbnail of Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort

Genetics in Medicine, 2015

Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic he... more Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES). After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes. We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects. We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.Genet Med advance online publication 30 July 2015Genetics in Medicine (2015); doi:10.1038/gim.2015.89.

Research paper thumbnail of MORFAN Syndrome: An Infantile Hypoinsulinemic Hypoketotic Hypoglycemia Due to an AKT2 Mutation

The Journal of pediatrics, Jan 21, 2015

We report a child with hypoinsulinemic hypoglycemia and distinctive facies, with a diagnosis of t... more We report a child with hypoinsulinemic hypoglycemia and distinctive facies, with a diagnosis of the previously described MORFAN (Mental retardation, pre- and post-natal Overgrowth, Remarkable Face, and Acanthosis Nigricans) syndrome of unknown etiology. Whole-exome sequencing revealed a de novo AKT2 mutation. Although AKT2 has been implicated in four patients with hypoinsulinemic hypoglycemia, our report expands phenotypic spectrum to include MORFAN syndrome characteristics.

Research paper thumbnail of Evaluation Of The Results Of Cordocentesis; 9 Years Experience

Journal of Turkish Society of Obstetric and Gynecology, 2013

... Correspondence: Turgay fiener, ‹. ‹nönü Cad No: 57/4, Eskiflehir e-mail: turgays@mail.com e-A... more ... Correspondence: Turgay fiener, ‹. ‹nönü Cad No: 57/4, Eskiflehir e-mail: turgays@mail.com e-Address: http://www.perinataldergi.com/20100182001 Page 2. Introduction ... In the study of Acar et al.15 which evaluated 250 cordocentesis cases, fetal loss rate was found as 4.8%. ...

Research paper thumbnail of Novel domain-specific POU3F4 mutations are associated with X-linked deafness: examples from different populations

BMC Medical Genetics, 2015

Mutations in the POU3F4 gene cause X-linked deafness type 3 (DFN3), which is characterized by inn... more Mutations in the POU3F4 gene cause X-linked deafness type 3 (DFN3), which is characterized by inner ear anomalies. Three Turkish, one Ecuadorian, and one Nigerian families were included based on either inner ear anomalies detected in probands or X-linked family histories. Exome sequencing and/or Sanger sequencing were performed in order to identify the causative DNA variants in these families. Four novel, c.707A>C (p.(Glu236Ala)), c.772delG (p.(Glu258ArgfsX30)), c.902C>T (p.(Pro301Leu)), c.987T>C (p.(Ile308Thr)), and one previously reported mutation c.346delG (p.(Ala116ProfsX26)) in POU3F4, were identified. All mutations identified are predicted to affect the POU-specific or POU homeo domains of the protein and co-segregated with deafness in all families. Expanding the spectrum of POU3F4 mutations in different populations along with their associated phenotypes provides better understanding of their clinical importance and will be helpful in clinical evaluation and counseling of the affected individuals.

Research paper thumbnail of Ceftriaxone-induced symptomatic pseudolithiasis mimicking ICP elevation

Neurochirurgie, 2006

In neurosurgery, ceftriaxone is a widely used, third generation cephalosporin for the treatment o... more In neurosurgery, ceftriaxone is a widely used, third generation cephalosporin for the treatment of CNS infections and perioperational prophylaxis. Recent studies have demonstrated that ceftriaxone induces reversible precipitates in the gallbladder. This complication is referred to as "biliary pseudolithiasis", and it has symptoms similar to the raised intracranial pressure (ICP) symptoms of the perioperative period. Symptomatic biliary pseudolithiasis should be kept in mind in all pediatric neurosurgery cases under ceftriaxone therapy in order to prevent unnecessary postoperative investigations and surgery.

Research paper thumbnail of Evidence for genotype–phenotype correlation for OTOF mutations

International Journal of Pediatric Otorhinolaryngology, 2014

The aim of this study is to evaluate the auditory phenotype in subjects with OTOF gene mutations ... more The aim of this study is to evaluate the auditory phenotype in subjects with OTOF gene mutations to describe genotype-phenotype correlations. Twenty-two affected members from three families with homozygous OTOF mutations were included. Nine subjects were evaluated audiologically with otoscopic examination, pure-tone audiometry, tympanometry with acoustic reflex testing, auditory brain stem responses, and otoacoustic emission tests. Homozygous c.4718T>C (p.Ile1573Thr) mutation was associated with the auditory neuropathy/auditory dys-synchrony (AN/AD) phenotype and with progressive sensorineural hearing loss in four siblings in one family, while homozygous c.4467dupC (p.I1490HfsX19) was associated with severe to profound sensorineural hearing loss without AN/AD in four relatives in another family. Homozygous c.1958delC (p.Pro653LeufsX13) mutation was associated with moderate sensorineural hearing loss without AN/AD in one affected person in an additional family. The audiological phenotype associated with different OTOF mutations appears to be consistently different suggesting the presence of a genotype-phenotype correlation.

Research paper thumbnail of Identification of copy number variants through whole-exome sequencing in autosomal recessive nonsyndromic hearing loss

Genetic testing and molecular biomarkers, 2014

Genetic variants account for more than half of the cases with congenital or prelingual onset hear... more Genetic variants account for more than half of the cases with congenital or prelingual onset hearing loss. Autosomal recessive nonsyndromic hearing loss (ARNSHL) is the most common subgroup. Whole-exome sequencing (WES) has been shown to be effective detecting deafness-causing single-nucleotide variants (SNVs) and insertion/deletions (INDELs). After analyzing the WES data for causative SNVs or INDELs involving previously reported deafness genes in 78 families with ARNSHL, we searched for copy number variants (CNVs) through two different tools in 24 families that remained unresolved. We detected large homozygous deletions in STRC and OTOA in single families. Thus, causative CNVs in known deafness genes explain 2 out of 78 (2.6%) families in our sample set. We conclude that CNVs can be reliably detected through WES and should be the part of pipelines used to clarify genetic basis of hearing loss.

Research paper thumbnail of Common genes for non-syndromic deafness are uncommon in sub-Saharan Africa: a report from Nigeria

International journal of pediatric otorhinolaryngology, 2014

Little is known about the molecular epidemiology of deafness in sub-Saharan Africa (SSA). Even in... more Little is known about the molecular epidemiology of deafness in sub-Saharan Africa (SSA). Even in Nigeria, the most populous African nation, no genetic studies of deafness have been conducted. This pioneering work aims at investigating the frequencies of gene mutations relatively common in other parts of the world (i.e. those in GJB2, GJB6, and mitochondrial DNA) among subjects from Nigeria with hearing loss (HL) with no evidence of acquired pathology or syndromic findings. In addition, we review the literature on the genetics of deafness in SSA. We evaluated 81 unrelated deaf probands from the Yoruba tribe residing in Ibadan, a suburban city in Nigeria, for the aetiology of their deafness. Subjects underwent genetic testing if their history was negative for an environmental cause and physical examination did not find evidence of a syndrome. Both exons of GJB2 and mitochondrial DNA flanking the 1555A>G mutations were PCR-amplified followed by Sanger sequencing. GJB6 deletions wer...

Research paper thumbnail of FAM65B is a membrane-associated protein of hair cell stereocilia required for hearing

Proceedings of the National Academy of Sciences, 2014

In a large consanguineous Turkish kindred with recessive nonsyndromic, prelingual, profound heari... more In a large consanguineous Turkish kindred with recessive nonsyndromic, prelingual, profound hearing loss, we identified in the gene FAM65B (MIM611410) a splice site mutation (c.102-1G>A) that perfectly cosegregates with the phenotype in the family. The mutation leads to exon skipping and deletion of 52-amino acid residues of a PX membrane localization domain. FAM65B is known to be involved in myotube formation and in regulation of cell adhesion, polarization, and migration. We show that wild-type Fam65b is expressed during embryonic and postnatal development stages in murine cochlea, and that the protein localizes to the plasma membranes of the stereocilia of inner and outer hair cells of the inner ear. The wild-type protein targets the plasma membrane, whereas the mutant protein accumulates in cytoplasmic inclusion bodies and does not reach the membrane. In zebrafish, knockdown of fam65b leads to significant reduction of numbers of saccular hair cells and neuromasts and to hearing loss. We conclude that FAM65B is a plasma membrane-associated protein of hair cell stereocilia that is essential for hearing.

Research paper thumbnail of Novel mutations confirm that COL11A2 is responsible for autosomal recessive non-syndromic hearing loss DFNB53

Molecular Genetics and Genomics, 2015

Hearing loss (HL) is a major public health issue. It is clinically and genetically heterogeneous.... more Hearing loss (HL) is a major public health issue. It is clinically and genetically heterogeneous.The identification of the causal mutation is important for early diagnosis, clinical follow-up, and genetic counseling. HL due to mutations in COL11A2, encoding collagen type XI alpha-2, can be non-syndromic autosomal-dominant or autosomal-recessive, and also syndromic as in Otospondylomegaepiphyseal Dysplasia, Stickler syndrome type III, and Weissenbacher-Zweymuller syndrome. However, thus far only one mutation co-segregating with autosomal recessive non-syndromic hearing loss (ARNSHL) in a single family has been reported. In this study, whole exome sequencing of two consanguineous families with ARNSHL from Tunisia and Turkey revealed two novel causative COL11A2 mutations, c.109G > T (p.Ala37Ser) and c.2662C > A (p.Pro888Thr). The variants identified co-segregated with deafness in both families. All homozygous individuals in those families had early onset profound hearing loss across all frequencies without syndromic findings. The variants are predicted to be damaging the protein function. The p.Pro888Thr mutation affects a -Gly-X-Y- triplet repeat motif. The novel p.Ala37Ser is the first missense mutation located in the NC4 domain of the COL11A2 protein. Structural model suggests that this mutation will likely obliterate, or at least partially compromise, the ability of NC4 domain to interact with its cognate ligands. In conclusion, we confirm that COL11A2 mutations cause ARNSHL and broaden the mutation spectrum that may shed new light on genotype-phenotype correlation for the associated phenotypes and clinical follow-up.

Research paper thumbnail of Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform

PLoS ONE, 2011

Despite the ever-increasing throughput and steadily decreasing cost of next generation sequencing... more Despite the ever-increasing throughput and steadily decreasing cost of next generation sequencing (NGS), whole genome sequencing of humans is still not a viable option for the majority of genetics laboratories. This is particularly true in the case of complex disease studies, where large sample sets are often required to achieve adequate statistical power. To fully leverage the potential of NGS technology on large sample sets, several methods have been developed to selectively enrich for regions of interest. Enrichment reduces both monetary and computational costs compared to whole genome sequencing, while allowing researchers to take advantage of NGS throughput. Several targeted enrichment approaches are currently available, including molecular inversion probe ligation sequencing (MIPS), oligonucleotide hybridization based approaches, and PCR-based strategies. To assess how these methods performed when used in conjunction with the ABI SOLID3+, we investigated three enrichment techniques: Nimblegen oligonucleotide hybridization array-based capture; Agilent SureSelect oligonucleotide hybridization solution-based capture; and Raindance Technologies' multiplexed PCRbased approach. Target regions were selected from exons and evolutionarily conserved areas throughout the human genome. Probe and primer pair design was carried out for all three methods using their respective informatics pipelines. In all, approximately 0.8 Mb of target space was identical for all 3 methods. SOLiD sequencing results were analyzed for several metrics, including consistency of coverage depth across samples, on-target versus off-target efficiency, allelic bias, and genotype concordance with array-based genotyping data. Agilent SureSelect exhibited superior on-target efficiency and correlation of read depths across samples. Nimblegen performance was similar at read depths at 206 and below. Both Raindance and Nimblegen SeqCap exhibited tighter distributions of read depth around the mean, but both suffered from lower on-target efficiency in our experiments. Raindance demonstrated the highest versatility in assay design.

Research paper thumbnail of Identifying Consensus Disease Pathways in Parkinson's Disease Using an Integrative Systems Biology Approach

PLoS ONE, 2011

Parkinson's disease (PD) has had six genome-wide association studies (GWAS) conducted as well as ... more Parkinson's disease (PD) has had six genome-wide association studies (GWAS) conducted as well as several gene expression studies. However, only variants in MAPT and SNCA have been consistently replicated. To improve the utility of these approaches, we applied pathway analyses integrating both GWAS and gene expression. The top 5000 SNPs (p,0.01) from a joint analysis of three existing PD GWAS were identified and each assigned to a gene. For gene expression, rather than the traditional comparison of one anatomical region between sets of patients and controls, we identified differentially expressed genes between adjacent Braak regions in each individual and adjusted using average control expression profiles. Over-represented pathways were calculated using a hyper-geometric statistical comparison. An integrated, systems metaanalysis of the over-represented pathways combined the expression and GWAS results using a Fisher's combined probability test. Four of the top seven pathways from each approach were identical. The top three pathways in the metaanalysis, with their corrected p-values, were axonal guidance (p = 2.8E-07), focal adhesion (p = 7.7E-06) and calcium signaling (p = 2.9E-05). These results support that a systems biology (pathway) approach will provide additional insight into the genetic etiology of PD and that these pathways have both biological and statistical support to be important in PD.

Research paper thumbnail of Identification of Rare Variants in Parkinson Disease Using Next-Generation Sequencing (S22.007)

Research paper thumbnail of Whole exome sequencing of rare variants in EIF4G1 and VPS35 in Parkinson disease

Neurology, 2013

Recently, vacuolar protein sorting 35 (VPS35) and eukaryotic translation initiation factor 4 gamm... more Recently, vacuolar protein sorting 35 (VPS35) and eukaryotic translation initiation factor 4 gamma 1 (EIF4G1) have been identified as 2 causal Parkinson disease (PD) genes. We used whole exome sequencing for rapid, parallel analysis of variations in these 2 genes. We performed whole exome sequencing in 213 patients with PD and 272 control individuals. Those rare variants (RVs) with <5% frequency in the exome variant server database and our own control data were considered for analysis. We performed joint gene-based tests for association using RVASSOC and SKAT (Sequence Kernel Association Test) as well as single-variant test statistics. We identified 3 novel VPS35 variations that changed the coded amino acid (nonsynonymous) in 3 cases. Two variations were in multiplex families and neither segregated with PD. In EIF4G1, we identified 11 (9 nonsynonymous and 2 small indels) RVs including the reported pathogenic mutation p.R1205H, which segregated in all affected members of a large family, but also in 1 unaffected 86-year-old family member. Two additional RVs were found in isolated patients only. Whereas initial association studies suggested an association (p = 0.04) with all RVs in EIF4G1, subsequent testing in a second dataset for the driving variant (p.F1461) suggested no association between RVs in the gene and PD. We confirm that the specific EIF4G1 variation p.R1205H seems to be a strong PD risk factor, but is nonpenetrant in at least one 86-year-old. A few other select RVs in both genes could not be ruled out as causal. However, there was no evidence for an overall contribution of genetic variability in VPS35 or EIF4G1 to PD development in our dataset.

Research paper thumbnail of A rare novel deletion of the tyrosine hydroxylase gene in Parkinson disease

Human Mutation, 2010

Tyrosine hydroxylase (TH) enzyme is a rate limiting enzyme in dopamine biosynthesis. Missense mut... more Tyrosine hydroxylase (TH) enzyme is a rate limiting enzyme in dopamine biosynthesis. Missense mutation in both alleles of the TH gene is known to cause dopamine-related phenotypes, including dystonia and infantile Parkinsonism. However, it is not clear if single allele mutation in TH modifies the susceptibility to the adult form of Parkinson disease (PD). We reported a novel deletion of entire TH gene in an adult with PD. The deletion was first identified by copy number variation (CNV) analysis in a genome-wide association study using Illumina Infinium BeadChips. After screening 635 cases and 642 controls, the deletion was found in one PD case but not in any control. The deletion was confirmed by multiple quantitative PCR (qPCR) assays. There is no additional exonic single nucleotide variant in the one copy of TH gene of the patient. The patient has an age-at-onset of 54 years, no evidence for dystonia, and was responsive to L-DOPA. This case supports the importance of the TH gene in PD pathogenesis and raises more attention to rare variants in candidate genes being a risk factor for Parkinson disease.

Research paper thumbnail of Tyrosine Hydroxylase Gene: Another Piece of the Genetic Puzzle of Parkinson’s Disease

CNS & Neurological Disorders - Drug Targets, 2012

The tyrosine hydroxylase (TH) gene encodes a monoxygenase that catalyzes the rate limiting step i... more The tyrosine hydroxylase (TH) gene encodes a monoxygenase that catalyzes the rate limiting step in dopamine biosynthesis. A hallmark of Parkinson's disease (PD) is the loss of dopaminergic neurons in the substantia nigra. Consistent with the essential role of TH in dopamine homeostasis, missense mutations in both alleles of TH have been associated with severe Parkinsonism-related phenotypes including infantile Parkinsonism. It has been speculated for a long time that genetic variants in the TH gene modify adult-onset PD susceptibility but the answer has not been clear. Genetic variants (both sequence variations and structural variations) can be classified into three categories based on their relative frequency in population: common variants (polymorphisms), rare variants and mutations. Each of these factors has a different mode in influencing the genetic risk and often requires different approaches to decipher their contributions to the disease. In the past few years, the revolutionary advances in genomic technology have allowed systematic evaluations of these genetic variants in PD, such as the genome-wide association study (GWAS, to survey common variants), copy number variation analysis (to detect structural variations), and massive parallel next generation sequencing (to detect rare variants and mutations). In this review, we have summarized the latest evidence on TH genetic variants in PD, including our ongoing effort of using whole exome sequencing to search for rare variants in PD patients.

Research paper thumbnail of Is Recurrent Abortion an Indication for Subtelomeric Region Analysis?

Turkiye Klinikleri …, 2010

Yasal uyarı: Bu sitede yayınlanan resim, yazı ve diğer uygulamaların her hakkı Ortadoğu Reklam Ve... more Yasal uyarı: Bu sitede yayınlanan resim, yazı ve diğer uygulamaların her hakkı Ortadoğu Reklam Ve Yayıncılık A.Ş. 'ye aittir. Kaynak gösterilmeden kullanılamaz. Bu site hekimleri sağlık alanında bilgilendirmeye yönelik hazırlanmıştır. Sitede yer alan bilgiler tanı ve tedavi amaçlı ...

Research paper thumbnail of Comprehensive Analysis of Deafness Genes in Families with Autosomal Recessive Nonsyndromic Hearing Loss

PLOS ONE, 2015

Comprehensive genetic testing has the potential to become the standard of care for individuals wi... more Comprehensive genetic testing has the potential to become the standard of care for individuals with hearing loss. In this study, we investigated the genetic etiology of autosomal recessive nonsyndromic hearing loss (ARNSHL) in a Turkish cohort including individuals with cochlear implant, who had a pedigree suggestive of an autosomal recessive inheritance. A workflow including prescreening of GJB2 and a targeted next generation sequencing panel (Illumına TruSightTM Exome) covering 2761 genes that we briefly called as mendelian exome sequencing was used. This panel includes 102 deafness genes and a number of genes causing Mendelian disorders. Using this approach, we identified causative variants in 21 of 29 families. Three different GJB2 variants were present in seven families. Remaining 14 families had 15 different variants in other known NSHL genes (MYO7A, MYO15A, MARVELD2, TMIE, DFNB31, LOXHD1, GPSM2, TMC1, USH1G, CDH23). Of these variants, eight are novel. Mutation detection rate of our workflow is 72.4%, confirming the usefulness of targeted sequencing approach in NSHL.

Research paper thumbnail of Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome

Orphanet Journal of Rare Diseases, 2015

Background: 3MC1 syndrome is a rare autosomal recessive disorder characterized by intellectual di... more Background: 3MC1 syndrome is a rare autosomal recessive disorder characterized by intellectual disability, short stature and distinct craniofacial, umbilical, and sacral anomalies. Five mutations in MASP1, encoding lectin complement pathway enzymes MASP-1 and MASP-3, have thus far been reported to cause 3MC1 syndrome. Only one previously reported mutation affects both MASP-1 and MASP-3, while the other mutations affect only MASP-3. Methods: We evaluated six unrelated individuals with 3MC1 syndrome and performed Sanger sequencing for all coding exons of MASP1. We also measured complement lectin and alternative pathway activities in an affected individual's serum. Results: We found two novel splice site mutations, c.1012-2A > G in one and c.891 + 1G > T in two probands, and three novel missense mutations, c.1451G > A (p.G484E), c.1657G > A (p.D553N), and c.1987G > T (p.D663Y). Missense mutations affect only MASP-3, while splice site mutations affect both MASP-1 and MASP-3. In a proband who is homozygous for c.891 + 1G > T, we detected a total lack of lectin complement pathway activity and a 2.5-fold lower alternative pathway activity. The phenotype observed in patients whose both MASP-1 and MASP-3 are affected and in those whose only MASP-3 is affected does not appear to be different. We observed structural brain abnormalities, neonatal tooth, a vascular anomaly and a solid lesion in liver as novel phenotypic features of 3MC1 syndrome. Conclusion: Novel mutations and additional phenotypic features expand the genotypic and phenotypic spectrum of 3MC1 syndrome. Although patients with MASP-1 dysfunction in addition to disrupted MASP-3 have an altered complement system, their disease phenotype is not different from those having only MASP-3 dysfunction.

Research paper thumbnail of A mayan founder mutation is a common cause of deafness in guatemala

Clinical Genetics, 2015

Over 5% of the world population have varying degrees of hearing loss. Mutations in GJB2 are the m... more Over 5% of the world population have varying degrees of hearing loss. Mutations in GJB2 are the most common cause of autosomal recessive non-syndromic hearing loss (NSHL) in many populations. The frequency and type of mutations are influenced by ethnicity. Guatemala is a multi-ethnic country with four major populations: Maya, Ladino, Xinca, and Garifuna. To determine the mutation profile of GJB2 in a NSHL population from Guatemala, we sequenced both exons of GJB2 in 133 unrelated families. A total of six pathogenic variants were detected. The most frequent pathogenic variant is c.131G>A (p.Trp44*) detected in 21 of 266 alleles. We show that c.131G>A is associated with a conserved haplotype in Guatemala suggesting a single founder. The majority of Mayan population lives in the west region of the country from where all c.131G>A carriers originated. Further analysis of genome-wide variation of individuals carrying the c.131G>A mutation compared to those of Native American, European, and African populations shows a close match with the Mayan population.

Research paper thumbnail of Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort

Genetics in Medicine, 2015

Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic he... more Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES). After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes. We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects. We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.Genet Med advance online publication 30 July 2015Genetics in Medicine (2015); doi:10.1038/gim.2015.89.

Research paper thumbnail of MORFAN Syndrome: An Infantile Hypoinsulinemic Hypoketotic Hypoglycemia Due to an AKT2 Mutation

The Journal of pediatrics, Jan 21, 2015

We report a child with hypoinsulinemic hypoglycemia and distinctive facies, with a diagnosis of t... more We report a child with hypoinsulinemic hypoglycemia and distinctive facies, with a diagnosis of the previously described MORFAN (Mental retardation, pre- and post-natal Overgrowth, Remarkable Face, and Acanthosis Nigricans) syndrome of unknown etiology. Whole-exome sequencing revealed a de novo AKT2 mutation. Although AKT2 has been implicated in four patients with hypoinsulinemic hypoglycemia, our report expands phenotypic spectrum to include MORFAN syndrome characteristics.

Research paper thumbnail of Evaluation Of The Results Of Cordocentesis; 9 Years Experience

Journal of Turkish Society of Obstetric and Gynecology, 2013

... Correspondence: Turgay fiener, ‹. ‹nönü Cad No: 57/4, Eskiflehir e-mail: turgays@mail.com e-A... more ... Correspondence: Turgay fiener, ‹. ‹nönü Cad No: 57/4, Eskiflehir e-mail: turgays@mail.com e-Address: http://www.perinataldergi.com/20100182001 Page 2. Introduction ... In the study of Acar et al.15 which evaluated 250 cordocentesis cases, fetal loss rate was found as 4.8%. ...

Research paper thumbnail of Novel domain-specific POU3F4 mutations are associated with X-linked deafness: examples from different populations

BMC Medical Genetics, 2015

Mutations in the POU3F4 gene cause X-linked deafness type 3 (DFN3), which is characterized by inn... more Mutations in the POU3F4 gene cause X-linked deafness type 3 (DFN3), which is characterized by inner ear anomalies. Three Turkish, one Ecuadorian, and one Nigerian families were included based on either inner ear anomalies detected in probands or X-linked family histories. Exome sequencing and/or Sanger sequencing were performed in order to identify the causative DNA variants in these families. Four novel, c.707A>C (p.(Glu236Ala)), c.772delG (p.(Glu258ArgfsX30)), c.902C>T (p.(Pro301Leu)), c.987T>C (p.(Ile308Thr)), and one previously reported mutation c.346delG (p.(Ala116ProfsX26)) in POU3F4, were identified. All mutations identified are predicted to affect the POU-specific or POU homeo domains of the protein and co-segregated with deafness in all families. Expanding the spectrum of POU3F4 mutations in different populations along with their associated phenotypes provides better understanding of their clinical importance and will be helpful in clinical evaluation and counseling of the affected individuals.

Research paper thumbnail of Ceftriaxone-induced symptomatic pseudolithiasis mimicking ICP elevation

Neurochirurgie, 2006

In neurosurgery, ceftriaxone is a widely used, third generation cephalosporin for the treatment o... more In neurosurgery, ceftriaxone is a widely used, third generation cephalosporin for the treatment of CNS infections and perioperational prophylaxis. Recent studies have demonstrated that ceftriaxone induces reversible precipitates in the gallbladder. This complication is referred to as "biliary pseudolithiasis", and it has symptoms similar to the raised intracranial pressure (ICP) symptoms of the perioperative period. Symptomatic biliary pseudolithiasis should be kept in mind in all pediatric neurosurgery cases under ceftriaxone therapy in order to prevent unnecessary postoperative investigations and surgery.

Research paper thumbnail of Evidence for genotype–phenotype correlation for OTOF mutations

International Journal of Pediatric Otorhinolaryngology, 2014

The aim of this study is to evaluate the auditory phenotype in subjects with OTOF gene mutations ... more The aim of this study is to evaluate the auditory phenotype in subjects with OTOF gene mutations to describe genotype-phenotype correlations. Twenty-two affected members from three families with homozygous OTOF mutations were included. Nine subjects were evaluated audiologically with otoscopic examination, pure-tone audiometry, tympanometry with acoustic reflex testing, auditory brain stem responses, and otoacoustic emission tests. Homozygous c.4718T>C (p.Ile1573Thr) mutation was associated with the auditory neuropathy/auditory dys-synchrony (AN/AD) phenotype and with progressive sensorineural hearing loss in four siblings in one family, while homozygous c.4467dupC (p.I1490HfsX19) was associated with severe to profound sensorineural hearing loss without AN/AD in four relatives in another family. Homozygous c.1958delC (p.Pro653LeufsX13) mutation was associated with moderate sensorineural hearing loss without AN/AD in one affected person in an additional family. The audiological phenotype associated with different OTOF mutations appears to be consistently different suggesting the presence of a genotype-phenotype correlation.

Research paper thumbnail of Identification of copy number variants through whole-exome sequencing in autosomal recessive nonsyndromic hearing loss

Genetic testing and molecular biomarkers, 2014

Genetic variants account for more than half of the cases with congenital or prelingual onset hear... more Genetic variants account for more than half of the cases with congenital or prelingual onset hearing loss. Autosomal recessive nonsyndromic hearing loss (ARNSHL) is the most common subgroup. Whole-exome sequencing (WES) has been shown to be effective detecting deafness-causing single-nucleotide variants (SNVs) and insertion/deletions (INDELs). After analyzing the WES data for causative SNVs or INDELs involving previously reported deafness genes in 78 families with ARNSHL, we searched for copy number variants (CNVs) through two different tools in 24 families that remained unresolved. We detected large homozygous deletions in STRC and OTOA in single families. Thus, causative CNVs in known deafness genes explain 2 out of 78 (2.6%) families in our sample set. We conclude that CNVs can be reliably detected through WES and should be the part of pipelines used to clarify genetic basis of hearing loss.

Research paper thumbnail of Common genes for non-syndromic deafness are uncommon in sub-Saharan Africa: a report from Nigeria

International journal of pediatric otorhinolaryngology, 2014

Little is known about the molecular epidemiology of deafness in sub-Saharan Africa (SSA). Even in... more Little is known about the molecular epidemiology of deafness in sub-Saharan Africa (SSA). Even in Nigeria, the most populous African nation, no genetic studies of deafness have been conducted. This pioneering work aims at investigating the frequencies of gene mutations relatively common in other parts of the world (i.e. those in GJB2, GJB6, and mitochondrial DNA) among subjects from Nigeria with hearing loss (HL) with no evidence of acquired pathology or syndromic findings. In addition, we review the literature on the genetics of deafness in SSA. We evaluated 81 unrelated deaf probands from the Yoruba tribe residing in Ibadan, a suburban city in Nigeria, for the aetiology of their deafness. Subjects underwent genetic testing if their history was negative for an environmental cause and physical examination did not find evidence of a syndrome. Both exons of GJB2 and mitochondrial DNA flanking the 1555A>G mutations were PCR-amplified followed by Sanger sequencing. GJB6 deletions wer...

Research paper thumbnail of FAM65B is a membrane-associated protein of hair cell stereocilia required for hearing

Proceedings of the National Academy of Sciences, 2014

In a large consanguineous Turkish kindred with recessive nonsyndromic, prelingual, profound heari... more In a large consanguineous Turkish kindred with recessive nonsyndromic, prelingual, profound hearing loss, we identified in the gene FAM65B (MIM611410) a splice site mutation (c.102-1G>A) that perfectly cosegregates with the phenotype in the family. The mutation leads to exon skipping and deletion of 52-amino acid residues of a PX membrane localization domain. FAM65B is known to be involved in myotube formation and in regulation of cell adhesion, polarization, and migration. We show that wild-type Fam65b is expressed during embryonic and postnatal development stages in murine cochlea, and that the protein localizes to the plasma membranes of the stereocilia of inner and outer hair cells of the inner ear. The wild-type protein targets the plasma membrane, whereas the mutant protein accumulates in cytoplasmic inclusion bodies and does not reach the membrane. In zebrafish, knockdown of fam65b leads to significant reduction of numbers of saccular hair cells and neuromasts and to hearing loss. We conclude that FAM65B is a plasma membrane-associated protein of hair cell stereocilia that is essential for hearing.

Research paper thumbnail of Novel mutations confirm that COL11A2 is responsible for autosomal recessive non-syndromic hearing loss DFNB53

Molecular Genetics and Genomics, 2015

Hearing loss (HL) is a major public health issue. It is clinically and genetically heterogeneous.... more Hearing loss (HL) is a major public health issue. It is clinically and genetically heterogeneous.The identification of the causal mutation is important for early diagnosis, clinical follow-up, and genetic counseling. HL due to mutations in COL11A2, encoding collagen type XI alpha-2, can be non-syndromic autosomal-dominant or autosomal-recessive, and also syndromic as in Otospondylomegaepiphyseal Dysplasia, Stickler syndrome type III, and Weissenbacher-Zweymuller syndrome. However, thus far only one mutation co-segregating with autosomal recessive non-syndromic hearing loss (ARNSHL) in a single family has been reported. In this study, whole exome sequencing of two consanguineous families with ARNSHL from Tunisia and Turkey revealed two novel causative COL11A2 mutations, c.109G > T (p.Ala37Ser) and c.2662C > A (p.Pro888Thr). The variants identified co-segregated with deafness in both families. All homozygous individuals in those families had early onset profound hearing loss across all frequencies without syndromic findings. The variants are predicted to be damaging the protein function. The p.Pro888Thr mutation affects a -Gly-X-Y- triplet repeat motif. The novel p.Ala37Ser is the first missense mutation located in the NC4 domain of the COL11A2 protein. Structural model suggests that this mutation will likely obliterate, or at least partially compromise, the ability of NC4 domain to interact with its cognate ligands. In conclusion, we confirm that COL11A2 mutations cause ARNSHL and broaden the mutation spectrum that may shed new light on genotype-phenotype correlation for the associated phenotypes and clinical follow-up.

Research paper thumbnail of Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform

PLoS ONE, 2011

Despite the ever-increasing throughput and steadily decreasing cost of next generation sequencing... more Despite the ever-increasing throughput and steadily decreasing cost of next generation sequencing (NGS), whole genome sequencing of humans is still not a viable option for the majority of genetics laboratories. This is particularly true in the case of complex disease studies, where large sample sets are often required to achieve adequate statistical power. To fully leverage the potential of NGS technology on large sample sets, several methods have been developed to selectively enrich for regions of interest. Enrichment reduces both monetary and computational costs compared to whole genome sequencing, while allowing researchers to take advantage of NGS throughput. Several targeted enrichment approaches are currently available, including molecular inversion probe ligation sequencing (MIPS), oligonucleotide hybridization based approaches, and PCR-based strategies. To assess how these methods performed when used in conjunction with the ABI SOLID3+, we investigated three enrichment techniques: Nimblegen oligonucleotide hybridization array-based capture; Agilent SureSelect oligonucleotide hybridization solution-based capture; and Raindance Technologies' multiplexed PCRbased approach. Target regions were selected from exons and evolutionarily conserved areas throughout the human genome. Probe and primer pair design was carried out for all three methods using their respective informatics pipelines. In all, approximately 0.8 Mb of target space was identical for all 3 methods. SOLiD sequencing results were analyzed for several metrics, including consistency of coverage depth across samples, on-target versus off-target efficiency, allelic bias, and genotype concordance with array-based genotyping data. Agilent SureSelect exhibited superior on-target efficiency and correlation of read depths across samples. Nimblegen performance was similar at read depths at 206 and below. Both Raindance and Nimblegen SeqCap exhibited tighter distributions of read depth around the mean, but both suffered from lower on-target efficiency in our experiments. Raindance demonstrated the highest versatility in assay design.

Research paper thumbnail of Identifying Consensus Disease Pathways in Parkinson's Disease Using an Integrative Systems Biology Approach

PLoS ONE, 2011

Parkinson's disease (PD) has had six genome-wide association studies (GWAS) conducted as well as ... more Parkinson's disease (PD) has had six genome-wide association studies (GWAS) conducted as well as several gene expression studies. However, only variants in MAPT and SNCA have been consistently replicated. To improve the utility of these approaches, we applied pathway analyses integrating both GWAS and gene expression. The top 5000 SNPs (p,0.01) from a joint analysis of three existing PD GWAS were identified and each assigned to a gene. For gene expression, rather than the traditional comparison of one anatomical region between sets of patients and controls, we identified differentially expressed genes between adjacent Braak regions in each individual and adjusted using average control expression profiles. Over-represented pathways were calculated using a hyper-geometric statistical comparison. An integrated, systems metaanalysis of the over-represented pathways combined the expression and GWAS results using a Fisher's combined probability test. Four of the top seven pathways from each approach were identical. The top three pathways in the metaanalysis, with their corrected p-values, were axonal guidance (p = 2.8E-07), focal adhesion (p = 7.7E-06) and calcium signaling (p = 2.9E-05). These results support that a systems biology (pathway) approach will provide additional insight into the genetic etiology of PD and that these pathways have both biological and statistical support to be important in PD.

Research paper thumbnail of Identification of Rare Variants in Parkinson Disease Using Next-Generation Sequencing (S22.007)

Research paper thumbnail of Whole exome sequencing of rare variants in EIF4G1 and VPS35 in Parkinson disease

Neurology, 2013

Recently, vacuolar protein sorting 35 (VPS35) and eukaryotic translation initiation factor 4 gamm... more Recently, vacuolar protein sorting 35 (VPS35) and eukaryotic translation initiation factor 4 gamma 1 (EIF4G1) have been identified as 2 causal Parkinson disease (PD) genes. We used whole exome sequencing for rapid, parallel analysis of variations in these 2 genes. We performed whole exome sequencing in 213 patients with PD and 272 control individuals. Those rare variants (RVs) with <5% frequency in the exome variant server database and our own control data were considered for analysis. We performed joint gene-based tests for association using RVASSOC and SKAT (Sequence Kernel Association Test) as well as single-variant test statistics. We identified 3 novel VPS35 variations that changed the coded amino acid (nonsynonymous) in 3 cases. Two variations were in multiplex families and neither segregated with PD. In EIF4G1, we identified 11 (9 nonsynonymous and 2 small indels) RVs including the reported pathogenic mutation p.R1205H, which segregated in all affected members of a large family, but also in 1 unaffected 86-year-old family member. Two additional RVs were found in isolated patients only. Whereas initial association studies suggested an association (p = 0.04) with all RVs in EIF4G1, subsequent testing in a second dataset for the driving variant (p.F1461) suggested no association between RVs in the gene and PD. We confirm that the specific EIF4G1 variation p.R1205H seems to be a strong PD risk factor, but is nonpenetrant in at least one 86-year-old. A few other select RVs in both genes could not be ruled out as causal. However, there was no evidence for an overall contribution of genetic variability in VPS35 or EIF4G1 to PD development in our dataset.

Research paper thumbnail of A rare novel deletion of the tyrosine hydroxylase gene in Parkinson disease

Human Mutation, 2010

Tyrosine hydroxylase (TH) enzyme is a rate limiting enzyme in dopamine biosynthesis. Missense mut... more Tyrosine hydroxylase (TH) enzyme is a rate limiting enzyme in dopamine biosynthesis. Missense mutation in both alleles of the TH gene is known to cause dopamine-related phenotypes, including dystonia and infantile Parkinsonism. However, it is not clear if single allele mutation in TH modifies the susceptibility to the adult form of Parkinson disease (PD). We reported a novel deletion of entire TH gene in an adult with PD. The deletion was first identified by copy number variation (CNV) analysis in a genome-wide association study using Illumina Infinium BeadChips. After screening 635 cases and 642 controls, the deletion was found in one PD case but not in any control. The deletion was confirmed by multiple quantitative PCR (qPCR) assays. There is no additional exonic single nucleotide variant in the one copy of TH gene of the patient. The patient has an age-at-onset of 54 years, no evidence for dystonia, and was responsive to L-DOPA. This case supports the importance of the TH gene in PD pathogenesis and raises more attention to rare variants in candidate genes being a risk factor for Parkinson disease.

Research paper thumbnail of Tyrosine Hydroxylase Gene: Another Piece of the Genetic Puzzle of Parkinson’s Disease

CNS & Neurological Disorders - Drug Targets, 2012

The tyrosine hydroxylase (TH) gene encodes a monoxygenase that catalyzes the rate limiting step i... more The tyrosine hydroxylase (TH) gene encodes a monoxygenase that catalyzes the rate limiting step in dopamine biosynthesis. A hallmark of Parkinson's disease (PD) is the loss of dopaminergic neurons in the substantia nigra. Consistent with the essential role of TH in dopamine homeostasis, missense mutations in both alleles of TH have been associated with severe Parkinsonism-related phenotypes including infantile Parkinsonism. It has been speculated for a long time that genetic variants in the TH gene modify adult-onset PD susceptibility but the answer has not been clear. Genetic variants (both sequence variations and structural variations) can be classified into three categories based on their relative frequency in population: common variants (polymorphisms), rare variants and mutations. Each of these factors has a different mode in influencing the genetic risk and often requires different approaches to decipher their contributions to the disease. In the past few years, the revolutionary advances in genomic technology have allowed systematic evaluations of these genetic variants in PD, such as the genome-wide association study (GWAS, to survey common variants), copy number variation analysis (to detect structural variations), and massive parallel next generation sequencing (to detect rare variants and mutations). In this review, we have summarized the latest evidence on TH genetic variants in PD, including our ongoing effort of using whole exome sequencing to search for rare variants in PD patients.

Research paper thumbnail of Is Recurrent Abortion an Indication for Subtelomeric Region Analysis?

Turkiye Klinikleri …, 2010

Yasal uyarı: Bu sitede yayınlanan resim, yazı ve diğer uygulamaların her hakkı Ortadoğu Reklam Ve... more Yasal uyarı: Bu sitede yayınlanan resim, yazı ve diğer uygulamaların her hakkı Ortadoğu Reklam Ve Yayıncılık A.Ş. 'ye aittir. Kaynak gösterilmeden kullanılamaz. Bu site hekimleri sağlık alanında bilgilendirmeye yönelik hazırlanmıştır. Sitede yer alan bilgiler tanı ve tedavi amaçlı ...