Publications by authors named "Guney Bademci"

47 Publications

First reported adult patient with retinal dystrophy and leukodystrophy caused by a novel ACBD5 variant: A case report and review of literature.

Am J Med Genet A 2021 Jan 11. Epub 2021 Jan 11.

Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA.

Peroxisomes play an essential role in lipid metabolism via interaction with other intracellular organelles. The information about the role of the Acyl-CoA-binding domain containing-protein 5 (ACBD5) in these interactions in human cells is emerging. Moreover, a few patients with retinal dystrophy and leukodystrophy caused by pathogenic variants in ACBD5 have been recently introduced. Here, we present a 36-year-old female with retinal dystrophy, leukodystrophy, and psychomotor regression due to a novel homozygous variant in ACBD5. Our study adds to the growing knowledge of this peroxisomal disorder by providing phenotypic details of the first adult patient.
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http://dx.doi.org/10.1002/ajmg.a.62073DOI Listing
January 2021

Radixin modulates the function of outer hair cell stereocilia.

Commun Biol 2020 Dec 23;3(1):792. Epub 2020 Dec 23.

Department of Biomedical and Clinical Sciences, Linköping University, SE-581 83, Linköping, Sweden.

The stereocilia of the inner ear sensory cells contain the actin-binding protein radixin, encoded by RDX. Radixin is important for hearing but remains functionally obscure. To determine how radixin influences hearing sensitivity, we used a custom rapid imaging technique to visualize stereocilia motion while measuring electrical potential amplitudes during acoustic stimulation. Radixin inhibition decreased sound-evoked electrical potentials. Other functional measures, including electrically induced sensory cell motility and sound-evoked stereocilia deflections, showed a minor amplitude increase. These unique functional alterations demonstrate radixin as necessary for conversion of sound into electrical signals at acoustic rates. We identified patients with RDX variants with normal hearing at birth who showed rapidly deteriorating hearing during the first months of life. This may be overlooked by newborn hearing screening and explained by multiple disturbances in postnatal sensory cells. We conclude radixin is necessary for ensuring normal conversion of sound to electrical signals in the inner ear.
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http://dx.doi.org/10.1038/s42003-020-01506-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758333PMC
December 2020

A founder noncoding GALT variant interfering with splicing causes galactosemia.

J Inherit Metab Dis 2020 11 21;43(6):1199-1204. Epub 2020 Aug 21.

Division of Clinical and Translational Genetics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA.

Galactosemia is a rare, treatable hereditary disorder of carbohydrate metabolism. We investigated the etiology of decreased GALT enzyme activity in a cohort of newborns referred by the Florida Newborn Screening Program with no detectable GALT variants in diagnostic molecular tests. Six affected individuals from four families with Guatemalan heritage were included. GALT enzyme activity ranged from 20% to 34% of normal. Clinical findings were unremarkable except for speech delay in two children. Via genome sequencing followed by Sanger confirmation we showed that all affected individuals were homozygous for a deep intronic GALT variant, c.1059+390A>G, which segregated as an autosomal recessive trait in all families. The intronic variant disrupts splicing and leads to a premature termination and is associated with a single haplotype flanking GALT, suggesting a founder effect. In conclusion, we present a deep intronic GALT variant leading to a biochemical variant form of galactosemia. This variant remains undiagnosed until it is specifically targeted in molecular testing.
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http://dx.doi.org/10.1002/jimd.12293DOI Listing
November 2020

Long-range cis-regulatory elements controlling GDF6 expression are essential for ear development.

J Clin Invest 2020 08;130(8):4213-4217

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.

Molecular mechanisms governing the development of the mammalian cochlea, the hearing organ, remain largely unknown. Through genome sequencing in 3 subjects from 2 families with nonsyndromic cochlear aplasia, we identified homozygous 221-kb and 338-kb deletions in a noncoding region on chromosome 8 with an approximately 200-kb overlapping section. Genomic location of the overlapping deleted region started from approximately 350 kb downstream of GDF6, which codes for growth and differentiation factor 6. Otic lineage cells differentiated from induced pluripotent stem cells derived from an affected individual showed reduced expression of GDF6 compared with control cells. Knockout of Gdf6 in a mouse model resulted in cochlear aplasia, closely resembling the human phenotype. We conclude that GDF6 plays a necessary role in early cochlear development controlled by cis-regulatory elements located within an approximately 500-kb region of the genome in humans and that its disruption leads to deafness due to cochlear aplasia.
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http://dx.doi.org/10.1172/JCI136951DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410044PMC
August 2020

Spectrum of Genetic Variants Associated with Anterior Segment Dysgenesis in South Florida.

Genes (Basel) 2020 03 26;11(4). Epub 2020 Mar 26.

John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.

Anterior segment dysgenesis (ASD) comprises a wide spectrum of developmental conditions affecting the cornea, iris, and lens, which may be associated with abnormalities of other organs. To identify disease-causing variants, we performed exome sequencing in 24 South Florida families with ASD. We identified 12 likely causative variants in 10 families (42%), including single nucleotide or small insertion-deletion variants in B3GLCT, BMP4, CYP1B1, FOXC1, FOXE3, GJA1, PXDN, and TP63, and a large copy number variant involving PAX6. Four variants were novel. Each variant was detected only in one family. Likely causative variants were detected in 1 out of 7 black and 9 out of 17 white families. In conclusion, exome sequencing for ASD allows us to identify a wide spectrum of rare DNA variants in South Florida. Further studies will explore missing variants, especially in the black communities.
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http://dx.doi.org/10.3390/genes11040350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230952PMC
March 2020

Analyses of del(GJB6-D13S1830) and del(GJB6-D13S1834) deletions in a large cohort with hearing loss: Caveats to interpretation of molecular test results in multiplex families.

Mol Genet Genomic Med 2020 04 17;8(4):e1171. Epub 2020 Feb 17.

Department of Science, Technology, & Mathematics, Gallaudet University, Washington, DC, USA.

Background: Mutations involving the closely linked GJB2 and GJB6 at the DFNB1 locus are a common genetic cause of profound congenital hearing loss in many populations. In some deaf GJB2 heterozygotes, a 309 kb deletion involving the GJB6 has been found to be the cause for hearing loss when inherited in trans to a GJB2 mutation.

Methods: We screened 2,376 probands from a National DNA Repository of deaf individuals.

Results: Fifty-two of 318 heterozygous probands with pathogenic GJB2 sequence variants had a GJB6 deletion. Additionally, eight probands had an isolated heterozygous GJB6 deletion that did not explain their hearing loss. In two deaf subjects, including one proband, a homozygous GJB6 deletion was the cause for their hearing loss, a rare occurrence not reported to date.

Conclusion: This study represents the largest US cohort of deaf individuals harboring GJB2 and GJB6 variants, including unique subsets of families with deaf parents. Testing additional members to clarify the phase of GJB2/GJB6 variants in multiplex families was crucial in interpreting clinical significance of the variants in the proband. It highlights the importance of determining the phase of GJB2/GJB6 variants when interpreting molecular test results especially in multiplex families with assortative mating.
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http://dx.doi.org/10.1002/mgg3.1171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196463PMC
April 2020

Novel variant p.E269K confirms causative role of PLS1 mutations in autosomal dominant hearing loss.

Clin Genet 2019 12 27;96(6):575-578. Epub 2019 Aug 27.

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.

Auditory reception relies on the perception of mechanical stimuli by stereocilia and its conversion to electrochemical signal. Mechanosensory stereocilia are abundant in actin, which provides them with structural conformity necessary for perception of auditory stimuli. Out of three major classes of actin-bundling proteins, plastin 1 encoded by PLS1, is highly expressed in stereocilia and is necessary for their regular maintenance. A missense PLS1 variant associated with autosomal dominant hearing loss (HL) in a small family has recently been reported. Here, we present another PLS1 missense variant, c.805G > A (p.E269K), in a Turkish family with autosomal dominant non-syndromic HL confirming the causative role of PLS1 mutations in HL. We propose that HL due to the p.E269K variant is from the loss of a stable PLS1-ACTB interaction.
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http://dx.doi.org/10.1111/cge.13626DOI Listing
December 2019

Identification of Main Genetic Causes Responsible for Non-Syndromic Hearing Loss in a Peruvian Population.

Genes (Basel) 2019 07 31;10(8). Epub 2019 Jul 31.

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.

Hearing loss (HL) is a common sensory disorder affecting over 5% of the global population. The etiology underlying HL includes congenital and acquired causes; genetic factors are the main cause in over 50% of congenital cases. Pathogenic variants in the gene are a major cause of congenital non-syndromic hearing loss (NSHL), while their distribution is highly heterogeneous in different populations. To the best of our knowledge, there is no data regarding the genetic etiologies of HL in Peru. In this study, we screened 133 Peruvian families with NSHL living in Lima. We sequenced both exons of the gene for all probands. Seven probands with familial NSHL that remained negative for variants underwent whole genome sequencing (WGS). We identified biallelic pathogenic variants in in 43 probands; seven were heterozygous for only one allele. The c.427C>T variant was the most common pathogenic variant followed by the c.35delG variant. WGS revealed three novel variants in in two probands, one of them was predicted to affect splicing and the others produce a premature stop codon. The Peruvian population showed a complex profile for genetic variants in the gene, this particular profile might be a consequence of the admixture history in Peru.
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http://dx.doi.org/10.3390/genes10080581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723399PMC
July 2019

A truncating CLDN9 variant is associated with autosomal recessive nonsyndromic hearing loss.

Hum Genet 2019 Oct 7;138(10):1071-1075. Epub 2019 Jun 7.

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue BRB-610 (M-860), Miami, FL, USA.

While the importance of tight junctions in hearing is well established, the role of Claudin- 9 (CLDN9), a tight junction protein, in human hearing and deafness has not been explored. Through whole-genome sequencing, we identified a one base pair deletion (c.86delT) in CLDN9 in a consanguineous family from Turkey with autosomal recessive nonsyndromic hearing loss. Three affected members of the family had sensorineural hearing loss (SNHL) ranging from moderate to profound in severity. The variant is predicted to cause a frameshift and produce a truncated protein (p.Leu29ArgfsTer4) in this single-exon gene. It is absent in public databases as well as in over 1000 Turkish individuals, and co-segregates with SNHL in the family. Our in vitro studies demonstrate that the mutant protein does not localize to cell membrane as demonstrated for the wild-type protein. Mice-lacking Cldn9 have been shown to develop SNHL. We conclude that CLDN9 is essential for proper audition in humans and its disruption leads to SNHL in humans.
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http://dx.doi.org/10.1007/s00439-019-02037-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6745279PMC
October 2019

Dysfunction of , encoding the GRB2-related adaptor protein, is linked to sensorineural hearing loss.

Proc Natl Acad Sci U S A 2019 01 4;116(4):1347-1352. Epub 2019 Jan 4.

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136;

We have identified a variant (c.311A>T; p.Gln104Leu) cosegregating with autosomal recessive nonsyndromic deafness in two unrelated families. encodes a member of the highly conserved growth factor receptor-bound protein 2 (GRB2)/Sem-5/drk family of proteins, which are involved in Ras signaling; however, the function of the growth factor receptor-bound protein 2 (GRB2)-related adaptor protein (GRAP) in the auditory system is not known. Here, we show that, in mouse, is expressed in the inner ear and the protein localizes to the neuronal fibers innervating cochlear and utricular auditory hair cells. Downstream of receptor kinase (), the homolog of human , is expressed in Johnston's organ (JO), the fly hearing organ, and the loss of in JO causes scolopidium abnormalities. mutant flies present deficits in negative geotaxis behavior, which can be suppressed by human wild-type but not mutant GRAP. Furthermore, drk specifically colocalizes with synapsin at synapses, suggesting a potential role of such adaptor proteins in regulating actin cytoskeleton dynamics in the nervous system. Our findings establish a causative link between mutation and nonsyndromic deafness and suggest a function of GRAP/drk in hearing.
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http://dx.doi.org/10.1073/pnas.1810951116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347722PMC
January 2019

FOXF2 is required for cochlear development in humans and mice.

Hum Mol Genet 2019 04;28(8):1286-1297

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.

Molecular mechanisms governing the development of the human cochlea remain largely unknown. Through genome sequencing, we identified a homozygous FOXF2 variant c.325A>T (p.I109F) in a child with profound sensorineural hearing loss (SNHL) associated with incomplete partition type I anomaly of the cochlea. This variant is not found in public databases or in over 1000 ethnicity-matched control individuals. I109 is a highly conserved residue in the forkhead box (Fox) domain of FOXF2, a member of the Fox protein family of transcription factors that regulate the expression of genes involved in embryogenic development as well as adult life. Our in vitro studies show that the half-life of mutant FOXF2 is reduced compared to that of wild type. Foxf2 is expressed in the cochlea of developing and adult mice. The mouse knockout of Foxf2 shows shortened and malformed cochleae, in addition to altered shape of hair cells with innervation and planar cell polarity defects. Expressions of Eya1 and Pax3, genes essential for cochlear development, are reduced in the cochleae of Foxf2 knockout mice. We conclude that FOXF2 plays a major role in cochlear development and its dysfunction leads to SNHL and developmental anomalies of the cochlea in humans and mice.
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http://dx.doi.org/10.1093/hmg/ddy431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452198PMC
April 2019

Identification of candidate gene FAM183A and novel pathogenic variants in known genes: High genetic heterogeneity for autosomal recessive intellectual disability.

PLoS One 2018 30;13(11):e0208324. Epub 2018 Nov 30.

John P. Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America.

The etiology of intellectual disability (ID) is heterogeneous including a variety of genetic and environmental causes. Historically, most research has not focused on autosomal recessive ID (ARID), which is a significant cause of ID, particularly in areas where parental consanguinity is common. Identification of genetic causes allows for precision diagnosis and improved genetic counseling. We performed whole exome sequencing to 21 Turkish families, seven multiplex and 14 simplex, with nonsyndromic ID. Based on the presence of multiple affected siblings born to unaffected parents and/or shared ancestry, we consider all families as ARID. We revealed the underlying causative variants in seven families in MCPH1 (c.427dupA, p.T143Nfs*5), WDR62 (c.3406C>T, p.R1136*), ASPM (c.5219_5225delGAGGATA, p.R1740Tfs*7), RARS (c.1588A>G, p.T530A), CC2D1A (c.811delG, p.A271Pfs*30), TUSC3 (c.793C>T, p.Q265*) and ZNF335 (c.808C>T, p.R270C and c.3715C>A, p.Q1239K) previously linked with ARID. Besides ARID genes, in one family, affected male siblings were hemizygous for PQBP1 (c.459_462delAGAG, p.R153Sfs*41) and in one family the proband was female and heterozygous for X-chromosomal SLC9A6 (c.1631+1G>A) variant. Each of these variants, except for those in MCPH1 and PQBP1, have not been previously published. Additionally in one family, two affected children were homozygous for the c.377G>A (p.W126*) variant in the FAM183A, a gene not previously associated with ARID. No causative variants were found in the remaining 11 families. A wide variety of variants explain half of families with ARID. FAM183A is a promising novel candidate gene for ARID.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208324PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6267965PMC
May 2019

Ripor2 is involved in auditory hair cell stereociliary bundle structure and orientation.

J Mol Med (Berl) 2018 11 3;96(11):1227-1238. Epub 2018 Oct 3.

Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.

RIPOR2 (previously known as FAM65B) localizes to stereocilia of auditory hair cells and causes deafness when its function is disturbed by mutations. Here, we demonstrate that during the morphogenesis of the hair cell bundle, absence of Ripor2 affects the orientation of this key subcellular structure. We show that Ripor2 interacts with Myh9, a protein encoded by a known deafness gene. Absence of Ripor2 is associated with low Myh9 abundance in the mouse cochlea despite increased amount of Myh9 transcripts. While Myh9 is mainly expressed in stereocilia, a phosphorylated form of Myh9 is particularly enriched in the kinocilium. In Ripor2-deficient mice, kinocilium shows an aberrant localization which associates with a reduced content of phosphorylated Myh9. Acetylated alpha tubulin, another specific kinociliary protein which contributes to microtubule stabilization, is reduced in the absence of Ripor2 as well. We propose that Ripor2 deficiency influences abundance and/or post-translational modifications of proteins expressed in both stereocilia and kinocilia. This effect may have a negative impact on the structure and function of the auditory hair cell bundle.
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http://dx.doi.org/10.1007/s00109-018-1694-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238639PMC
November 2018

Monosomy chromosome 21 compensated by 21q22.11q22.3 duplication in a case with small size and minor anomalies.

Mol Cytogenet 2018 1;11:43. Epub 2018 Aug 1.

1Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, 1601 NW 12th Avenue, Miami, FL 33136 USA.

Background: Partial monosomy 21 is a rare finding with variable sizes and deletion breakpoints, presenting with a broad spectrum of phenotypes.

Case Presentation: We report a 10-month-old boy with short stature, minor anomalies and mild motor delay. The patient had a monosomy 21 and duplication of the 21q22.11q22.3 region on the remaining derivative chromosome 21 which represents a partial 21q uniparental disomy of paternal origin, upd(21q22.11q22.3)pat. The abnormalities were characterized by karyotyping, FISH, chromosomal microarray, and genotyping.

Conclusions: This is the first case showing a monosomy 21 compensated by upd(21q22.11q22.3) as a mechanism of genomic rescue. Because there is no strong evidence showing imprinting on chromosome 21, the uniparental disomy itself is not associated with abnormal phenotype but has reduced phenotype severity of monosomy 21. We reviewed the previously published cases with isolated 21q deletions and identified a common deletion of 5.7 Mb associated with low birth weight, length and head circumference in the 21q21.2 region.
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http://dx.doi.org/10.1186/s13039-018-0390-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090943PMC
August 2018

MPZL2 is a novel gene associated with autosomal recessive nonsyndromic moderate hearing loss.

Hum Genet 2018 Jul 7;137(6-7):479-486. Epub 2018 Jul 7.

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.

While recent studies have revealed a substantial portion of the genes underlying human hearing loss, the extensive genetic landscape has not been completely explored. Here, we report a loss-of-function variant (c.72delA) in MPZL2 in three unrelated multiplex families from Turkey and Iran with autosomal recessive nonsyndromic hearing loss. The variant co-segregates with moderate sensorineural hearing loss in all three families. We show a shared haplotype flanking the variant in our families implicating a single founder. While rare in other populations, the allele frequency of the variant is ~ 0.004 in Ashkenazi Jews, suggesting that it may be an important cause of moderate hearing loss in that population. We show that Mpzl2 is expressed in mouse inner ear, and the protein localizes in the auditory inner and outer hair cells, with an asymmetric subcellular localization. We thus present MPZL2 as a novel gene associated with sensorineural hearing loss.
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http://dx.doi.org/10.1007/s00439-018-1901-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478175PMC
July 2018

Whole Exome Sequencing of a Consanguineous Turkish Family Identifies a Mutation in GTF2H3 in Brothers With Spermatogenic Failure.

Urology 2018 Oct 30;120:86-89. Epub 2018 Jun 30.

Department of Urology, University of Miami Miller School of Medicine, Miami, FL.

In this case report we describe our investigation into the genetic cause of infertility due to idiopathic nonobstructive azoospermia in a consanguineous Turkish family. We extracted DNA from blood and applied whole exome sequencing on 4 infertile brothers in this family diagnosed with oligo- and azoospermia. Standard bioinformatics analysis pipelines were run including alignment to the reference genome, variant calling, and quality control filtering. Potentially pathogenic variants were identified and prioritized using genetic variant annotation software and public variant frequency databases, followed by validation with Sanger sequencing. A nonsynonymous variant in "general transcription factor TFIIH subunit 3" (GTF2H3) was identified in this consanguineous family. This variant in chromosome 12 (12chr: 124144111 T>C, p.Ser222Pro) of GTF2H3 represents a likely a disease-causing mutation as it is predicted to be damaging, rare, segregates with the disease, and is highly evolutionarily conserved. Familial segregation analysis of the variant showed that it was present as a homozygous mutation in the brothers with nonobstructive azoospermia, and heterozygous mutation in the oligospermic brothers. We propose a mechanism by which this variant leads to deficits in Vitamin A signaling, which is essential for spermatogenesis.
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http://dx.doi.org/10.1016/j.urology.2018.06.031DOI Listing
October 2018

A MECOM variant in an African American child with radioulnar synostosis and thrombocytopenia.

Clin Dysmorphol 2018 Jan;27(1):9-11

aGenomic Medicine ProgrambDr John T. Macdonald Foundation Department of Human GeneticscDivision of Pediatric Hematology and Oncology, Department of PediatricsdJohn P. Hussman Institute for Human GenomicseDepartment of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida, USA.

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http://dx.doi.org/10.1097/MCD.0000000000000200DOI Listing
January 2018

Research of genetic bases of hereditary non-syndromic hearing loss.

Turk Pediatri Ars 2017 Sep 1;52(3):122-132. Epub 2017 Sep 1.

Department of Medical Genetics, Erciyes University Faculty of Medicine, Kayseri, Turkey.

Aim: Hearing loss is the most common sensory disorder that affects approximately one per 1000 live births. With this project, we aimed to identify gene variants that were common causes of hearing loss in Turkey to contribute to the planning of genetic screening programs for hearing loss, as well as to improve genetic counseling to affected families.

Material And Methods: Twenty-one families with at least two affected individuals and parental consanguinity who presented with non-syndromic severe-to-profound sensorineural hearing loss were included in this study. We first screened for mutations in GJB2 and mitochondrial DNA 12S RNA genes. Subsequently, we genotyped the TMIE c.250C>T and SNP markers flanking the genes in the remaining twelve families without mutations in GJB2.

Results: Screening for mutations in GJB2 gene showed c.[35delG];[35delG] mutation in four families, c.[35delG];[507C>A] mutation in two families, c.[35delG];[-23+1G>A] mutation in one family, and c.457G>A heterozygous mutation in one family. Genotyping SNP markers showed the c.[250C>T];[250C>T] mutation in TMIE in one family. A homozygous region with SNP genotypes was detected with the gene in one family, the gene in another family, and also a homozygous region was detected with , and genes in another family.

Conclusions: Further research will be required to determine the genetic bases of hearing loss in families with non-syndromic hearing loss.
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http://dx.doi.org/10.5152/TurkPediatriArs.2017.4254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644578PMC
September 2017

Novel pathogenic variants underlie SLC26A4-related hearing loss in a multiethnic cohort.

Int J Pediatr Otorhinolaryngol 2017 Oct 8;101:167-171. Epub 2017 Aug 8.

John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA; Department of Otorhinolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA. Electronic address:

Objectives: The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. Despite this heterogeneity, DNA variants found within SLC26A4 have been reported to be the second most common contributor after those of GJB2 in many populations.

Methods: Whole exome sequencing and/or Sanger sequencing of SLC26A4 in 117 individuals with sensorineural hearing loss with or without inner ear anomalies but not with goiter from Turkey, Iran, and Mexico were performed.

Results: We identified 27 unique SLC26A4 variants in 31 probands. The variants c.1673A > G (p.N558S), c.1708-1G > A, c.1952C > T (p.P651L), and c.2090-1G > A have not been previously reported. The p.N558S variant was detected in two unrelated Mexican families.

Conclusion: A range of SLC26A4 variants without a common recurrent mutation underlies SLC26A4-related hearing loss in Turkey, Iran, and Mexico.
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http://dx.doi.org/10.1016/j.ijporl.2017.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679420PMC
October 2017

Novel EYA1 variants causing Branchio-oto-renal syndrome.

Int J Pediatr Otorhinolaryngol 2017 Jul 26;98:59-63. Epub 2017 Apr 26.

John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA. Electronic address:

Introduction: Branchio-oto-renal (BOR) syndrome is an autosomal dominant genetic disorder characterized by second branchial arch anomalies, hearing impairment, and renal malformations. Pathogenic mutations have been discovered in several genes such as EYA1, SIX5, and SIX1. However, nearly half of those affected reveal no pathogenic variant by traditional genetic testing.

Methods And Materials: Whole Exome sequencing and/or Sanger sequencing performed in 10 unrelated families from Turkey, Iran, Ecuador, and USA with BOR syndrome in this study.

Results: We identified causative DNA variants in six families including novel c.525delT, c.979T > C, and c.1768delG and a previously reported c.1779A > T variants in EYA1. Two large heterozygous deletions involving EYA1 were detected in additional two families. Whole exome sequencing did not reveal a causative variant in the remaining four families.

Conclusions: A variety of DNA changes including large deletions underlie BOR syndrome in different populations, which can be detected with comprehensive genetic testing.
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http://dx.doi.org/10.1016/j.ijporl.2017.04.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516569PMC
July 2017

Novel Causative Variants in , and Associated with Intellectual Disability and Additional Phenotypic Features.

J Pediatr Genet 2017 Jun 14;6(2):77-83. Epub 2017 Feb 14.

Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, United States.

Patients with unclear patterns of developmental and cognitive delay may go years without a definitive diagnosis despite extensive testing due to overlapping phenotypes of many genetic disorders. In this study, we identified causative variants in , , or in four individuals with global developmental delay and various findings including microcephaly and sensorineural hearing loss using whole exome sequencing. We present the cognitive, neurologic, and physical findings of four individuals to expand the clinical knowledge of possible features of the phenotypes of three rare genetic disorders. Through this process, we provide support for the use of whole exome sequencing in the setting of severe, intellectual disability or in those in whom a genetic disorder is suspected despite initial negative testing.
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http://dx.doi.org/10.1055/s-0037-1598639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423827PMC
June 2017

Dominant deafness-onychodystrophy syndrome caused by an mutation.

Clin Case Rep 2017 04 8;5(4):376-379. Epub 2017 Feb 8.

John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA; Department of Human Genetics Dr. John T. Macdonald Foundation University of Miami Miller School of Medicine Miami Florida USA.

Our report clarifies the role of in patients with deafness and onycho-osteodystrophy and confirms that a recurring c.1516C>T [p.(Arg506*)], variant causes dominant deafness-onychodystrophy (DDOD) syndrome.
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http://dx.doi.org/10.1002/ccr3.761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378843PMC
April 2017

Targeted Resequencing of Deafness Genes Reveals a Founder MYO15A Variant in Northeastern Brazil.

Ann Hum Genet 2016 Nov;80(6):327-331

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.

Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil. Haplotype analysis of this variant was consistent with a single founder. No other cases with this variant were detected among 105 simplex cases from other cities of northeastern Brazil, suggesting that this variant is confined to a geographical region. This study suggests that it is feasible to develop population-specific screening for deafness variants once causative variants are identified in different geographical groups.
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http://dx.doi.org/10.1111/ahg.12177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127167PMC
November 2016

Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents.

Hum Genet 2016 08 25;135(8):953-61. Epub 2016 Jun 25.

Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.

Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.
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http://dx.doi.org/10.1007/s00439-016-1697-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5497215PMC
August 2016

ROR1 is essential for proper innervation of auditory hair cells and hearing in humans and mice.

Proc Natl Acad Sci U S A 2016 May 9;113(21):5993-8. Epub 2016 May 9.

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL 33136; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136

Hair cells of the inner ear, the mechanosensory receptors, convert sound waves into neural signals that are passed to the brain via the auditory nerve. Little is known about the molecular mechanisms that govern the development of hair cell-neuronal connections. We ascertained a family with autosomal recessive deafness associated with a common cavity inner ear malformation and auditory neuropathy. Via whole-exome sequencing, we identified a variant (c.2207G>C, p.R736T) in ROR1 (receptor tyrosine kinase-like orphan receptor 1), cosegregating with deafness in the family and absent in ethnicity-matched controls. ROR1 is a tyrosine kinase-like receptor localized at the plasma membrane. At the cellular level, the mutation prevents the protein from reaching the cellular membrane. In the presence of WNT5A, a known ROR1 ligand, the mutated ROR1 fails to activate NF-κB. Ror1 is expressed in the inner ear during development at embryonic and postnatal stages. We demonstrate that Ror1 mutant mice are severely deaf, with preserved otoacoustic emissions. Anatomically, mutant mice display malformed cochleae. Axons of spiral ganglion neurons show fasciculation defects. Type I neurons show impaired synapses with inner hair cells, and type II neurons display aberrant projections through the cochlear sensory epithelium. We conclude that Ror1 is crucial for spiral ganglion neurons to innervate auditory hair cells. Impairment of ROR1 function largely affects development of the inner ear and hearing in humans and mice.
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http://dx.doi.org/10.1073/pnas.1522512113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889368PMC
May 2016

A next-generation sequencing gene panel (MiamiOtoGenes) for comprehensive analysis of deafness genes.

Hear Res 2016 Mar 2;333:179-184. Epub 2016 Feb 2.

Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.

Extreme genetic heterogeneity along with remarkable variation in the distribution of causative variants across in different ethnicities makes single gene testing inefficient for hearing loss. We developed a custom capture/next-generation sequencing gene panel of 146 known deafness genes with a total target size of approximately 1 MB. The genes were identified by searching databases including Hereditary Hearing Loss Homepage, the Human Genome Mutation Database (HGMD), Online Mendelian Inheritance in Man (OMIM) and most recent peer-reviewed publications related to the genetics of deafness. The design covered all coding exons, UTRs and 25 bases of intronic flanking sequences for each exon. To validate our panel, we used 6 positive controls with variants in known deafness genes and 8 unsolved samples from individuals with hearing loss. Mean coverage of the targeted exons was 697X. On average, each sample had 99.8%, 96.2% and 92.7% of the targeted region coverage of 1X, 50X and 100X reads, respectively. Analysis detected all known variants in nuclear genes. These results prove the accuracy and reliability of the custom capture experiment.
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http://dx.doi.org/10.1016/j.heares.2016.01.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798889PMC
March 2016

Comprehensive Analysis of Deafness Genes in Families with Autosomal Recessive Nonsyndromic Hearing Loss.

PLoS One 2015 11;10(11):e0142154. Epub 2015 Nov 11.

Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Ege University, Izmir, Turkey.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142154PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641619PMC
June 2016

Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome.

Orphanet J Rare Dis 2015 Sep 30;10:128. Epub 2015 Sep 30.

Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, 1501 NW 10th Avenue, BRB-610 M-860, Miami, FL, 33136, USA.

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.
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http://dx.doi.org/10.1186/s13023-015-0345-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589207PMC
September 2015

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort.

Genet Med 2016 Apr 30;18(4):364-71. Epub 2015 Jul 30.

Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.

Purpose: 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).

Methods: 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.

Results: 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.

Conclusion: 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 18 4, 364-371.
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http://dx.doi.org/10.1038/gim.2015.89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733433PMC
April 2016

MORFAN Syndrome: An Infantile Hypoinsulinemic Hypoketotic Hypoglycemia Due to an AKT2 Mutation.

J Pediatr 2015 Aug 23;167(2):489-91. Epub 2015 May 23.

Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL. Electronic address:

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.
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http://dx.doi.org/10.1016/j.jpeds.2015.04.069DOI Listing
August 2015