Developmental anomalies of the hearing organ, the cochlea, are diagnosed in approximately one-fourth of individuals with congenital. The majority of patients with cochlear malformations remain etiologically undiagnosed due to insufficient knowledge about underlying genes or the inability to make conclusive interpretations of identified genetic variants. We used exome sequencing for the genetic evaluation of hearing loss associated with cochlear malformations in three probands from unrelated families deafness. We subsequently generated monoclonal induced pluripotent stem cell (iPSC) lines, bearing patient-specific knockins and knockouts using CRISPR/Cas9 to assess pathogenicity of candidate variants. We detected FGF3 (p.Arg165Gly) and GREB1L (p.Cys186Arg), variants of uncertain significance in two recognized genes for deafness, and PBXIP1(p.Trp574*) in a candidate gene. Upon differentiation of iPSCs towards inner ear organoids, we observed developmental aberrations in knockout lines compared to their isogenic controls. Patient-specific single nucleotide variants (SNVs) showed similar abnormalities as the knockout lines, functionally supporting their causality in the observed phenotype. Therefore, we present human inner ear organoids as a potential tool to validate the pathogenicity of DNA variants associated with cochlear malformations.

Genetic factors contributing to hearing loss (HL) are heterogeneous, and effective medical treatments remain limited. We identified 3 distinct missense variants in CPD, encoding carboxypeptidase D, in 5 individuals with congenital deafness from 3 unrelated families, affecting the catalytically active CP domain 2 of this protein. Subsequent analysis of a larger cohort from the 100,000 Genomes Project revealed an enrichment of rare protein-altering CPD variants in individuals with HL. We show that CPD localizes to sensory epithelium and nerve cells in the mouse cochlea, and the enzymatic activity of CPD, crucial for nitric oxide (NO) production through arginine processing, is impaired in affected individuals. The levels of arginine, NO, and cGMP in patient-derived fibroblasts are also decreased, leading to endoplasmic reticulum stress-mediated responses being triggered in the cells. Silencing of Cpd in organotypic mouse cochlea cultures leads to increased apoptosis. Finally, Drosophila models of CPD deficiency display defective Johnston's organ, impaired auditory transduction, and sensory and movement abnormalities. Notably, these phenotypes are partially rescued by supplementation with arginine or sildenafil, a cGMP enhancer. Our findings establish CPD mutations as a cause of congenital HL, highlighting that the NO signaling pathway offers a promising therapeutic avenue.

Objective: Vaccinia-related kinase 1 (VRK1)-related disease is an extremely rare autosomal recessive disorder primarily affecting the peripheral and/or central nervous system. In this report, we describe the genetic and clinical features of two siblings from a Turkish family presenting with an amyotrophic lateral sclerosis (ALS) phenotype due to a novel homozygous VRK1 mutation, and discuss the broad phenotypic spectrum associated with pathogenic variants in this gene. Methods: We analyzed the demographic data, clinical histories, neurological examinations, laboratory findings, and genetic results of 53 patients, including our cases, derived from 27 different reports. Results: Whole-exome sequencing identified a novel homozygous missense mutation, c.700A > G (p.Asn234Asp), in the VRK1 gene in two affected siblings. The characteristic features of the ALS phenotype included a recessive inheritance pattern, motor deficits with onset in the lower limbs, pyramidal tract signs, and a muscle magnetic resonance imaging (MRI) pattern demonstrating preferential involvement of the posterior compartments of the leg and thigh. The most common phenotypes associated with VRK1 mutations were ALS (18/53, 34%) and distal hereditary motor neuropathy (dHMN) (14/53, 26.4%), followed by pontocerebellar hypoplasia type 1 (7/53, 13.2%), hereditary motor and sensory neuropathy (5/53, 9.4%), autosomal recessive primary microcephaly with brain malformations (4/53, 7.5%), and spastic paraplegia (2/53, 3.8%). The ALS phenotype exhibited a significantly earlier mean age of onset compared to the dHMN phenotype (p = 0.015; 15.3 ± 11.5 and 27 ± 15.5 years, respectively). Conclusion: Our findings highlight the importance of investigating VRK1 mutations in patients with young-onset familial ALS. Furthermore, this report provides a systematic classification of the phenotype definitions associated with VRK1 mutations.

BackgroundMultilocus Inherited Neoplasia Allele Syndrome (MINAS) describes individuals who harbor pathogenic or likely pathogenic (LP/P) germline variants in two or more distinct cancer predisposition genes. With the broader implementation of next-generation sequencing (NGS) and multigene panel testing, MINAS has been increasingly recognized.MethodsWe retrospectively evaluated 655 Turkish patients referred for hereditary cancer testing using two validated NGS panels. MINAS was defined as the presence of LP/P variants in at least two different genes.Results14 patients (2.13%) met the criteria for MINAS. An additional 156 patients (23.8%) had single-gene LP/P variants. MINAS cases accounted for 8.2% of mutation-positive individuals. These patients showed diverse tumor types. Common gene combinations included BRCA1+MUTYH and CHEK2+PALB2.ConclusionThis is the first MINAS-focused analysis from a Turkish cohort. Although uncommon, MINAS represents a significant subset of genetically high-risk individuals requiring tailored clinical management.

Autosomal dominant sensorineural hearing loss (ADSNHL) is a genetically heterogeneous disorder caused by pathogenic variants in various genes, including MYH14. However, the interpretation of pathogenicity for MYH14 variants remains a challenge due to incomplete penetrance and the lack of functional studies and large families. In this study, we performed exome sequencing in six unrelated families with ADSNHL and identified five MYH14 variants, including three novel variants. Two of the novel variants, c.571G > C (p.Asp191His) and c.571G > A (p.Asp191Asn), were classified as likely pathogenic using ACMG and Hearing Loss Expert panel guidelines. In silico modeling demonstrated that these variants, along with p.Gly1794Arg, can alter protein stability and interactions among neighboring molecules. Our findings suggest that MYH14 causative variants may be more contributory and emphasize the importance of considering this gene in patients with nonsyndromic mainly post-lingual severe form of hearing loss. However, further functional studies are needed to confirm the pathogenicity of these variants.

Genomic repeat sequences are patterns of nucleic acids that exist in multiple copies throughout the genome. More than 60 Mendelian disorders are caused by the expansion or contraction of these repeats. Various specific methods for determining tandem repeat variations have been developed. However, these methods are highly specific to the genomic region being studied and sometimes require specialized tools. In this study, we have investigated the use of Optical Genome Mapping (OGM) as a diagnostic tool for detecting repeat disorders. We evaluated 19 patients with a prediagnosis of repeat disorders and explained the molecular etiology of 9 of them with OGM (5 patients with Facioscapulohumeral Muscular Dystrophy (FSHD), 2 patients with Friedreich's Ataxia (FA), 1 patient with Fragile X Syndrome (FXS), and 1 patient with Progressive Myoclonic Epilepsy 1A (EPM1A)). We confirmed OGM results with more widely used fragment analysis techniques. This study highlights the utility of OGM as a diagnostic tool for repeat expansion and contraction diseases such as FA, FXS, EPM1A, and FSHD.

Hearing loss (HL) is a common heterogeneous trait that involves variants in more than 200 genes. In this study, we utilized exome (ES) and genome sequencing (GS) to effectively identify the genetic cause of presumably non-syndromic HL in 322 families from South and West Asia and Latin America. Biallelic GJB2 variants were identified in 58 probands at the time of enrollment these probands were excluded. In addition, upon review of phenotypic findings, 38/322 probands were excluded based on syndromic findings at the time of ascertainment and no further evaluation was performed on those samples. We performed ES as a primary diagnostic tool on one or two affected individuals from 212/226 families. Via ES we detected a total of 78 variants in 30 genes and showed their co-segregation with HL in 71 affected families. Most of the variants were frameshift or missense and affected individuals were either homozygous or compound heterozygous in their respective families. We employed GS as a primary test on a subset of 14 families and a secondary tool on 22 families which were unsolved by ES. Although the cumulative detection rate of causal variants by ES and GS is 40% (89/226), GS alone has led to a molecular diagnosis in 7 of 14 families as the primary tool and 5 of 22 families as the secondary test. GS successfully identified variants present in deep intronic or complex regions not detectable by ES.

Hereditary hearing loss (HL) is a genetically heterogeneous disorder affecting people worldwide. The implementation of advanced sequencing technologies has significantly contributed to the identification of novel genes involved in HL. In this study, probands of two Turkish families with non-syndromic moderate HL were subjected to exome sequencing. The data analysis identified the c.600G > A (p.Thr200Thr) and c.1863dupG (p.His622fs) variants in GPR156, which co-segregated with the phenotype as an autosomal recessive trait in the respective families. The in silico predictions and a minigene assay showed that the c.600G > A variant disrupts mRNA splicing. This gene belongs to the family of G protein-coupled receptors whose function is not well established in the inner ear. GPR156 variants have very recently been reported to cause HL in three families. Our study from a different ethnic background confirms GPR156 as a bona fide gene involved in HL in humans. Further investigation towards the understanding of the role of GPCRs in the inner ear is warranted.

Objectives:The aim was to point out the importance of the diagnosis rate of breast cancer (BC) by analyzing the cancer predisposition genes except BRCA1/2 with multigene testing. Methods: In this study, 232 non-BRCA cases with BC and/or BC family history (FH) were analyzed using the next-generation sequencing method. Results: Twenty-two different pathogenic/likely pathogenic variants were determined in 24 (10.34%) of cases, and these variants were detected in the CHEK2 (7/24, 29.1%), ATM (5/24, 20.8%), MUTYH (3/24, 12.5%), BLM (2/24, 8.3%), WRN (2/24, 8.3%), TP53 (1/24, 4.1%), BRIP1 (1/24, 4.1%), MSH2 (1/24, 4.1%), NBN (1/24, 4.1%), and PTEN (1/24, 4.1%) genes including three novel variants which were identified in the BLM, ATM, and MSH2 (3/22, 13.6%) genes. Fourteen of 24 (58.3%) cases had BC diagnosis, and 10 of 24 (41.6%) cases had a FH of BC. Conclusion: Among non-BRCA BC and/or BC FH cases, cancer susceptibility gene frequency was 10.34% in this study. CHEK2 and ATM genes had relatively high mutation rates.

BACKGROUND Neutrophil-lymphocyte ratio (NLR), lymphocyte-monocyte ratio (LMR), and platelet-lymphocyte ratio (PLR) are inflammation markers in inflammatory, cardiovascular, and malignant diseases and are important to assess prognosis. The aim of the study is to show the correlation between the inflammation markers of NLR, LMR, and PLR identified in total blood count of patients with Coronavirus disease 2019 (COVID-19) with the disease severity. METHODS A total of 409 patients attending hospital with clinical symptoms of COVID-19 and with positive quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) test were divided into two groups as 61 severe patients and 348 non-severe patients. The levels of inflammation markers NLR, LMR, PLR, and c-reactive protein (CRP) were assessed. RESULTS The mean age of 409 patients was 49.9 ± 18.3 years and 48.7% of all patients were female. In the severe patient group, NLR 8.94 ± 13.24, LMR 2.24 ± 1.46, and PLR 248 ± 254 were identified. NLR exhibited the largest area under the curve at 0.698, with the highest specificity (67%) and sensitivity (67.3%) among the other inflammation markers such as LMR and PLR. Consistent with the severity of disease in severe COVID-19 patients, NLR, PLR, CRP and other inflammation markers increase, while LMR is observed to reduce. CONCLUSIONS NLR and PLR, calculated with the simple, cheap, and easily accessible hemogram test requested for diagnosis and follow-up of COVID-19 disease, were correlated with the total score for radiological findings and duration of hospitalization, and we observed NLR and LMR may predict disease severity.

Background: Pneumonia due to Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is spreading rapidly all over the world and air travel is the leading transmission route of the virus among countries. The aim of the study is to determine the frequency of SARS-CoV-2 Immunoglobulin G (IgG) antibodies in aircrew, to determine occupa-tional exposure, and to understand the spread of immunity in social groups. Method: The study was designed as a cross-sectional retrospective study. SARS-CoV-2 IgG levels were measured in patients who applied to between December 1, 2020 and January 13, 2021. Coronavirus disease-2019 (COVID-19) Reverse transcription polymerase chain reaction (RT-PCR) positivity was investigated before December 1, 2020. Results: The patients were divided into three groups according to their jobs such as 313 aircrew; 451 healthcare workers; 4258 other patients. The PCR positivity rate was found to be 39% in the aircrew group, 32% in the healthcare workers and %20 other patient group (p < 0.001). The IgG antibody positivity rate was 46% in the aircrew, 41% in healthcare workers, and 35.3% in the other patient group (p < 0.001).The group with the highest IgG antibody titer is in the aircrew; there was a significant difference between the groups (p < 0.001). Conclusions: In our study, it was observed that aircrew, similar to healthcare workers, are at serious risk against SARS-CoV-2. In this process, it is suggested that the vaccination processes included repeated doses of aircrew should be accelerated and protective measures and equipment should be increased in terms of reinfection.

Introduction: This study aimed to assess the correlation between nucleic acid amplification test (real-time reverse transcription-polymerase chain reaction, RT-PCR) positivity of patients presenting with suspected COVID-19 and pneumonic infiltration consistent with COVID-19-specific pneumonia diagnosis on thoracic computed tomography (CT), with symptoms, laboratory findings, and clinical progression. Methods: The study included 286 patients (female:male 131:155; mean age, 53.3 +/- 17.9 years) who were divided into two groups according to their RT-PCR test results. The symptoms, laboratory examinations, clinical findings, and thoracic CT imaging of the patients were evaluated. Results: While the physical examination, comorbidities, and total CT scores were similar between the groups, taste/smell abnormalities were observed more frequently in the PCR-positive group. The use of moxifloxacin, lopinavir/ritonavir, and tocilizumab was higher in the PCR-positive group (p = 0.016, p < 0.001, and p = 0.002, respectively). The duration of hospitalization, intensive care requirement, and mortality rate of the studied groups did not differ between the groups. Conclusions: Among patients presenting with suspected COVID-19 and pneumonic infiltration consistent with COVID-19 on thoracic CT, the symptoms, physical examination, total CT scores, duration of hospitalization, intensive care requirement, and mortality rate were similar between RT-PCR-positive and RT-PCR-negative patients. However, PCR-positive patients appeared to require more specific treatments.

Objective: Advances in the science of genetics and the development of assisted reproductive techniques focus on the genetic causes of infertility. The aim of this research is to reveal genetic abnormalities in terms of sex chromosome aneuploidy and Y chromosome microdeletions. Material and Methods: A total of 350 patients with azoospermia or severe oligozoospermia were selected. After general examination of the patients and laboratory investigations were performed, cartoypes and Y chromosome microdeletions were examined. Results: A total of 225 infertile men with non-obstructive azoospermia (NOA) and 125 infertile men with oligozoospermia were enrolled into the study. The overall cytogenetic anomaly rate was 16%. Chromosomal changes were detected in 32 of 350 (9.1%) cases. The most common genetic anomaly was 47, XXY (Klinefelter syndrome) and the incidence was 11.5% in NOA group. This rate was 3.2% in oligozoospermia group. Y chromosome microdeletions were detected in 24 (6.8%) patients and similarly, it was observed more frequently in the NOA group than in the oligozoospermia group. Conclusion: The incidence of genetic causes have been increasing with the severity of infertility. As a result, genetic screening and appropriate genetic counseling are needed before the use of assisted reproductive techniques. Keywords: azospermia, chromosome, infertility, microdeletion, oligozoospermiaage

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.

Background: Leber congenital amaurosis (LCA) is both genetically and phenotypically heterogeneous group of retinal disorder. Mutations in retinal degeneration 3 (RD3) have been reported as an infrequent cause of LCA which account for less than 1% of all known LCA cases. This case report provides Optical Coherence Tomography (OCT) and Fundus Autofluorescence (FAF) findings of an infant with LCA related to a mutation in RD3. Materials and Methods: Single retrospective case report. Results: TruSight One Expanded Sequencing Panel was applied to the patient on the Illumina NextSeq. Homozygous pathogenic variant (c.112 C > T, p.Arg38Ter) was detected in the RD3 gene. Well-demarcated central foveal atrophy was noted in the infrared imaging. FAF imaging showed perifoveal hyperautofluorescent ring and irregular hyperautofluorescence outside the vascular arcade. An arrest in foveal development and loss of outer retinal structure including outer nuclear layer, external limiting membrane, ellipsoid zone and interdigitation zone at the fovea were detected in the OCT imaging. Conclusion: This study indicates that RD3-related LCA has a very severe phenotype with foveal development arrest and very early loss of all photoreceptor layer and external limiting membrane at the fovea.

We aimed to evaluate type, frequency, and variety of pathogenic variants according to clinical and demographic features of children diagnosed with cystic fibrosis (CF). Twenty-five CF patients were evaluated retrospectively. Patients' demographics, physical examination, imaging, laboratory, and molecular pathogenic variant analysis findings were evaluated. Phe508del was the most frequently (33.3%) detected pathogenic variant, followed by point pathogenic variants E92K, 1898 + lGA/7T/7T, and 2789 + 5GA, respectively. Statistically higher rates of pathogenic variants were detected in male patients. The most frequently detected pathogenic variant was Phe508del. The identification of nine additional pathogenic variants of Phe508del revealed the heterogeneous nature of the CF.

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.

Nonketotic hyperglycinemia (NKH) is caused by defects in the glycine cleavage system. Hyperglycinemia without biallelic mutations in one of the 4 genes that encode the constituents of the glycine cleavage system is classified as 'variant NKH'. The defects in these cases are in the iron-sulphur cluster biogenesis and lipoate synthesis pathways. The GLRX5 gene is one of the genes in these new pathways. We report here an 8.5-year-old male patient presented with spasticity, ataxia and optic atrophy. He lost his ability to walk after a febrile infection at the age of 1.5 year. The patient's cognitive functions were preserved. His plasma glycine level and cerebrospinal fluid/plasma glycine ratio were high. A novel homozygous mutation p.Gly116Asp (c.347G>A) in the GLRX5 gene was identified by whole exome sequencing. In conclusion, in a child, who have neurological regression, spasticity, ataxia, and whom cognitive functions are partially preserved, if plasma glycine level is high, variant NKH should be considered in the differential diagnosis.

BACKGROUND:Genetic defects in the NFU1, an iron-sulfur cluster scaffold protein coding gene, which is vital in the final stage of assembly for iron sulfur proteins, have been defined as multiple mitochondrial dysfunctions syndrome I. This disorder is a severe autosomal recessive disease with onset in early infancy. It is characterized by disruption of the energy metabolism, resulting in weakness, neurological regression, hyperglycinemia, lactic acidosis, and early death. PATIENT DESCRIPTION:This report documents the case of a 27-month-old girl, who showed clinical signs and symptoms of spastic paraparesis with a relapsing-remitting course. The patient had a sister with a severe phenotype who died at the age of 16 months. RESULTS:Magnetic resonance imaging revealed hyperintensity of the cerebral white matter that was more prominent in the frontal regions, with milder involvement in the posterior periventricular regions. There was also evidence of partial cystic degeneration and cavitation in the frontal regions. In addition, she had hyperglycinemia. Homozygous NM_001002755.4:c.565G>A (p.Gly189Arg) mutation was identified in the NFU1 gene; this had not previously been reported as homozygous. CONCLUSION:Hyperglycinemia and cavitating leukodystrophy are suggestive of an NFU1 mutation diagnosis. An intrafamilial phenotypic variation has not been published in NFU1-associated disorders before. Presenting with spasticity as a rare phenotype, NFU1 mutations could be considered a genetic mimic of cerebral palsy.

Background 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. Mutations in over 20 genes have been shown to cause ASD. To identify disease-causing variants, we performed exome sequencing in 24 South Florida families with ASD. Results 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. Conclusions Presence of rare variants in multiple genes leading to ASD explains its genetic basis in over 40% of patients from South Florida. Exome sequencing for ASD allows us to identify causative variants, thus improving our ability to explain the underlying etiology in more families and to assist them with genetic counseling.