DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing

The discovery of low-coverage (i.e. uncovered) regions containing clinically significant variants, especially when they are related to the patient's clinical phenotype, is critical for whole-exome sequencing (WES) based clinical diagnosis. Therefore, it is essential to develop tools to identify the existence of clinically important variants in low-coverage regions. Here, we introduce a desktop application, namely DEVOUR (DEleterious Variants On Uncovered Regions), that analyzes read alignments for WES experiments, identifies genomic regions with no or low-coverage (read depth < 5) and then annotates known variants in the low-coverage regions using clinical variant annotation databases. As a proof of concept, DEVOUR was used to analyze a total of 28 samples from a publicly available Hirschsprung disease-related WES project (NCBI Bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19327), revealing the potential existence of 98 disease-associated variants in low-coverage regions. DEVOUR is available from https://github.com/projectDevour/DEVOUR under the MIT license.

Shared Biological Pathways and Processes in Patients with Intellectual Disability: A Multicenter Study

BACKGROUND

 Although the underlying genetic causes of intellectual disability (ID) continue to be rapidly identified, the biological pathways and processes that could be targets for a potential molecular therapy are not yet known. This study aimed to identify ID-related shared pathways and processes utilizing enrichment analyses.

METHOD

 In this multicenter study, causative genes of patients with ID were used as input for Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes enrichment analysis.

RESULTS

 Genetic test results of 720 patients from 27 centers were obtained. Patients with chromosomal deletion/duplication, non-ID genes, novel genes, and results with changes in more than one gene were excluded. A total of 558 patients with 341 different causative genes were included in the study. Pathway-based enrichment analysis of the ID-related genes via ClusterProfiler revealed 18 shared pathways, with lysine degradation and nicotine addiction being the most common. The most common of the 25 overrepresented DO terms was ID. The most frequently overrepresented GO biological process, cellular component, and molecular function terms were regulation of membrane potential, ion channel complex, and voltage-gated ion channel activity/voltage-gated channel activity, respectively.

CONCLUSION

 Lysine degradation, nicotine addiction, and thyroid hormone signaling pathways are well-suited to be research areas for the discovery of new targeted therapies in ID patients.

Clinical and laboratory evaluation of children with congenital hyperinsulinism: a single center experience

OBJECTIVES

To evaluate and present the data regarding clinical, laboratory, radiological and the results of molecular genetic analysis of patients with hyperinsulinemic hypoglycemia in our clinics.

METHODS

A total of 9 patients with CHI followed at Istanbul Medipol University. Data related to gender, age at presentation, birth weight, gestational age, consanguinity, glucose and insulin levels at diagnosis, treatment modalities, response to treatment, the results of genetic analysis and radiological evaluation were gathered from the files.

RESULTS

The oldest age at presentation was 6 months. K_ATP channel mutation was detected in 55% (n: 5). Diazoxide unresponsiveness was seen in 55% (n: 5). Octreotide was effective in 3 of them. ¹⁸F-DOPA PET performed in 4 diazoxide unresponsive patients revealed focal lesion in 3 of them. Spontaneous remission rate was 66% (n:6). All the patients with normal genetic result achieved spontaneous remission. Spontaneous remission was even noted in diazoxide unresponsive patients and in patients with focal lesion on ¹⁸F-DOPA PET.

CONCLUSIONS

Clinical presentation of patients with congenital hypereinsulinism is heterogeneous. Spontaneous remission rate is quite high even in patients with severe clinical presentation. It is important to develop methods that can predict which patients will have spontaneous remission. Reporting the clinical and laboratory data of each patient is important and will help to guide the management of patients with hyperinsulinemic hypoglycemia.

Clinical and genetic spectrum from a prototype of ciliopathy: Joubert syndrome

OBJECTIVE

Joubert syndrome is a neurodevelopmental disorder with a distinctive hindbrain malformation called molar tooth sign, causing motor and cognitive impairments. More than 40 genes have been associated with Joubert syndrome. We aim to describe a group of Joubert syndrome patients clinically and genetically emphasizing organ involvement.

METHODS

We retrospectively collected clinical information and molecular diagnosis data of 22 patients with Joubert syndrome from multiple facilities. Clinical exome or whole-exome sequencing were performed to identify causal variations in genes.

RESULTS

The most common variants were in the CPLANE1, CEP290, and TMEM67 genes, and other causative genes were AHI1, ARMC9, CEP41, CSPP1, HYLS1, KATNIP, KIAA0586, KIF7, RPGRIP1L, including some previously unreported variants in these genes. Multi-systemic organ involvement was observed in nine (40%) patients, with the eye being the most common, including Leber's congenital amaurosis, ptosis, and optic nerve coloboma. Portal hypertension and esophageal varices as liver and polycystic kidney disease and nephronophthisis as kidney involvement was encountered in our patients. The HYLS1 gene, which commonly causes hydrolethalus syndrome 1, was also associated with Joubert syndrome in one of our patients. A mild phenotype with hypophyseal hormone deficiencies without the classical molar tooth sign was observed with compound heterozygous and likely pathogenic variants not reported before in the KATNIP gene.

CONCLUSION

Some rare variants that display prominent genetic heterogeneity with variable severity are first reported in our patients. In our study of 22 Joubert syndrome patients, CPLANE1 is the most affected gene, and Joubert syndrome as a ciliopathy is possible without a classical molar tooth sign, like in the KATNIP gene-affected patients.

Prevalence of SARS-CoV-2 Variants in COVID-19 Positive Patients

Objective: Of the existing variants, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2), and omicron (B.1.1.529) were defined as variants of concern (VOCs) by World Health Organization. We aimed to retrospectively assess the distribution of VOCs in patients with positive COVID-19 real-time polymerase chain reaction (RT-PCR) test. Methods: Between April 2021 and December 31, 2021, 4260 patients whose clinical samples were sent with a COVID-19 PCR test request were included in the study. Of the patients whose samples were evaluated, 2173 (51%) were male, and 2087 (49%) were female. Viral nucleic acid isolation was performed by treating nasopharyngeal swabs, bronchoalveolar lavage, and tracheal aspirate samples with viral nucleic acid buffer (vNAT). SARS-CoV-2 variants were detected by Bio-Speedy® SARS-CoV-2 Variant Plus kit (Bioeksen AR-GE Technologies, Turkey), which targets variant-specific genome regions only found in B.1.1.7, B.1.351, and P.1 as well as ORF1ab and N gene regions. We used Bio-Speedy® SARS-CoV-2 Emerging Plus kit and CFX96 DX real-time PCR system to detect SARS-Cov-2 variants; N D3L mutation was targeted to detect the alpha variant, SL452R mutation to detect the delta variant, and S E484K mutation, which is widespread, to detect the gamma and the mu variants. Results: SARS-CoV-2 RT-PCR was positive in 773 (18.14%) of 4260 samples, and different SARS-CoV-2 variants were detected in 316 (40.88%) of positive samples. 407 (52.65%) of the patients with real-time polymerase chain reaction (RT-PCR) positive test were women, and the mean age was 41.7 years. While no variant type was detected in 457 (59.12%) of the patients, the alpha variant was detected in 156 (20.18%) and the delta variants in 137 (17.72%) patients. Conclusion: In our study, we found that the alpha variant was the dominant type in April, May, and June, and the delta variant became dominant as of July until the end of the year. Decreased rates of delta variants towards the end of 2021 and an increase in the other variants suggest the omicron variant, widely spread globally. Therefore, we believe that the omicron variant has been our country’s dominant type since November 2021. In conclusion, molecular surveillance studies that are planned in the light of epidemiological data and assessment of the frequency and genomic analyzes of regional and global variants are required.

Chronic Neutropenia in Childhood: Laboratory and Clinical Features

OBJECTIVES

To describe the clinical characteristics of patients with chronic neutropenia.

METHODS

Data of 36 patients with chronic neutropenia, who were followed up in the authors' clinic between May 2013 and May 2020, were analyzed retrospectively. Patients were diagnosed based on their clinical and laboratory characteristics.

RESULTS

A total of 36 patients (23 females, 13 males) were included in the study. The mean age at diagnosis was 9.85 ± 9.17 mo while the mean follow-up time was 21.83 ± 20.03 mo. The mean absolute neutrophil count (ANC) at admission was 462.5 ± 388.8 cells/mm³ (median = 375 cells/mm³), and the lowest and highest ANC mean was 241.2 ± 262.1 cells/mm³ (median = 125 cells/mm³), and 1362.9 ± 1127.9 cells/mm³ (median = 925 cells/mm³), respectively. Idiopathic neutropenia was found in 28 (77.8%) patients, autoimmune neutropenia in 6 (16.7%) patients, and congenital neutropenia in 2 (5.6%) patients. Neutrophil normalization was observed in 19 (52.8%) of the patients.

CONCLUSIONS

Chronic neutropenia is a heterogeneous picture that presents with different clinical symptoms in childhood. The cause of neutropoenia in children is usually benign and resolves spontaneously but especially in those with severe neutropoenia genetic examination should be performed.

First case with RANBP2 biallelic mutation and severe acute necrotizing encephalopathy phenotype

Familial acute necrotizing encephalopathy (ANE) is a rapidly progressive encephalopathy that can occur after common viral infections at different stages of life. The clinical findings of 2 siblings diagnosed with ANE were shared and the whole-exome-sequencing study of the index case was performed. It was confirmed by the Sanger method. We found the RANBP2 gene p.I656V variant homozygous in the index case. We found the variant in the parents as heterozygous. We argue that biallelic mutations in the RANBP2 gene may result in ANE with early onset and severe prognosis by increasing penetrance.

Clinical, Genetic, and Outcome Characteristics of Pediatric Patients with Primary Hemophagocytic Lymphohistiocytosis

Objectİive:

In this study, we sought to describe the clinical, laboratory, and genetic characteristics of patients diagnosed with primary hemophagocytic lymphohistiocytosis. Thus, we aimed to evaluate the early diagnosis and appropriate treatment options for pediatric hemophagocytic lymphohistiocytosis patients.

Materials and Methods:

Medical records of 9 patients diagnosed with primary hemophagocytic lymphohistiocytosis between November 2013 and December 2019 were analyzed retrospectively. Clinical, genetic, and laboratory characteristics, family histories, initial complaints, physical examination findings, age at diagnosis, treatment choices, and clinical follow-up of all patients were investigated.

Results:

The mean age at diagnosis was 11 months (range: 1.5 months to 17 years). Genetic analysis was performed in all patients, and a disease-related mutation was detected in 8 (89%) of them. Among clinical features, 6 (66%) patients had fever, 5 (56%) had splenomegaly, 4 (44%) had lymphadenopathy, 4 (44%) had skin rash, and 4 (44%) had neurological findings. Hemophagocytosis was observed in the bone marrow samples of 6 (66%) patients. Disease remission was achieved in 7 (78%) patients. Hematopoietic stem cell transplantation was performed in 7 (78%) patients.

Conclusion:

Hemophagocytic lymphohistiocytosis may present with different clinical symptoms that can cause a significant diagnostic delay. The only curative treatment option in primary hemophagocytic lymphohistiocytosis patients is hematopoietic stem cell transplantation. The chemotherapy should be started as early as possible, in order to achieve a disease remission. Patients should be referred to the appropriate bone marrow transplant center for hematopoietic stem cell transplantation as soon as they reach the disease remission.

Clinical and molecular genetic findings of Crisponi / cold-induced sweating syndrome (CS/CISS) spectrum in patients from Turkey

Crisponi / cold-induced sweating syndrome (CS/CISS) is a rare autosomal recessive disorder characterized by episodic hyperthermia, arthrogryposis, impaired feeding ability, and respiratory distress. The classic CS/CISS is mainly associated with CRLF1 and, rarely, CLCF1. PERCHING syndrome, previously known as CS/CISS type-3 associated with biallelic pathogenic variants in KLHL7, is notable for its few overlapping manifestations. This study presents genotype-phenotype relationships in CS/CISS-like spectrum associated with CRLF1 and KLHL7. Clinical findings of 19 patients from 14 families and four patients from three families were found in association with six different CRLF1 and three different KLHL7 variants, respectively. c.167 T > C and c.713delC of the CRLF1 gene and the c.642G > C of the KLHL7 were novel. The c.708_709delCCinsT allele of CRLF1 was identified in 10 families from the Mardin province of Turkey, underlining that an ancestral haplotype has become widespread. CRLF1-associated phenotypes revealed novel manifestations such as prenatal oligohydramnios, benign external hydrocephalus, previously unreported dysmorphic features emerging with advancing age, severe palmoplantar keratoderma and facial erythema, hypopigmented macules and streaks, and recurrent cardiac arrests. KLHL7 variants presented with glabellar nevus flammeus, blepharophimosis, microcephaly, thin corpus callosum, and cleft palate. Abnormalities of sweating, observed in one patient reported herein, is known to be very rare among KLHL7-related phenotypes. This article is protected by copyright. All rights reserved.

Further clinical and genetic evidence of ASC-1 complex dysfunction in congenital neuromuscular disease

Transcriptional coregulators modulate the efficiency of transcription factors. Bi-allelic variants in TRIP4 and ASCC1, two genes that encode members of the tetrameric coregulator ASC-1, have recently been associated with congenital bone fractures, hypotonia, and muscular dystrophy in a total of 22 unrelated families. Upon exome sequencing and data repository mining, we identified six new patients with pathogenic homozygous variants in either TRIP4 (n = 4, two novel variants) or ASCC1 (n = 2, one novel variant). The associated clinical findings confirm and extend previous descriptions. Considering all patients reported to date, we provide supporting evidence suggesting that ASCC1-related disease has a more severe phenotype compared to TRIP4-related disorder regarding higher incidence of perinatal bone fractures and shorter survival.

HLA - matched related donor hematopoietic stem cell transplantation in a patient with polynucleotide kinase 3-phosphatase mutation developed acute myeloid leukemia

BACKGROUND

PNPK gene mutations result in DNA repair disorders and have a spectrum of neurodevelopmental manifestations. To date, cancer predisposition has not been described in patients with PNKP mutations.

OBSERVATION

Here, we report a patient with PNKP mutation, who developed AML at age of five and underwent reduced-intensity HSCT.

CONCLUSION

Although many DNA repair disorders are known to have increased risk of malignancy, association between PNKP mutations and malignancy is not well-described. This report is the first description of a PNPK mutation patient developing a malignancy and undergoing curative HSCT.

Interacting with AP1 complex mutated synergin gamma (SYNRG) reveals a novel coatopathy in the form of complicated hereditary spastic paraplegia

BACKGROUND

Today, it is known that about 80 genes are involved in the etiology of hereditary spastic paraplegia. However, there are many cases whose etiology could not be determined by extensive genetic tests such as whole-exome sequencing, clinical exome.

METHODS

Candidate genes were determined, since no clinically illuminating variant was detected in the whole-exome sequencing analysis of three patients, two of whom were siblings, with a complex hereditary spastic paraplegia phenotype.

RESULTS

The p.Leu1202Pro variant in the SYNRG gene in the 1st and 2nd cases, and the p.Gly533* variant in the 3rd case were homozygous.

DISCUSSION

We suggest that the SYNRG gene interacting with AP-1 (adaptor-related protein) from the AP complex family may cause the complex hereditary spastic paraplegia phenotype with extensive clinical spectrum. It may be important to evaluate SYNRG gene variants in patients with hereditary spastic paraplegia whose etiology has not been clarified.

How to Manage Low Estriol Levels in Pregnancies, One Center Experience

Objective:

Low estriol (uE3) levels in the second-trimester screening for Down syndrome may be the result of fetal demise, congenital abnormalities, or some genetic hormonal disorders of the fetus. Although X-linked ichthyosis, a microdeletion syndrome with mild ichthyosis, which causes steroid sulfatase (STS) deficiency, is the most common genetic cause, second-trimester screening tests calculate the risk for a less common and severe disorder known as the Smith Lemli Opitz syndrome (SLOS). We aimed to investigate the outcomes of pregnancies with low uE3 levels in Down syndrome screening and emphasize the high prevalence of STS deficiency instead of SLOS in such cases.

Methods:

Fifteen pregnancies with very low uE3 levels and high risk for trisomy and/or SLOS in screening tests were evaluated and tested for STS deficiency and SLOS.

Results:

Seven of the pregnancies had STS microdeletion syndrome, while additional two cases were supposed to have STS gene mutation according to family and/or postnatal history. Although one fetal death was recorded, no chromosomal abnormality, SLOS, or congenital malformation was recorded in our series.

Conclusions:

SLOS is a very severe and rare syndrome. The risk estimation for SLOS in screening tests causes stress for pregnant women and healthcare givers. We recommend the addition of risk estimation for STS deficiency when a low uE3 level is detected in the screening test.

High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population

Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.

COVID-19: pathogenesis, genetic polymorphism, clinical features and laboratory findings

COVID-19 caused by a novel agent SARS-CoV-2 progressed to a pandemic condition and resulted in a major public health concern worldwide, leading to social and economic issues at the same time. The pathogenesis of COVID-19 starts with the bonding of the virus to ACE2 receptors expressed in many tissues, and the triggered excessive immune response plays a critical role in the course of the disease. The cytokine storm that occurs upon excessive production of pro-inflammatory cytokines is considered responsible for the severe progression of the disease and the organ damage. However, the accurate pathophysiological mechanism of the disease, which progresses with various clinical presentations, is still substantially unknown. While various studies have been conducted on the effect of genetic polymorphism on the course and severity of the disease, the presence of a significant effect has not been proven yet. The clinical course of the disease is variable, with clinical representation ranging from 81% mild course to 14% severe course along with 5% critical course in patients. Asymptomatic course is considered to be higher than expected, although its frequency is not known exactly. Older adults and those with comorbidities are exposed to a more severe disease course. The disease progress with various symptoms, such as fever, cough, dyspnea, malaise, myalgia, taste and smell dysfunctions, diarrhea, and headache. A range of complications (acute respiratory distress syndrome, thromboembolic conditions, arrhythmia and cardiac events, secondary infections) could be seen during the course of the disease. Varied laboratory tests are vital to determine these verity and prognosis of the disease, along with the condition and exposure of the affected systems during thecourse of COVID-19.

A case with Rubinstein-Taybi syndrome: A novel frameshift mutation in the CREBBP gene

Rubinstein-Taybi syndrome (RSTS) is a developmental disorder characterized by a wide spectrum of multiple congenital anomalies and cognitive impairment. RSTS is primarily due to mutations in CREBBP (approximately 55% of cases) or EP300 (approximately 8% of cases) genes. A 2 month-old boy had atypical facial findings such as low anterior hairline, triangular face, hirsutism on forehead, down-slanting palpebral fissures, beaked nose, broad nasal bridge, triangular mouth and pointed chin and skeletal finding including broad great thumbs and halluces, and accessory nipple. With this paper, we reported a novel frameshift mutation which is led to premature stop codon in CREBBP gene. As a result, c.2057dupC, reported in this paper enlarges the molecular spectrum of disease-causing CREBBP gene.

Proteomic analysis of sperm proteins in infertile men with high levels of reactive oxygen species

Oxidative stress is a significant risk factor for male infertility. A pro-oxidant testicular environment may alter the expression profile of functional sperm proteins and result in poor sperm quality. Patients and donors were divided into ROS (-) and ROS (+) groups. Using computational studies, and data mining of available literature on spermatozoa, oxidative stress and proteomics, we identified three core regulatory proteins angiotensin-converting enzyme (ACE), heat-shock protein (Hsp70) family A member 2 (HSPA2) and ribosomal protein subunit 27A (RPS27A) and seven interlink proteins NOS2, SUMO2, UBL4A, FBXO25, MAP3K3, APP and UBC. HSPA2 was validated by Western Blot, while the localisation of ACE, RPS27A, MAP3K3 and APP was identified by immunocytochemistry. The obtained results showed that HSPA2 was 1.2 (ROS+) and 2.1 (ROS-) fold downregulated in spermatozoa from patients with high levels of reactive oxygen species (ROS). ACE and APP were localised in the post-acrosomal region of spermatozoa, whereas RPS27A and MAP3K3 were localised either in the tail or sperm neck area. Our data show that these proteins may play a role in ROS-induced male infertility.

Performance and stability analysis of curcumin dye as a photo sensitizer used in nanostructured ZnO based DSSC

Environmental friendly natural dye curcumin extracted from low-cost Curcumina longa stem is used as a photo-sensitizer for the fabrication of ZnO-based dye-sensitized solar cells (DSSC). Nanostructured ZnO is fabricated on a transparent conducting glass (TCO), using a cost-effective chemical bath deposition technique. Scanning electron microscopic images show hexagonal patterned ZnO nano-towers decorated with several nanosteps. The average length of ZnO nano-tower is 5μm and diameter is 1.2μm. The UV-Vis spectroscopic study of the curcumin dye is used to understand the light absorption behavior as well as band gap energy of the extracted natural dye. The dye shows wider absorption band-groups over 350-470nm and 500-600nm with two peaks positioned at 425nm and 525nm. The optical band gap energy and energy band position of the dye is derived which supports its stability and high electron affinity that makes it suitable for light harvesting and effortless electron transfer from dye to the semiconductor or interface between them. FTIR spectrum of curcumin dye-sensitized ZnO-based DSSC shows the presence of anchoring groups and colouring constitutes. The I-V and P-V curves of the fabricated DSSC are measured under simulated light (100mW/cm²). The highest visible light to electric conversion efficiency of 0.266% (using ITO) and 0.33% (using FTO) is achieved from the curcumin dye-sensitized cell.

Haploinsufficiency of the DMRT Gene Cluster in a Case with 46,XY Ovotesticular Disorder of Sexual Development

Background

Ovotesticular disorder is characterized by the presence of testicular and ovarian tissues in the same individual. Single gene mutations in SRY, SOX9, DMRT1 and DAX1 can lead to ovotesticular disorder of sexual development.

Case Report

Herein, we report a 3-month-old phenotypically female baby in whom differentiated tissues of both Müllerian and Wolffian ducts were detected on pathological analysis of laparoscopic biopsy material. Chromosomal analysis observed 46,XY, der(9)t(3;9)(p25;p24) with deletion of 9p24.3p23 including the DMRT gene cluster and duplication of 3p26.3p24.3 on array comparative genomic hybridisation.

Conclusion

In support of previous literature, we found that haploinsufficiency of the DMRT gene cluster leads to ovotesticular disorder of sexual development. In addition, we emphasize that array comparative genomic hybridisation is an important technique in the molecular diagnosis of ovotesticular disorder of sexual.

A novel homozygous HOXB1 mutation in a Turkish family with hereditary congenital facial paresis

Hereditary congenital facial paresis (HCFP) is characterized by isolated dysfunction of the facial nerve (CN VII) due to congenital cranial dysinnervation disorders. HCFP has genetic heterogeneity and HOXB1 is the first identified gene. We report the clinical, radiologic and molecular investigations of three patients admitted for HCFP in a large consanguineous Turkish family. High-throughput sequencing and Sanger sequencing of all patients revealed a novel homozygous mutation p.Arg230Trp (c.688C>T) within the HOXB1 gene. The report of the mutation brings the total number of HOXB1 mutations identified in HCFP to four. The results of this study emphasize that in individuals with congenital facial palsy accompanied by hearing loss and dysmorphic facial features, HOXB1 mutation causing HCFP should be kept in mind.

Familial mutation in Caffey disease with reduced penetrance: A case report

Caffey disease is a rare condition of early infancy, characterized by soft tissue swelling, bone lesions, and hyperirritability. Its typical radiological finding is periosteal new bone formation. It can be sporadic or inherited in an autosomal dominant manner. There is no specific treatment. In symptomatic cases, non-steroidal anti-inflammatory drugs such as ibuprofen, indomethacin, or naproxen can be used. This is a report of an infant who presented with restlessness, irritability, and swelling over his shins, diagnosed as Caffey disease. Although there was no family history, the genetic analysis revealed heterozygous missense mutation (c.3040C > T) in type-I-collagen-alpha-1-chain gene in the patient in addition to his mother, grandmother, aunt, and cousin. After indomethacin therapy, the complaints of the patient were completely resolved and his bone lesions were significantly improved. This case report is a familial form of Caffey disease from Turkey, with proven heterozygous mutation in the patient and the family members.

Detection of α-Thalassemia by Using Multiplex Ligation-Dependent Probe Amplification as an Additional Method for Rare Mutations in Southern Turkey

α-thalassemia is the most common single gene disorder in the Cukurova Region in Turkey. It is therefore routinely screened, including premaritally, in our region. The heterogeneous molecular basis of the disease makes α-thalassemia mutation detection difficult and complex. Besides well established methods, multiplex ligation dependent probe amplification (MLPA) is known as an effective, simple and specific method for the detection and characterization of deletions and duplications. We employed MLPA testing to 30 patients with hematological parameters suggestive of α-thalassemia carrier status but was negative for α-thalassemia with conventional reverse dot blot hybridization (RDB). We found α-globin gene deletions in 3 out of 30 (10 %) patients with MLPA. We propose that MLPA can be used as a second tier test in addition to other techniques such as RDB to identify α-thalassemia carriers in high prevalence regions such as ours, thereby allowing clinicians to provide accurate genetic counselling.

Effects of methylene blue in acute lung injury induced by blunt chest trauma

BACKGROUND

We studied whether methylene blue (MB) treatment blunts chest trauma-induced lung injury in rats.

MATERIAL AND METHODS

Forty male Sprague-Dawley rats, 200-300g, were used. The rats were divided into five groups (n=8): control, early contusion (EC), early contusion + methylene blue (2 mg/kg, EC+MB), late contusion (LC), and late contusion + methylene blue (2 mg/kg, LC+MB).

RESULTS

Histopathological analysis showed increased hemorrhage, alveolar wall thickness, edema, and inflammatory cell infiltrates in the EC and LC rats, which decreased upon MB treatment. Immunohistochemical studies revealed that MB reduced activation of inducible nitric oxide synthase (iNOS) and the number of active terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells. A significant increase was observed in the malondialdehyde (MDA) and nitric oxide (NO) levels in the EC group compared to the control group (p<0.05). In addition, a significant decrease was reported in the glutathione (GSH), superoxide dismutase (SOD), and glutathione peroxidase (GPx) levels (p<0.01), but no significant difference was observed in the catalase (CAT) levels among the groups. The MDA level was significantly higher in the LC group compared to the control group, whereas the GSH level was significantly lower compared to the control group. The NO level in the EC+MB group was significantly lower when compared to the NO level in the EC group (p<0.05).

CONCLUSION

The present study provides evidence that MB might serve as a therapeutic treatment for blunt chest trauma.

Efficacy of combined metformin-clomiphene citrate in comparison with clomiphene citrate alone in infertile women with polycystic ovarian syndrome (PCOS)

BACKGROUND

Polycystic ovary syndrome (PCOS) is the most common endocrinopathy in women and is associated with the reproductive and metabolic disorders.

OBJECTIVES

To compare the ovulation and conception rates after the treatment with Clomiphene Citrate (CC) alone and in combination with metformin in infertile patients presented with polycystic ovarian syndrome (PCOS).

MATERIAL & METHODS

This randomized controlled trial of independent cases and controls was conducted in the Department of Obstetrics and Gynecology, Hera General Hospital, Makkah, Saudi Arabia, during 2008. The 42 subjects diagnosed as PCOS were divided into group A and B (21 subjects in each) for the management with CC + metformin and CC alone, respectively. Group A received 500mg of metformin continuously, three times a day from the first cycle, for 6 months or until the pregnancy was confirmed. In both groups, CC was started with a dose of 50 mg from day-2 until day-6 of the menstrual cycle. The dose of CC was increased to 100 mg in the second and 150 mg in the third cycle, and then 150 mg remained for the rest of three cycles. With ovulation, the dose of CC was unaltered in both groups. Data were analyzed by using SPSS version 16.

RESULTS

More than 50% of the females in both groups had a body mass index of >25. Group A achieved a higher rate of regular cycles, ovulation success, and conception than group B (71.4% vs. 38.1%; p=0.03), (76.2% vs. 38.1%; p=0.021) and (66.6% vs. 28.6%, p=0.01), respectively.

CONCLUSION

Management with metformin + CC increased the ovulation and conception rates.

An ontology for collaborative construction and analysis of cellular pathways

MOTIVATION

As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated.

RESULTS

We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology.

Lemierre's syndrome

This is a case report of Lemierre's syndrome in a 17-year-old male patient. Lemierre's disease consists of suppurative thrombophlebitis of the internal jugular vein (SIJVT) in the presence of oropharyngeal infection and can be complicated by septic pulmonary embolism. Other causes of SIJVT include deep neck infections and central venous catheterization. The disease usually results from Gram-negative anaerobic organisms such as Fusobacterium necrophorum.

Use of pleural fluid C-reactive protein in diagnosis of pleural effusions

The aims of the study were to assess whether C-reactive protein (CRP) is a sensitive marker for discriminating between transudative and exudative and pleural effusions to evaluate whether it can be used to distinguish inflammatory pleural effusions from other types of effusion. Pleural fluid and serum CRP levels were obtained in 97 patients with pleural effusion, using an immunoturbidimetric method (Olympus AU-600 autoanalyser). We compared CRP levels between transudates and exudates, inflammatory effusions and other types of effusion. According to the criteria used, 16 patients were included in the transudate group and 81 patients in the exudate group. Pleural fluid CRP levels were significantly lower in the transudate group (P<0.04; 14.9 +/- 4.9 mg l(-1) and 35.5 +/- 4.9 mg l(-1) respectively). Also, the ratio of pleural fluid to serum was significantly lower in the transudate group (P<0.009; 0.8 +/- 0.5 mg l(-1) and 2.8 +/- 0.7 mg l(-1), respectively). In the exudate group, 35 patients had neoplastic effusions, 10 chronic non-specific pleurisy, 19 tuberculous pleurisy, 16 parapneumonic effusion and one Dressler Syndrome. When these sub-groups were compared, the parapneumonic effusion subgroup CRP levels (mean 89 +/- 16.3 mg l(-1)) were significantly higher than those in the other subgroups, other exudate of neoplastic effusion, tuberculous pleurisy and chronic non-specific effusion and the transudate group (P<0.0001; P<0.0001; P<0.0004 and P<0.0001, respectively). The ratio between pleural fluid and serum CRP was significantly higher in the parapneumonic effusion subgroup than in the neoplastic subgroup (P<0.0002; 6.6 +/- 2.7 mg l(-1) and 1 +/- 0.2 mg l(-1), respectively). Pleural fluid CRP levels > 30 mg l(-1) had a high sensitivity (93.7%) and specificity (76.5%) and a positive predictive value of 98.4%. In the differential diagnosis of pleural effusions, higher CRP levels may prove to be a rapid, practical and accurate method of differentiating parapneumonic effusions from other exudate types. Although the high level of CRP obtained in the exudate group may be due to the number of patients with parapneumonic effusion who were included, the pleural CRP level may also be helpful in discriminating between exudative and transudative pleural effusions.