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

Renal Cell Carcinoma in A Patient with Kartagener Syndrome: First Case Report in English Language

Cardiac and pulmonary anomalies are common among patients with situs inversus totalis. Renal anomalies, including renal agenesis, dysplasia, hypoplasia, ectopia, polycystic kidney, and horseshoe kidney have been reported. We report a case of renal cell carcinoma in a patient with situs inversus totalis (SIT). Our case represents the fourth case report of renal cell carcinoma in a patient with situs inversus totalis and to the best of our knowledge this is the first report in English language. Due to the higher frequency of cardiac, pulmonary, renal, and vascular anomalies the management of patients with situs inversus and urologic disease requires careful preoperative evaluation

The incidence of renal oncocytoma in renal tumours and the location of imaging for indication of fine needle aspiration biopsy in diagnosis

Amaç: Böbrek tümörü nedeniyle tedavi edilen hastalar içerisinde renal onksitom sıklığını ve tanı için görüntüleme yöntemlerinin ince iğne aspirasyon biyopsisi indikasyonundaki yerini araştırdık. Gereç ve Yöntemler: Hastanemizde 2005 ile 2011 yılları arasında böbrek tümörü nedeniyle radikal nefrektomi veya nefron koruyucu cerrahi uygulanan 420 hasta retrospektif olarak incelendi. Renal onkositom saptanan hastalar radyolojik bulgu ve semptom varlığı, bu hastalara uygulanan tedaviler ve ince iğne aspirasyon biyopsisi ile böbrek biyopsisi uygulanabilirliği açısından değerlendirildi. Bulgular: Renal onkositom sıklığı %2.8 olarak tespit edildi. Bu hastaların 7’sinde (%58) radyolojik bulgu izlendi. Hastaların 8’i (%67) tanı anında semptomatikti. 2 hastaya (%17) nefron koruyucu cerrahi, 10 hastaya (%83) ise radikal nefrektomi uygulandı. Sonuç: Renal onkositom sıklığı literatür ile uyumlu bulundu. Radyolojik bulgusu olan veya benin-malin ayrımı yapılamayan hastalarda ince iğne aspirasyon biyopsisi veya böbrek biyopsisi yapılmasının gereksiz radikal cerrahileri engelleyeceği kanaatindeyiz.Objective: We’ve investigated the incidence of renal oncocytoma in patients with renal tumour who underwent surgery and the location of imaging for indication of fine needle aspiration biopsy in diagnosis. Material and Methods: 420 patients who underwent radical nephrectomy or nephron sparing surgery between 2005 and 2011 in our hospital were evaluated retrospectively. Patients who diagnosed Renal Oncocytoma (RO) were determined in terms of presence of symptoms and radiological signs, treatment modalities and applicability of fine needle aspiration biopsy or renal biopsy. Results: The incidence of renal oncocytoma was 2.8% and in 7 patients (58%) who diagnosed renal oncocytoma had radiological signs. 8 patients (67%) were symptomatic at the time of diagnosis. 2 patients (17%) were treated with radical nephrectomy while 10 patients (83%) with nephron sparing surgery. Conclusion: The incidence of renal oncocytoma was consistent with the literature. We believe that performing fine needle aspiration biopsy or renal biopsy in patients who have radiological signs or difficulty in differentiation between benign and malignant will prevent unnecessary radical surgeries

A very rare fact occurring after V/P shunt in the surgical treatment of Pseudotumor Serebri Syndrome: Liver subcapsular pseudocysts

Introduction: In this study, it is aimed to present a very rare liver subcapsular accumulation of a patient after ventriculoperitoneal shunt surgery who was diagnosed with Pseudotumor cerebri syndrome with progressive sight loss.&nbsp; &nbsp;&nbsp; Case:&nbsp;The patient is a 38-year-old female who was diagnosed with lomber spondylose and later operated with stabilization and fusion surgery. Seven days after the operation her headaches became clear and blackout in her left eye was seen and she was observed with medical treatment. CSF &nbsp;pressure of her was measured to be 25 cm/ water, so she was diagnosed as pseudotumour cerebri and taken to the operation immediately. On the 3rd day of post-operation, there occurred to be intense stomach ache and abdominal sensitivity of the case. After the scanning of abdominal CT,&nbsp; 7 cm of liquid collection was detected in the shunt distal of liver subcapsular area. Discussion: Liver pseudocyst should be considered, even if it is a rare complication when back striking abdominal pain and high liver enzymes are seen in patients with shunt dysfunction. USG and abdominal bt tests should be made for these patients. The drainage of the cyst and then the removal of the abdominal catheter should be applied

Editör Yardımcıları / Associate Editors

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