Contribution of Inherited Variants to Hereditary Cancer Syndrome Predisposition.

Cancer is a clonal disease that develops as a result of the changes on the genetic material by various factors in micro/macro environment. It has a multi-step development process. In some cancer types, genetic factors allow this multi-step process to proceed easily. These cancer types are also called hereditary cancer syndromes. Targeted gene panels are important diagnostic methods in hereditary cancer syndromes to detect the causative variants associated with these hereditary cancer syndromes. We reviewed the data of 94 patients who applied to Ankara City Hospital Genetic Diseases Evaluation Center from March 2019 to July 2021. Qiagen familial cancer susceptibility gene panel kit was used for next generation sequencing to detect the single nucleotide variants for the targeted genes. Sixty-one genes which are associated with increased cancer risk or well characterized hereditary cancer syndromes were included to this panel. Twenty five patients (27%), including 8 males and 17 females, had pathogenic/likely pathogenic variants in 13 of the 61 genes analyzed. Forty patients (43%) had variants which were assessed as variant of unknown significant. In our study, targeted multi-gene panel was diagnostic in nearly one third of the patients with personal/familial cancer syndromes. Molecular diagnosis in familial cancer syndromes is important in terms of predictive diagnosis and family screening, as well as patient follow-up and early prophylactic surgery. The predisposition for hereditary cancer syndromes can be determined according to pre-test evaluation, figuring out the inheritance type with pedigree analysis, cancer type and the genetic analysis for appropriate susceptibility genes.

Predictive Factors for Molecular Response in Chronic Myeloid Leukemia: Reduction Ratio and Halving Time of BCR::ABL1 IS Transcript Levels

Objective: Achieving an early molecular response (EMR) is crucial for improving the prognosis of patients with chronic myeloid leukemia (CML). The halving time (HT) and reduction ratio (RR) of BCR::ABL1 transcript levels have recently emerged as additional prognostic indexes besides the BCR::ABL1 International Scale (IS). We aimed to investigate the prognostic role of BCR::ABL1 transcript levels, HT, and RR on molecular response kinetics at 3 months in patients with newly diagnosed chronic-phase (CP)-CML. Materials and Methods: Forty patients with CP-CML who received first-line imatinib treatment were included in this study. BCR::ABL1 transcript levels and molecular responses at baseline and at 3, 6, 12, and 24 months of treatment were evaluated retrospectively. Major molecular response (MMR) at 12 months and event-free survival (EFS) were determined as primary endpoints and the effects of treatment kinetics on these parameters were examined. Results: Of the 40 patients, BCR::ABL1 IS was ≤10% at 3 months in 72.5%, representing EMR. The rate of event occurrence was 45.5% in patients with BCR::ABL1 IS of >10%, whereas it was 6.9% in those with BCR::ABL1 IS of ≤10% (p=0.004). MMR was detected in 62.1% of the patients with EMR and in 9.1% of those without EMR (p=0.003). The cut-off value for achieving MMR was 24 days for HT and 0.04 for RR. Deep molecular response (DMR) at 24 months was associated with HT of ≤24 days and RR of ≤0.04. EFS was found to be significantly better in the group with BCR::ABL1 IS of ≤10% and HT of ≤24 days (p=0.001) and in the group with BCR::ABL1 IS of ≤10% and RR of ≤0.04 (p=0.007) compared to others. Conclusion: Our findings revealed that MMR could be predicted via EMR as well as by HT and RR. Additionally, HT of ≤24 days and RR of ≤0.04 were more important than BCR::ABL1 IS of ≤10% in achieving DMR at 24 months, and the combination of BCR::ABL1 IS of ≤10% with both HT of ≤24 days and RR of ≤0.04 has the best predictive value for EFS.

Frequency of germline BRCA1/2 mutations and association with clinicopathological characteristics in Turkish women with epithelial ovarian cancer.

AIM: This study aims to determine the frequency of germline BRCA 1/2 mutations in Turkish women with epithelial ovarian cancer (EOC) and evaluate its relationship with clinicopathological characteristics. METHODS: In this cross-sectional study, all women with recently diagnosed EOC presenting to Zekai Tahir Burak Women's Health Training and Research Hospital Medical Oncology Clinic between 2016 and 2019 were referred for BRCA testing. Peripheral blood samples were obtained from 76 patients applying to Medical Genetics and BRCA1/2 genes were sequenced using next-generation sequencing. The American College of Medical Genetics and Genomics 2015 criteria were followed for classification of genetic variants. RESULTS: Twenty-four women (31.6%) had pathogenic germline BRCA1/2 mutations. Of these, 17 patients (22.4%) harbored germline BRCA1 mutations and 7 (9.2%) had BRCA2 mutations. When we compared the patients with and without BRCA mutations, there was significant difference in terms of family history (41.7% vs 9.6%, respectively, P = .001). Among all patients, 15 (19.7%) had history of breast or ovarian cancer in first- or second-degree relatives. Germline BRCA1/2 mutations were detected in 66.7% of patients with family history, while these mutations were found in 22.9% of patients without family history (P = .001). CONCLUSION: In this sample 31.6% of Turkish women with EOC harbored germline BRCA1/2 mutations, which seems higher compared to other ethnic groups except for the Ashkenazi Jews population. All women with EOC should be referred for BRCA testing regardless of family history, age at diagnosis, and histological subtype.

Severe isolated sulfide oxidase deficiency with a novel mutation.

BACKGROUND: Isolated sulfite oxidase deficiency (ISOD), caused by mutations in SUOX gene, is an autosomal recessive disease manifesting with early onset seizures, developmental delay, microcephaly, and spasticity. It mimics hypoxic-ischemic encephalopathy (HIE) in the neonatal period and is characterized by progressive severe neurological impairment due to accumulation of toxic metabolites. CASE: This report presents a late diagnosed male patient with ISOD manifesting with neonatal-onset seizures, developmental delay, microcephaly, and spastic quadriplegia. Brain magnetic resonance imaging of the patient showed bilateral subcortical multi-cystic encephalomalacia involving bilateral parieto-occipital regions. A novel homozygous c.590_595delAGCCTC in-frame deletion in SUOX gene was identified in the patient, while both parents were heterozygous for that mutation. CONCLUSION: The mutation identified in our patient causes severe ISOD. Early diagnosis of ISOD is essential for accurate genetic counseling and achieving prenatal diagnosis. Screening for urinary sulfite in patients with neonatal or early infantile onset seizures, developmental delay, microcephaly and cystic encephalomalacia in neuroimaging mimicking HIE helps in early diagnosis.

Acromesomelic dysplasia-Maroteaux type, nine patients with two novel NPR2 variants.

OBJECTIVES: Acromesomelic dysplasia, type Maroteaux, is an autosomal recessive skeletal dysplasia caused by biallelic loss of function variations of NPR2, which encodes a cartilage regulator C-type natriuretic peptide receptor B. NPR2 variations impair skeletal growth. It is a rare type of dwarfism characterized by shortening of the middle and distal segments of the limbs with spondylar dysplasia. METHODS: We performed detailed clinical and radiological evaluation and sequence analysis for NPR2. RESULTS: Herein, we report nine patients from eight families with two novel NPR2 pathogenic variants. CONCLUSIONS: This study describes typical clinical phenotypes of Maroteaux type acromesomelic dysplasia, and enriches the variant spectrum of NPR2 by reporting one nonsense and one missense novel variant. We emphasize the importance of detailed clinical evaluation before genetic testing in diagnosing rare skeletal disorders.

Hematopoietic stem cell transplantation complicated with EBV associated hemophagocytic lymphohistiocytosis in a patient with DOCK2 deficiency.

BACKGROUND: Dedicator of cytokinesis 2 (DOCK2) deficiency is a rare autosomal recessive combined immunodeficiency presenting with very early onset, severe bacterial and viral infections. In DOCK2 deficiency; T, B and NK cell numbers are decreased and functions are impaired resulting in severe atrophy of secondary lymphoid tissues. The aim of this report is to provide information on clinical and laboratory features and hematopoietic stem cell transplantation (HSCT) outcomes of a DOCK2 deficient patient. The patient was diagnosed by using a targeted next generation sequencing primary immunodeficiency (PID) panel. Lymphocyte subsets were measured by flow-cytometry. CASE: Here, we describe a patient with DOCK2 deficiency presented with severe combined immunodeficiency. He underwent HSCT without conditioning regimen before the genetic diagnosis and developed hemophagocytic lymphohistiocytosis(HLH) due to Epstein-Barr virus (EBV) infection. CONCLUSIONS: Genetic testing is necessery for early diagnosis of DOCK2 deficiency. The curative treatment should be HSCT soon after diagnosis.

Optical coherence tomography-angiographic vascular densities in Familial Mediterranean Fever (FMF) Patients with M694V Mutations.

Familial Mediterranean fever (FMF) is a hereditary auto-inflammatory disease with accompanying findings of amyloidosis and vasculitis. M694V is one of the most common mutations associated with amyloidosis. This study compared the macular optical coherence tomography angiography measurements in FMF patients who were genetically verified to carry the M694V mutation of the MEFV gene to those in healthy controls. The vessel densities (VDs) of superficial (SVP) and deep vascular plexus (DVP) of the retina, and choriocapillaris, foveal avascular zone (FAZ) perimetry, foveal VD 300µ around the FAZ (FD-300), acirculatory index (AI) and non-flow area were measured with  optical coherence tomography angiography (OCT-A). The FMF and control groups were matched for age and gender. Compound heterozygous pathogenic variants were excluded. Thirty-eight FMF patients with M694V mutations (28 heterozygous and 10 homozygous) and 40 healthy controls were included. The two groups were similar with the regard to age and gender (P=0.88 and P=0.49, respectively). None of the investigated parameters, including the vessel densities of the SVP and DVP, and choriocapillaris, FAZ perimetry, FD-300, AI, and non-flow area showed a statistically significant difference between the FMF and control groups. The macular vessel density measurements and FAZ parameters of FMF patients with M694V mutations do not differ from age- and sex-matched healthy controls.

Regression of macular edema with topical brinzolamide and nepafenac alone and identification of a novel gyrate atrophy mutation.

Gyrate atrophy is a rare metabolic autosomal recessive disorder caused by ornithine aminotransferase enzyme deficiency that leads to characteristic progressive, degenerative chorioretinal findings. Patients complain mostly of low vision, night blindness, and peripheral vision loss. Posterior subcapsular cataract, myopia, choroid neovascularization, and intraretinal cysts may be accompanying factors related to vision loss. We encountered a patient with vision loss secondary to posterior subcapsular cataract and intraretinal cysts. After treatment with topical brinzolamide and nepafenac (and without any diet mo dification and/or supplementation), we observed 143- and 117-mm macular thickness resolutions with 2 and 1 Snellen lines of visual gain in his right and left eyes, respectively. Also, we detected a novel homozygous mutation in the ornithine aminotransferase gene: c.1253T>C (p.Leu418Pro). Carbonic anhydrase inhibitors and/or non-steroid anti-inflammatory drugs can control macular edema in patients with gyrate atrophy-associated intraretinal cysts. The genetic variants may also be a determinant in the responsiveness to the therapy type.

The Effect of BRAF V600E Mutation on Lymph Node Involvement in Papillary Thyroid Cancer.

OBJECTIVES: Papillary thyroid cancer (PTC) is the most common well-differentiated thyroid cancer. Lymph node (LN) metastasis is frequently seen in PTC. The effect of BRAFV600E mutation on PTC-associated LN metastasis has not been clearly established. Therefore, we aimed to evaluate the effect of the BRAFV600E mutation in patients with PTC on regional LN metastasis. MATERIAL AND METHODS: Between January 2013 and 2017, sixty-three PTC patients who underwent central lymph node dissection were included into the study. The patients were divided into two groups according to the pathology results of the LN dissection, and these groups were compared for positive BRAFV600E mutations and other clinicopathological findings. RESULTS: BRAFV600E mutation was found to be more significant in the pLN1 group (p= 0.005). Multivariate analysis revealed that nodule size, microcalcifications, and BRAFV600E mutation were associated with lymph node metastasis independent of other parameters. ROC analysis also evaluated the adequacy of the BRAFV600E mutation in predicting the presence of LN involvement. AUC: 0.738 (95%CI:0.6110.866,p: 0.002). CONCLUSION: In our study, independent of other parameters, BRAFV600E gene mutation was found to be effective on lymph node involvement.

Duplication 4q associated with chronic cholestatic changes in liver biopsy.

We report a 15-day-old girl with partial trisomy 4q syndrome who presented with neonatal cholestasis. She had dysmorphic facial features and preaxial polysyndactyly of the right hand. The other findings were generalized hypertrichosis, pes equinovarus, oedema on feet and mild hepatomegaly. No specific reason for the cholestasis with elevated liver enzymes and direct bilirubinemia were characterized. Cytogenetic analyses revealed a karyotype 46,XX,der(13)t(4;13)(q25;p13). This is the first patient with partial trisomy 4q syndrome presented with neonatal cholestasis.