Germline genetic variants in Turkish familial multiple myeloma/monoclonal gammopathy of undetermined significance cases.

Multiple myeloma (MM) is a haematological malignancy primarily affecting the elderly, with a striking male predilection and ethnic disparities in incidence. Familial predisposition to MM has long been recognized, but the genetic underpinnings remain elusive. This study aimed to investigate germline variants in Turkish families with recurrent MM cases. A total of 37 MM-affected families, comprising 77 individuals, were included. Targeted next-generation sequencing analysis yielded no previously reported rare variants. Whole exome sequencing analysis in 11 families identified rare disease-causing variants in various genes, some previously linked to familial MM and others not previously associated. Notably, genes involved in ubiquitination, V(D)J recombination and the PI3K/AKT/mTOR pathway were among those identified. Furthermore, a specific variant in BNIP1 (rs28199) was found in 13 patients across nine families, indicating its potential significance in MM pathogenesis. While this study sheds light on genetic variations in familial MM in Turkey, its limitations include sample size and the absence of in vivo investigations. In conclusion, familial MM likely involves a polygenic inheritance pattern with rare, disease-causing variants in various genes, emphasizing the need for international collaborative efforts to unravel the intricate genetic basis of MM and develop targeted therapies.

Contribution of genotypes in Prothrombin and Factor V Leiden to COVID-19 and disease severity in patients at high risk for hereditary thrombophilia.

Thrombotic and microangiopathic effects have been reported in COVID-19 patients. This study examined the contribution of the hereditary thrombophilia factors Prothrombin (FII) and Factor V Leiden (FVL) genotypes to the severity of COVID-19 disease and the development of thrombosis. This study investigated FII and FVL alleles in a cohort of 9508 patients (2606 male and 6902 female) with thrombophilia. It was observed that 930 of these patients had been infected by SARS-CoV-2 causing COVID-19. The demographic characteristics of the patients and their COVID-19 medical history were recorded. Detailed clinical manifestations were analyzed in a group of cases (n = 4092). This subgroup was age and gender-matched. FII and FVL frequency data of healthy populations without thrombophilia risk were obtained from Bursa Uludag University Medical Genetic Department's Exome Databank. The ratio of males (31.08%; 27.01%) and the mean age (36.85 ± 15.20; 33.89 ± 14.14) were higher among COVID-19 patients compared to non-COVID-19 patients. The prevalence of FVL and computerized tomography (CT) positivity in COVID-19 patients was statistically significant in the thrombotic subgroup (p < 0.05). FVL prevalence, CT positivity rate, history of thrombosis, and pulmonary thromboembolism complication were found to be higher in deceased COVID-19 patients (p < 0.05). Disease severity was mainly affected by FVL and not related to genotypes at the Prothrombin mutations. Overall, disease severity and development of thrombosis in COVID-19 are mainly affected by the variation within the FVL gene. Possible FVL mutation should be investigated in COVID-19 patients and appropriate treatment should be started earlier in FVL-positive patients.

ROHMM-A flexible hidden Markov model framework to detect runs of homozygosity from genotyping data.

Runs of long homozygous (ROH) stretches are considered to be the result of consanguinity and usually contain recessive deleterious disease-causing mutations. Several algorithms have been developed to detect ROHs. Here, we developed a simple alternative strategy by examining X chromosome non-pseudoautosomal region to detect the ROHs from next-generation sequencing data utilizing the genotype probabilities and the hidden Markov model algorithm as a tool, namely ROHMM. It is implemented purely in java and contains both a command line and a graphical user interface. We tested ROHMM on simulated data as well as real population data from the 1000G Project and a clinical sample. Our results have shown that ROHMM can perform robustly producing highly accurate homozygosity estimations under all conditions thereby meeting and even exceeding the performance of its natural competitors.

Phenotypic and molecular characterization of five patients with PIK3CA-related overgrowth spectrum (PROS).

Somatic and germline PI3K-AKT-mTOR pathway pathogenic variants are involved in several segmental overgrowth phenotypes such as the PIK3CA-related overgrowth spectrum (PROS), Proteus syndrome, and PTEN hamartoma tumor syndrome. In this study, we describe five patients with PROS. We identified by high-throughput sequencing four different somatic PIK3CA pathogenic variants in five individuals. The Glu726Lys variant, which was previously reported in megalencephaly-capillary malformation-polymicrogyria (MCAP) syndrome, was identified in two patients with unclassified PROS. The Cys420Arg substitution, which was previously reported in CLOVES, was found in a patient with fibroadipose hyperplasia. Additionally, relatively rare pathogenic variants, His1047Tyr and Tyr1021Cys, were detected in two patients with MCAP. Therefore, we suggest performing deep sequencing of PIK3CA in all patients with suspected PROS, instead of targeted polymerase chain reaction for hotspot pathogenic variants.

A Novel PTCH1 Frameshift Mutation Leading to Nevoid Basal Cell Carcinoma Syndrome.

Nevoid basal cell carcinoma syndrome (NBCCS), also known as Gorlin syndrome, is a rare multisystemic autosomal dominant disorder typically presenting with cutaneous basal cell carcinomas, multiple keratocysts, and skeletal anomalies. NBCCS is caused by heterozygous mutations in the PTCH1 gene in chromosome 9q22, in the PTCH2 gene in 1p34, or the SUFU gene in 10q24.32. Here, we report on an 18-month-old boy presenting with medulloblastoma, frontal bossing, and multiple skeletal anomalies and his father who has basal cell carcinomas, palmar pits, macrocephaly, bifid ribs, calcification of falx cerebri, and a history of surgery for odontogenic keratocyst. These clinical findings were compatible with the diagnosis of NBCCS, and a novel mutation, c.1249delC; p.Gln417Lysfs*15, was found in PTCH1 causing a premature stop codon.

Epstein-barr virus-negative post-transplant lymphoproliferative diseases: three distinct cases from a single center.

Three cases of Epstein-Barr virus (EBV)-negative post-transplant lymphoproliferative disease that occurred 6 to 8 years after renal transplantation are reported. The patients respectively had gastric mucosa-associated lymphoid tissue lymphoma, gastric diffuse large B-cell lymphoma, and atypical Burkitt lymphoma. Absence of EBV in the tissue samples was demonstrated by both in situ hybridization for EBV early RNA and polymerase chain reaction for EBV DNA. Patients were treated with reduction in immunosuppression and combined chemotherapy plus an anti-CD20 monoclonal antibody, rituximab. Despite the reduction in immunosuppression, patients had stable renal functions without loss of graft functions. The patient with atypical Burkitt lymphoma had an abnormal karyotype, did not respond to treatment completely, and died due to disease progression. The other patients are still alive and in remission 5 and 3 years after diagnosis, respectively. EBV-negative post-transplant lymphoproliferative diseases are usually late-onset and are reported to have poor prognosis. Thus, reduction in immunosuppression is usually not sufficient for treatment and more aggressive approaches like rituximab with combined chemotherapy are required.

X-linked Dyskeratosis Congenita Case with Mutation 1058C>T(p.Ala353Val) in Dyskerine Gene.

Dyskeratosis congenita (DC) is a rare inherited bone marrow failure syndrome and telomere biology disorder, usullay consisting of a triad of oral leucoplakia, dystrophic nails, reticular skin pigmentation. The diagnosis in the majority of cases can be made following all the clinical findings of this triad are established. Here we report 7 years-old boy who had oral leukoplakia and nail abnormality without skin involvement, associated with bone marrow failure diagnosed with X-linked DC due to dyskerin (DKC1) mutation. Our report emphasizes the fact that clinical suspicion can prevent fatal consequences since all manifestations may not always be seen collectively.

Oesophageal achalasia misdiagnosed as uncontrolled asthma.

Achalasia is characterized by incomplete lower oesophageal sphincter relaxation and aperistalsis of the oesophagus. It may present with dyspnea symptom. An 18-years-old male patient applied to a clinic with the complaints of cough, dyspnea, wheezing and diagnosed as asthma. Although his asthma treatment was increased in time while he did not recover, he was reffered to our hospital with the diagnosis of uncontrolled asthma. On chest X-ray there was a mild upper mediastinal enlargement and chest computed tomography revealed an over-dilated oesophagus constricting the trachea. The patient was referred to chest surgery clinic with a suspected diagnosis of achalasia. Barium-oesophagogram and endoscopic evaluation of the oesophagus confirmed the diagnosis of achalasia. The patient underwent Heller myotomy and oesophagogastrostomy. He was recovered in one week after the surgery without any complaint of dyspnea. Spirometry tests and chest X-ray resulted normal in one year. With this case of achalasia who used asthma treatment unnecessarily,we wanted to emphasize the importance of differential diagnosis of difficult asthma.

Right Anterior Theta Hypersynchrony as a Quantitative Measure Associated with Autistic Traits and K-Cl Cotransporter KCC2 Polymorphism.

Our aim was to use theta coherence as a quantitative trait to investigate the relation of the polymorphisms in NKCC1 (rs3087889) and KCC2 (rs9074) channel protein genes to autistic traits (AQ) in neurotypicals. Coherence values for candidate connection regions were calculated from eyes-closed resting EEGs in two independent groups. Hypersynchrony within the right anterior region was related to AQ in both groups (p < 0.05), and variability in this hypersynchrony was related to the rs9074 polymorphism in the total group (p < 0.05). In conclusion, theta hypersynchrony within the right anterior region during eyes-closed rest can be considered a quantitative measure for autistic traits. Replicating our findings in two independent populations with different backgrounds strengthens the validity of the current study.

Coexistence of Ovarian Granulose Cell Tumor, Congenital Adrenal Hyperplasia, and Triple Translocation: Is a Consequence or Coincidence?

PURPOSE: Congenital adrenal hyperplasia (CAH) is rare autosomal recessive disease. CAH due to 21-hydroxylase deficiency accounts for 95% of cases. We aimed to share the first case of coexistence of simple virilizing-type congenital adrenal hyperplasia [I172N mutation in the CYP21A], triple translocation [t(9;11;12)], and ovarian granulose cell tumor. METHODS: A 59-year-old female patient was presented to our clinic, complaining with abdominal pain and distension. Physical examination revealed palpable abdominal mass, virilism, ambiguous genitalia, clitoramegaly, and hyperpigmentation. Contrast-enhanced abdominal computed tomography showed a giant mass originating from the right tubo-ovarian structure. RESULTS: The patient was operated in the light of the clinico-radiological features mentioned above. A giant mass weighing 3500 g was detected on the right tubo-ovarian structure during laparotomy, and mass was excised with right tubo-ovarian structure. Immunohistochemical examination revealed ovarian granulosa cell tumor. The high serum concentration of 17-OH progesterone was measured at baseline and after 250-µg bolus of synthetic ACTH. In genetic analysis, we screened for six-point mutations, large deletions, and non-common mutations using restriction fragment length polymorphism (RFLP) methods, PCR, and sequencing of CYP21 gene respectively. The patient was detected to be homozygous for the I172N mutation. In addition, 50% of the metaphases examined had triple translocation [t(9;11;12)]. CONCLUSION: The coexistence of congenital adrenal hyperplasia, triple chromosomal translocations, and ovarian granulosa cell tumor has not been described previously. This coexistence may be a sign of a new syndrome.

TBX1 gene mutation screening in patients with non-syndromic Fallot tetralogy.

Fallot tetralogy (FT) is the most frequently observed conotruncal heart defect (CTHD) and accompanies 15% of the 22q11 deletion syndromes, DiGeorge/ velocardiofacial (DGS/VCFS) syndromes. TBX1 is a gene located in the 22q11 region and has a role in neural crest migration and conotruncal development. The mouse Tbx1 locus shows 98% homology with TBX1. DGS/VCFS-like aortic arch abnormalities in the mouse were attributed to deletions in this locus. The T-box region, common to both mice and humans, is part of TBX1 with proven effects on heart outflow track anomalies. The role of TBX1 in non-syndromic CTHDs is still unclear. In this study, we screened the TBX1 gene T-box region exons in 50 FT patients without 22q11 deletion and in 50 healthy volunteers. Our study did not show any disease causing mutations, but one polymorphic change. These results do not support a major role of the T-box region in the etiology of isolated FT. Furthermore, this study also confirms that mouse cardiac-development study models do not always provide an explanation for human phenotype-genotype correlations.

Lack of the Association of the PTPN22 C1858T Gene Polymorphism With Susceptibility to Familial Mediterranean Fever.

OBJECTIVES: This study aims to investigate whether the protein tyrosine phosphatase non-receptor type 22 (PTPN22) C1858T gene polymorphism plays a role in the pathogenesis of familial Mediterranean fever (FMF) through T-lymphocyte activation. PATIENTS AND METHODS: We conducted a case-control study with 180 FMF patients (68 males, 112 females; mean age 38.2±1.6 years; range 16 to 81 years) and 184 healthy controls (86 males, 98 females; mean age 32.9±9.2 years; range 18 to 58 years). The PTPN22 C1858T polymorphism (rs2476601) was genotyped by polymerase chain reaction restriction fragment length polymorphism. In patients with FMF, clinical features, disease severity score, the frequencies of amyloidosis, positive family history, and Mediterranean fever gene mutations were determined. RESULTS: The frequencies of heterozygous genotype (CT) were 4.5% in FMF patients and 2.8% in healthy controls, respectively. The frequencies of polymorphic homozygous genotypes (TT) were 0.5% in both FMF patients and healthy controls. There were no statistically significant differences in the frequencies of CT and TT genotypes between FMF patients and healthy controls (odds ratio: 1.65, 95% confidence interval: 0.53-5.14, p>0.05 for CT genotype). The frequencies of clinical features, sex, amyloidosis, positive family history, Mediterranean fever gene mutations, and disease severity score were not significantly different between the patients. CONCLUSION: The distribution of PTPN22 C1858T polymorphism did not reveal any association with FMF in a Turkish population.

Is vitamin D hypothesis for schizophrenia valid? Independent segregation of psychosis in a family with vitamin-D-dependent rickets type IIA.

The vitamin D hypothesis of schizophrenia is a recent concept bringing together old observations on environmental risk factors and new findings on the neurodevelopmental effects of vitamin D. Candidate genes related to the vitamin D endocrine system have not yet been fully explored for this purpose. The coexistence of vitamin-D-dependent-rickets type II with alopecia (VDDR IIA) and different forms of psychosis in the same inbred family has provided us with an opportunity to investigate the presumed relationship between vitamin D deficiency and psychosis. Psychiatric examination and molecular genetic studies were performed in this family overloaded with psychotic disorders and VDDR IIA. Forty members were evaluated in order to describe their phenotypic features. The family was tested for a linkage to the chromosome 12q12-q14 region where the vitamin D receptor (VDR) gene is located. Psychosis was the common phenotype in the 18 psychiatrically affected members. Pedigree analysis did not show a cosegregation of psychosis and rickets. Lod scores were not significant to prove a linkage between psychosis and VDR locus. The authors concluded that (1) the neurodevelopmental consequences of vitamin D deficiency do not play a causative role in psychotic disorders, (2) these two syndromes are inherited independently, and (3) vitamin D deficiency does not act as a risk factor in subjects susceptible to psychosis.

The contribution of genotypes at the MICA gene triplet repeat polymorphisms and MEFV mutations to amyloidosis and course of the disease in the patients with familial Mediterranean fever.

OBJECTIVE: To evaluate the effects of MEFV genotypes and the major histocompatibility complex class I chain-related gene A (MICA) triplet repeat polymorphism on the severity and clinical features of familial Mediterranean fever (FMF) and amyloidosis in a group of Turkish FMF patients. METHODS: We evaluated 105 adult FMF patients (with or without amyloidosis, 33 and 72, respectively) along with 107 healthy controls who were neither related to the patients nor had a family history of FMF or Behcet's disease. After recording the demographic and clinical data, the predominant mutations in the MEFV gene locus (M694V, M680I, V726A, M694I, and E148Q) were investigated by direct sequencing. MICA transmembrane polymorphisms in exon 5 were studied by vertical gel electrophoresis and fragment analysis of the amplicons obtained from MICA locus with appropriate primers. RESULTS: Earlier age at onset, increased frequency of attacks, arthritis attacks, erysipelas-like erythema, increased severity scores and amyloidosis were significantly more common in M694V homozygous patients compared to the patients not M694V homozygous (P = 0.005, OR 4.55; P = 0.001, OR 7.60; P = 0.003, OR 4.57; P = 0.002, OR 7.58; P = 0.004, OR 5.15 and P = 0.018, OR 3.33, respectively). We did not detect any modifying effects of MICA alleles as an independently risk factor on the amyloidosis development. However, when we examined the effects of MICA alleles on the course of the disease and development of amyloidosis in the M694V homozygous patients, A5 allele had a protective effect against the development of amyloidosis (P = 0.038, OR(adj) 0.26 with A5 and P = 0.009, OR(adj) 4.42 without A5). CONCLUSION: Though the effects of the MEFV genotypes seem clear, there are definitely other modifying factors or genes on the development of amyloidosis and on the course of the disease. For example, some MICA alleles have a protective effect on the prognostic factors in FMF.

Colobomatous macrophthalmia with microcornea syndrome maps to the 2p23-p16 region.

Colobomatous macrophthalmia with microcornea syndrome (OMIM 602499) is a rare, autosomal dominant malformation characterized by microcornea, uveal coloboma, axial enlargement of the globe, and myopia. Using what is currently the largest described pedigree and candidate localization approach, we first excluded the candidate genes PAX2, PAX3, PAX6, and PAX9. Subsequently, the chromosome 14q24 region containing the CHX10, SIX1, and SIX4 genes were also excluded. Positive LOD scores were obtained with the DNA markers selected from the 2p23-p16 region. A maximum pairwise LOD score of 3.61 (Theta = 0) was noted with the DNA marker D2S1788. Haplotype analysis positioned the locus between DNA markers D2S2263 and D2S1352 within a 22 Mb physical interval. This region contains major candidate genes, such as SIX2, SIX3, and CYP1B1; however, mutation analysis did not identify a causative mutation in these genes. Macrophthalmia, colobomatous, with microcornea (MACOM) is proposed as the gene symbol for this malformation linked to 2p23-p16.

A fourth locus for hereditary hemorrhagic telangiectasia maps to chromosome 7.

Hereditary hemorrhagic telangiectasia (HHT) is a genetically and clinically heterogeneous multisystem vascular dysplasia. Mutations of the endoglin and ACVRL1 genes are known to cause HHT. However, existence of HHT families in which linkage to these genes has been excluded has suggested that other gene(s) can cause HHT in some families. Recently, a family was reported to be linked to chromosome 5q, the HHT3 locus. Here we report on linkage results on a family with classic features of HHT, albeit a less severe phenotype with regards to epistaxis and telangiectases, in which linkage to HHT1, HHT2, and HHT3 is ruled out. Whole genome linkage analysis and fine mapping results suggested a 7 Mb region on the short arm of chromosome 7 (7p14) between STR markers D7S2252 and D7S510. We obtained a maximum two point LOD score of 3.60 with the STR marker D7S817. This region was further confirmed by haplotype analysis. These findings suggest the presence of another gene causing HHT (HHT4). The features in this family that strongly suggest the presence of a hereditary, multisystem vascular dysplasia would be easily missed during the typical evaluation and management of a patient with an AVM. This family helps emphasize the need to obtain a very detailed, targeted medical and family history for even mild, infrequent but recurring nosebleed, subtle telangiectases. Further studies of the candidate region and the identification of the gene responsible for the vascular anomalies in this family will add to our understanding of vascular morphogenesis and related disorders.