Multiplex PCR-Based Newborn Screening for Severe T and B-Cell Lymphopenia: The first Pilot Study in Turkey.

Objectives: Severe combined immunodeficiency disease (SCID), non-SCID T-cell lymphopenia, and other primary immunodeficiency diseases with T-cell and B-cell lymphopenia have low the T-cell-receptor-excision circles (TRECs) and κ-deleting-recombination-excision circles (KRECs) levels that can be measured in dried blood spots (DBS) of the newborn. The incidence of SCID and non-SCID T-cell lymphopenia in Western societies has been reported by TREC screening of newborns as 1: 58,000 and 1: 7300, respectively. Since there is no similar study in our country, we aimed to perform the first pilot study of TREC and KREC screening of newborn for SCID and non-SCID T-cell lymphopenia in Turkey. Methods: The heel blood samples of newborns born between 1st October 2015 and 31st December 2016 at two major hospitals in our city were included in this study. TREC and KREC copies were determined by a multiplex quantitative PCR-based method from newborn DBS. Cutoff levels were used as 7 copies per DBS for TRECs and KRECs, 1000 copies for ACTB (internal control). Failed samples or abnormal results in measurements were tested the second time. An immunologist evaluated data of newborns with low TREC and KREC copies clinically and through the laboratory. Results: A total of 1960 DBS were tested. The results of 1856 newborns were evaluated. The low TRECs and/or KRECs levels were detected in 71 newborns (3.8 %). The low TRECs rate was 1.1 %. Preterm newborns have lower levels of TRECs and KRECs than term newborns (both p <0.0001). As a result of immunological research, we did not detect any SCID, but we detected 2 newborns with non-SCID T-cell lymphopenia (1:928). These 2 newborns were found to have frequent and severe infectious diseases or hypogammaglobulinemia in their clinical follow-up, although they did not have absolute lymphopenia. Conclusion: Non-SCID T-cell lymphopenia is common in our country than in western societies. TRECs and KRECs assay should be considered for routine NBS programs in our country. Studies involving more newborns should be conducted to detect SCID.

Multiscale analysis of SRY-positive 46,XX testicular disorder of sex development: Presentation of nine cases.

46,XX testicular disorder of sex development (46,XX TDSD) is a relatively rare condition characterised by the presence of testicular tissue with 46,XX karyotype. The present study aims to reveal the phenotype to genotype correlation in a series of sex-determining region Y (SRY)-positive 46,XX TDSD cases. We present the clinical findings, hormone profiles and genetic test results of six patients with SRY-positive 46,XX TDSD and give the details and follow-up findings of our three of previously published patients. All patients presented common characteristics such as azoospermia, hypergonadotropic hypogonadism and an SRY gene translocated on the terminal part of the short arm of one of the X chromosomes. Mean ± standard deviation (SD) height of the patients was 164.78 ± 8.0 cm. Five patients had decreased secondary sexual characteristics, and three patients had gynaecomastia with varying degrees. Five of the seven patients revealed a translocation between protein kinase X (PRKX) and inverted protein kinase Y (PRKY) genes, and the remaining two patients showed a translocation between the pseudoautosomal region 1 (PAR1) of X chromosome and the differential region of Y chromosome. X chromosome inactivation (XCI) analysis results demonstrated random and skewed XCI in 5 cases and 1 case, respectively. In brief, we delineate the phenotypic spectrum of patients with SRY-positive 46,XX TDSD and the underlying mechanisms of Xp;Yp translocations.

Genetic Burden and Outcome of Cystic Hygromas Detected Antenatally: Results of 93 Pregnancies from a Single Center in the Northern Region of Turkey.

OBJECTIVE: Genetic burden, fetal malformations, and fetal outcomes of 93 fetuses with cystic hygroma (CH) are reported from a single center in Turkey. PATIENTS AND METHODS: Pregnancies, having a diagnosis of fetal CH, detected between January 2010 and October 2016, were included in the study except fetuses having increased nuchal translucency. Fetal age/gender, maternal age, the age of pregnancy, types of fetal malformations, karyotype, and outcomes were evaluated. RESULTS: The average gestational age was 16.2 weeks. Nearly 47% of the pregnancies had multiple congenital anomalies, of which 58% had a chromosomal anomaly. Chromosomal anomaly rate was 68.2% in patients with hydrops fetalis. Aneuploidies were major chromosomal defects. All trisomies were of regular type except one with Robertsonian translocation (46, XY, +13, rob[13;14][q10;q10]). Seventy-four percentage pregnancies were terminated due to either fetal/karyotype anomaly. CONCLUSION: Characteristics of fetal CH were similar in different ethnical backgrounds. Aneuploidy is the dominant chromosomal constitution of fetal CH. Little information was known about the genes involved. Gene dosage effect implies that fetal CH is a complex genetic situation involving multiple genes interactions. For proper genetic counseling, each fetus with CH should be karyotyped, and fetal ultrasound examination should be performed. In the case of normal chromosome set, application of aCGH should be considered.

Chromosomal and Y-chromosome microdeletion analysis in 1,300 infertile males and the fertility outcome of patients with AZFc microdeletions.

The present study investigated the frequency of chromosome aberrations and AZF microdeletions in infertile patients with nonobstructive azoospermia (NOA) or severe oligozoospermia. Additionally, the effect of the AZFc microdeletions on the success of microdissection testicular sperm extraction (microTESE) and intracytoplasmic sperm injection (ICSI) methods were evaluated. Peripheral blood samples were received from 1,300 infertile men with NOA and severe oligozoospermia. Karyotyping and FISH analysis were performed according to standard methods. AZF microdeletions were analysed using multiplex polymerase chain reaction or GML Y-chromosome Microdeletion Detection System consisting of 14 markers. The chromosomal aberrations and the AZF microdeletions frequency among 1,300 infertile men were 10.6% and 4.0% respectively. Either ejaculated spermatozoa or microTESE was performed on only in 19 out of 26 patients with AZFc deletions. Of the 19 patients, four had severe oligozoospermia and 15 had NOA. In eight out of 15 NOA patients, testicular mature spermatozoa were obtained (53.3%) and then ICSI was applied to mature oocytes. After undergoing ICSI treatment, clinical pregnancy and live birth outcome rates were found to be 37.5% and 25% respectively. These results suggest that infertile patients with AZFc microdeletion could achieve successful fertilisation pregnancies with the help of assisted reproductive technology.

Long-Term Outcome of Fetuses with Soft Marker and Without Genetic or Structural Abnormality.

PURPOSE: To determine long-term outcome of infants with isolated or multiple soft markers but no structural or chromosomal abnormalities. METHODS: A retrospective study of 78 pregnant women who were referred for amniocentesis and found to have soft markers including echogenic intracardiac focus/foci (EIF), echogenic bowel (EB), unilateral or bilateral choroid plexus cysts, (UCPCs or BCPCs) mild pyelectasis and single umbilical artery but no structural anomalies and outcomes of the liveborns with a 4- to 9-year follow-up was conducted. RESULTS: Among 28 fetuses with EIF, allergic asthma and epilepsy were diagnosed in two liveborns. We followed up nine pregnancies with EB, epilepsy was present in one case. Allergic asthma was detected in both UCPCs and BCPCs, whereas epilepsy and attention-deficit/hyperactivity disorder (ADHD) were diagnosed in two liveborns with BCPCs. Twelve liveborns with multiple soft markers were evaluated; no pathology was detected in most of them except one case of allergic asthma, one case of hearing impairment and one case of ADHD. CONCLUSIONS: This study shows longer-term favorable outcomes of the liveborns with isolated or multiple soft markers without any aneuploidy and may provide insight into this debated point.

ATP6V0A2-related cutis laxa in 10 novel patients: Focus on clinical variability and expansion of the phenotype.

In ATP6V0A2-related cutis laxa, the skin phenotype varies from a wrinkly skin to prominent cutis laxa and typically associates with skeletal and neurological manifestations. The phenotype remains incompletely characterized, especially in adult patients. Glycosylation defects and reduced acidification of secretory vesicles contribute to the pathogenesis, but the consequences at the clinical level remain to be determined. Moreover, the morphology of the elastic fibres has not been studied in ATP6V0A2-related cutis laxa, nor its relation with potential clinical risks. We report on the extreme variability in ATP6V0A2-related cutis laxa in 10 novel patients, expand the phenotype with emphysema and von Willebrand disease and hypothesize on the pathogenesis that might link both with deficiency of glycosylation and with elastic fibre anomalies. Our data will affect clinical management of patients with ATP6V0A2-related cutis laxa.

Impact of Fluorescent In Situ Hybridization Aberrations and CLLU1 Expression on the Prognosis of Chronic Lymphocytic Leukemia: Presentation of 156 Patients from Turkey.

OBJECTIVE: This study evaluates the impact of CLLU1 expression and fluorescent in situ hybridization (FISH) analysis of a group of Turkish chronic lymphocytic leukemia (CLL) patients. MATERIALS AND METHODS: A total of 156 CLL patients were analyzed by FISH method; 47 of them were also evaluated for CLLU1 expression. Results were correlated with clinical parameters. RESULTS: FISH aberrations were found in 62% of patients. These aberrations were del13q14 (67%), trisomy 12 (27%), del11q22 (19%), del17p (8%), and 14q32 rearrangements (20%). Overall del11q22 and del17p were associated with the highest mortality rates, shortest overall survival (OS), and highest need for medication. Homozygous del13q14, 14q32 rearrangements, and higher CLLU1 expression correlated with shorter OS. CONCLUSION: Cytogenetics/FISH analysis is still indicated for routine evaluation of CLL. Special consideration is needed for the poor prognostic implications of del11q22, del17p, 14q32 rearrangements, and homozygous del13q14. The impact of CLLU1 expression is not yet clear and it requires more data before becoming routine in genetic testing in CLL patients.

Hematopoietic Stem Cell Transplantation in Primary Immunodeficiency Patients in the Black Sea Region of Turkey.

Hematopoietic stem cell transplantation is a promising curative therapy for many combined primary immunodeficiencies and phagocytic disorders. We retrospectively reviewed pediatric cases of patients diagnosed with primary immunodeficiencies and scheduled for hematopoietic stem cell transplantation. We identified 22 patients (median age, 6 months; age range, 1 month to 10 years) with various diagnoses who received hematopoietic stem cell transplantation. The patient diagnoses included severe combined immunodeficiency (n=11), Chediak-Higashi syndrome (n=2), leukocyte adhesion deficiency (n=2), MHC class 2 deficiency (n=2), chronic granulomatous syndrome (n=2), hemophagocytic lymphohistiocytosis (n=1), Wiskott-Aldrich syndrome (n=1), and Omenn syndrome (n=1). Of the 22 patients, 7 received human leukocyte antigen-matched related hematopoietic stem cell transplantation, 12 received haploidentical hematopoietic stem cell transplantation, and 2 received matched unrelated hematopoietic stem cell transplantation. The results showed that 5 patients had graft failure. Fourteen patients survived, yielding an overall survival rate of 67%. Screening newborn infants for primary immunodeficiency diseases may result in timely administration of hematopoietic stem cell transplantation.

Biallelic Mutations in TMTC3, Encoding a Transmembrane and TPR-Containing Protein, Lead to Cobblestone Lissencephaly.

Cobblestone lissencephaly (COB) is a severe brain malformation in which overmigration of neurons and glial cells into the arachnoid space results in the formation of cortical dysplasia. COB occurs in a wide range of genetic disorders known as dystroglycanopathies, which are congenital muscular dystrophies associated with brain and eye anomalies and range from Walker-Warburg syndrome to Fukuyama congenital muscular dystrophy. Each of these conditions has been associated with alpha-dystroglycan defects or with mutations in genes encoding basement membrane components, which are known to interact with alpha-dystroglycan. Our screening of a cohort of 25 families with recessive forms of COB identified six families affected by biallelic mutations in TMTC3 (encoding transmembrane and tetratricopeptide repeat containing 3), a gene without obvious functional connections to alpha-dystroglycan. Most affected individuals showed brainstem and cerebellum hypoplasia, as well as ventriculomegaly. However, the minority of the affected individuals had eye defects or elevated muscle creatine phosphokinase, separating the TMTC3 COB phenotype from typical congenital muscular dystrophies. Our data suggest that loss of TMTC3 causes COB with minimal eye or muscle involvement.

Vesicourethral reflux-induced renal failure in a patient with ICF syndrome due to a novel DNMT3B mutation.

ICF syndrome is a primary immunodeficiency disease characterized by hypo- or agammaglobulinemia, centromeric instability mainly on chromosomes 1, 9, and 16 and facial anomalies. ICF syndrome presents with frequent respiratory tract infections in infancy. A 20-month-old female patient was referred to our clinic due to frequent lower respiratory tract infections. ICF syndrome was considered because of comorbidity of hypogammaglobulinemia, facial anomalies, and neuromotor growth retardation. Metaphase chromosome analysis revealed centromeric instability on chromosomes 1, 9, and 16 and through Sanger a previously unreported homozygous missense mutation (c.1805T>C; [p.V602A]) was identified in the DNMT3B, confirming ICF1. The patient was found to have a breakdown in renal function 1 year later; the urinary system was examined and bilateral vesicoureteral reflux was found, warranting the need for dialysis in time. This report expands the mutation spectrum of ICF1 and is the first to describe bilateral vesicoureteral reflux accompanying ICF syndrome. © 2016 Wiley Periodicals, Inc.

Could familial Mediterranean fever gene mutations be related to PFAPA syndrome?

BACKGROUND: The cause and pathophysiology of PFAPA syndrome is unknown. The aim of this study was to determine all MEFV gene variants relevant to familial Mediterranean fever in children with PFAPA syndrome. METHODS: All MEFV gene variants were analyzed in patients with PFAPA syndrome. All patients were evaluated using the Gaslini scoring system. Serum immunoglobulin levels were also determined upon admission. RESULTS: We evaluated 64 patients with PFAPA syndrome. The median age at diagnosis was 37.5 (min-max: 6-96) months, and the percentage of male patients was 55.0%. The Gaslini diagnostic score for periodic fever was high in 81.0% of the patients. An MEFV gene mutation was found in 42 (66.0%) children. Mostly, heterozygous or compound heterozygous variants of the MEFV gene were found. Two patients were homozygous for R202Q. MEFV gene mutations were not detected in 22 (34.0%) patients. No significant differences in clinical or laboratory findings were observed between the two groups (p > 0.05), and there were no significant differences in period and duration of the fever episodes (p > 0.05). The fever of all 47 patients (100.0%) who received prednisolone during the episodes decreased within hours and did not recur. Eighteen of the patients using prednisolone underwent prophylaxis with colchicine, and the fever episodes of 9/18 (50.0%) patients using colchicine decreased within months. CONCLUSIONS: Most patients presenting with PFAPA syndrome have heterozygous MEFV gene mutations. Whether carrying a heterozygous MEFV gene is the primary cause of this syndrome requires further investigation.

Absence of the lateral and third ventricles associated with holoprosencephaly.

We describe a 6-month-old boy suffering from motor and mental retardation. All radiological features were suggestive of holoprosencephaly with no identifiable lateral or third ventricles and fusion of the thalami.

Mutations in the human UBR1 gene and the associated phenotypic spectrum.

Johanson-Blizzard syndrome (JBS) is a rare, autosomal recessive disorder characterized by exocrine pancreatic insufficiency, typical facial features, dental anomalies, hypothyroidism, sensorineural hearing loss, scalp defects, urogenital and anorectal anomalies, short stature, and cognitive impairment of variable degree. This syndrome is caused by a defect of the E3 ubiquitin ligase UBR1, which is part of the proteolytic N-end rule pathway. Herein, we review previously reported (n = 29) and a total of 31 novel UBR1 mutations in relation to the associated phenotype in patients from 50 unrelated families. Mutation types include nonsense, frameshift, splice site, missense, and small in-frame deletions consistent with the hypothesis that loss of UBR1 protein function is the molecular basis of JBS. There is an association of missense mutations and small in-frame deletions with milder physical abnormalities and a normal intellectual capacity, thus suggesting that at least some of these may represent hypomorphic UBR1 alleles. The review of clinical data of a large number of molecularly confirmed JBS cases allows us to define minimal clinical criteria for the diagnosis of JBS. For all previously reported and novel UBR1 mutations together with their clinical data, a mutation database has been established at LOVD.

Premature ovarian failure due to tetrasomy X in an adolescent girl.

UNLABELLED: Tetrasomy X associated with premature ovarian failure has been described in a few patients, and the parental origin of the extra X chromosomes has not been investigated so far in this group. A 15-year-old girl with mental retardation and minor physical anomalies showed secondary amenorrhea, high gonadotropin levels, and osteoporosis. Molecular analysis of the fibroblast cells revealed pure 48,XXXX constitution despite 48,XXXX/47,XXX mosaicism in peripheral blood. Analysis of the polymorphic markers (X22, DXYS218, DXYS267, HPRT) on the X chromosome by the quantitative fluorescent polymerase chain reaction (QF-PCR) method demonstrated that the extra X chromosomes were maternal in origin. CONCLUSION: Patients with tetrasomy X syndrome should be screened for ovarian insufficiency during early adolescence because hormone replacement therapy may be required for prevention of osteoporosis. In order to understand a potential impact of the parental origin of the extra X chromosomes on ovarian development and function, further studies are needed.

Phenotypic spectrum and prevalence of INPP5E mutations in Joubert syndrome and related disorders.

Joubert syndrome and related disorders (JSRD) are clinically and genetically heterogeneous ciliopathies sharing a peculiar midbrain-hindbrain malformation known as the 'molar tooth sign'. To date, 19 causative genes have been identified, all coding for proteins of the primary cilium. There is clinical and genetic overlap with other ciliopathies, in particular with Meckel syndrome (MKS), that is allelic to JSRD at nine distinct loci. We previously identified the INPP5E gene as causative of JSRD in seven families linked to the JBTS1 locus, yet the phenotypic spectrum and prevalence of INPP5E mutations in JSRD and MKS remain largely unknown. To address this issue, we performed INPP5E mutation analysis in 483 probands, including 408 JSRD patients representative of all clinical subgroups and 75 MKS fetuses. We identified 12 different mutations in 17 probands from 11 JSRD families, with an overall 2.7% mutation frequency among JSRD. The most common clinical presentation among mutated families (7/11, 64%) was Joubert syndrome with ocular involvement (either progressive retinopathy and/or colobomas), while the remaining cases had pure JS. Kidney, liver and skeletal involvement were not observed. None of the MKS fetuses carried INPP5E mutations, indicating that the two ciliopathies are not allelic at this locus.

Two males with SRY-positive 46,XX testicular disorder of sex development.

The 46,XX testicular disorder of sex development (46,XX testicular DSD) is a rare phenotype associated with disorder of the sex chromosomes. We describe the clinical, molecular, and cytogenetic findings of a 16- and a 30-year-old male patient with sex-determining region Y (SRY)-positive 46,XX testicular DSD. Chromosomal analysis revealed 46,XX karyotype. Fluorescence in situ hybridization (FISH) showed the SRY region translocated to the short arm of the X chromosome. The presence of the SRY gene was also confirmed by polymerase chain reaction (PCR). The X chromosome inactivation (XCI) assay showed that both patients have a random pattern of X chromosome inactivation. This report compares the symptoms and features of the SRY-positive 46,XX testicular DSD patients.

Chromosomal anomalies and additional sonographic findings in fetuses with open neural tube defects.

OBJECTIVE: To evaluate the results and the necessity of chromosome analysis in fetuses prenatally detected with a neural tube defect and to determine the significance of ultrasonographic evaluation for the identification of underlying or accompanying chromosomal anomalies. METHODS: Ninety fetuses that underwent prenatal and/or postnatal chromosome analysis after being diagnosed with open neural tube defects (NTD) between the years 2006 and 2010 in the Department of Obstetrics and Gynecology at Ondokuz Mayis University School of Medicine were included in this study. Detailed fetal ultrasonography was performed in all cases in order to investigate any additional anomalies. Karyotype was determined in the prenatal period by amniocentesis in 72 (80%) of the 90 fetuses, and by cordocentesis in 5 (5.5%). In 13 (13.3%) fetuses, karyotype was determined in the postnatal period by blood sampling. RESULTS: Fourteen (15.5%) of the 90 fetuses were diagnosed with acrania/anencephaly, 14 (15.5%) with encephalocele, 2 (2.2%) with iniencephaly, 60 (66.6%) with open spina bifida. None of the 90 fetuses with open NTD who had undergone chromosome analysis was diagnosed with chromosomal anomalies. None of the 19 (21.1%) fetuses diagnosed with additional ultrasound findings had a chromosomal abnormality, either. Seventy-one (78.9%) fetuses having sonograhically isolated NTD were also isolated in postmortem examination. CONCLUSION: In fetuses with open NTD, we could not find the chromosomal anomaly rate as high as reported in previous literature. The necessity of fetal karyotyping should be questioned especially in isolated cases.

Simplified gyral pattern with cerebellar hypoplasia in Sedaghatian type spondylometaphyseal dysplasia: a clinical report and review of the literature.

We report on a patient with Sedaghatian type spondylometaphyseal dysplasia (SSMD) who presented with metaphyseal dysplasia, congenital atrioventricular block, simplified gyral pattern, hypogenesis of corpus callosum, and severe cerebellar hypoplasia. We want to emphasize that in this rare congenital lethal skeletal dysplasia with unknown etiology, central nervous system malformations might be a major component of the disorder and should be evaluated in detail to possibly uncover the underlying pathophysiology.

t(6;9)(p23;q34) presenting acute myeloid leukemia in a child with an unsuspected 45,X/46,X,derY [?t(Yp;Yq)] chromosomal constitution: yet another Y chromosome overdosage and malignancy association.

Development of leukemia in patients with sexual chromosome abnormalities is relatively rare and mostly involves cases of monosomy X, Turner syndrome. Here, we report on a child having a 45,X/46,X,derY [?t(Yp;Yq)] chromosomal constitution (variant Turner syndrome) presenting with concordant acute myeloid leukemia and a rarely seen clonal neoplasic cell lineage-related karyotype, t(6;9)(p23;q34).

KIF7 mutations cause fetal hydrolethalus and acrocallosal syndromes.

KIF7, the human ortholog of Drosophila Costal2, is a key component of the Hedgehog signaling pathway. Here we report mutations in KIF7 in individuals with hydrolethalus and acrocallosal syndromes, two multiple malformation disorders with overlapping features that include polydactyly, brain abnormalities and cleft palate. Consistent with a role of KIF7 in Hedgehog signaling, we show deregulation of most GLI transcription factor targets and impaired GLI3 processing in tissues from individuals with KIF7 mutations. KIF7 is also a likely contributor of alleles across the ciliopathy spectrum, as sequencing of a diverse cohort identified several missense mutations detrimental to protein function. In addition, in vivo genetic interaction studies indicated that knockdown of KIF7 could exacerbate the phenotype induced by knockdown of other ciliopathy transcripts. Our data show the role of KIF7 in human primary cilia, especially in the Hedgehog pathway through the regulation of GLI targets, and expand the clinical spectrum of ciliopathies.