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Multicolour FISH and quantitative PCR can detect submicroscopic deletions in holoprosencephaly patients with a normal karyotype.

Holoprosencephaly (HPE) is the most common structural malformation of the developing forebrain. At birth, nearly 50% of children with HPE have cytogenetic anomalies. Approximately 20% of infants with normal chromosomes have sequence mutations in one of the four main HPE genes (SHH, ZIC2, SIX3, and TGIF). The other non-syndromic forms of HPE may be due to environmental factors or mutations in other genes, or potentially due to submicroscopic deletions of HPE genes. We used two complementary assays to test for HPE associated submicroscopic deletions. Firstly, we developed a multicolour fluorescent in situ hybridisation (FISH) assay using probes for the four major HPE genes and for two candidate genes (DISP1 and FOXA2). We analysed lymphoblastoid cell lines (LCL) from 103 patients who had CNS findings of HPE, normal karyotypes, and no point mutations, and found seven microdeletions. We subsequently applied quantitative PCR to 424 HPE DNA samples, including the 103 samples studied by FISH: 339 with CNS findings of HPE, and 85 with normal CNS and characteristic HPE facial findings. Microdeletions for either SHH, ZIC2, SIX3, or TGIF were found in 16 of the 339 severe HPE cases (that is, with CNS findings; 4.7%). In contrast, no microdeletion was found in the 85 patients at the mildest end of the HPE spectrum. Based on our data, microdeletion testing should be considered as part of an evaluation of holoprosencephaly, especially in severe HPE cases.

Base Sequence↗

Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism.

The Y chromosome provides a unique opportunity to study mutational processes within the human genome, decoupled from the confounding effects of interchromosomal recombination. It has been suggested that the increased density of certain dispersed repeats on the Y could account for the high frequency of causative microdeletions relative to single nucleotide mutations in infertile males. Previously we localised breakpoints of an AZFa microdeletion close to two highly homologous complete human endogenous retroviral sequences (HERV), separated by 700 kb. Here we show, by sequencing across the breakpoint, that the microdeletion occurs in register within a highly homologous segment between the HERVs. Furthermore, we show that recurrent double crossovers have occurred between the HERVs, resulting in the loss of a 1.5 kb insertion from one HERV, an event underlying the first ever Y chromosomal polymorphism described, the 12f2 deletion. This event produces a substantially longer segment of absolute homology and as such may result in increased predisposition to further intrachromosomal recombination. Intrachromosomal crosstalk between these two HERV sequences can thus result in either homogenizing sequence conversion or a microdeletion causing male infertility. This represents a major subclass of AZFa deletions.

Chromosome Breakage↗

Deep clinical and genetic analysis of 17p13.3 region: 38 pediatric patients diagnosed using next-generation sequencing and literature review.

BACKGROUND: Chromosome 17p13.3 is a region of genomic instability associated with different neurodevelopmental diseases. The malformation spectrum of 17p13.3 microdeletions ranges from an isolated lissencephaly sequence to Miller-Dieker syndrome, while 17p13.3 microduplications result in autism, learning disabilities, microcephaly and other brain malformations. This study aims to provide a more comprehensive delineation of the clinical and genetic characteristics associated with 17p13.3 alterations. METHODS: We retrospectively analyzed the next-generation sequencing (NGS) data of more than 40 thousand patients from January 2016 to December 2021 and identified 38 pediatric patients with copy-number variations (CNVs) or single-nucleotide variations (SNVs) in 17p13.3 region. Published patients with CNVs in the 17p13.3 region were also collected and we performed a Chi-square test to compare the phenotype spectrum of microdeletions and microduplications. RESULTS: Among the 27 CNV patients, 20 patients with microdeletions and 7 patients with microduplications were found. PAFAH1B1 was the most frequently deleted gene and CRK was the most frequently duplicated gene. Affected genes in 11 SNV patients included PAFAH1B1 and PRPF8. Developmental delay was the most common abnormality detected in the 38 patients (29/38, 76.3%). Of note, Case 10 presented omphalocele and Case 23 presented scoliosis, webbed neck and bone cyst, all of which were unusual variant phenotypes in this region. The Chi-square test revealed that epilepsy, lissencephaly and short stature were statistically significant with microdeletions, while behavioral abnormalities and hand and foot abnormalities were significant with microduplications (p&#x2009;<&#x2009;0.01). CONCLUSIONS: While PAFAH1B1, YWHAE and CRK are associated with major phenotypes of 17p13.3, RTN4RL1 may be involved in white matter changes and HIC1 might contribute to the occurrence of omphalocele. This study provided a comprehensive understanding of genetic information and phenotype spectrum of the 17p13.3 region.

Humans↗

A high frequency of Y chromosome deletions in males with nonidiopathic infertility.

Microdeletions of the long arm of the human Y chromosome are associated with spermatogenic failure and have been used to define three regions of Yq (AZFa, AZFb, and AZFc) that are recurrently deleted in infertile males. In a blind study we screened 131 infertile males (46 idiopathic and 85 nonidiopathic) for Y chromosome microdeletions. Nineteen percent of idiopathic males, with an apparently normal 46,XY chromosome complement had microdeletions of either the AZFa, AZFb, or AZFc region. There was no strict correlation between the extent or location of the deletion and the phenotype. The AZFb deletions did not include the active RBM gene. Significantly, a high frequency of microdeletions (7%) was found in patients with known causes of infertility and a 46,XY chromosome complement. These included deletions of the AZFb and AZFc regions, with no significant difference in the location or extent of the deletion compared with the former group. It is recommended that all males with reduced or absence sperm counts seeking assisted reproductive technologies be screened for deletions of the Y chromosome.

Adult↗

Y-chromosome haplotypes in azoospermic Israeli men.

Among azoospermic and severely oligozoospermic men, 7-15% present microdeletions of a region on the long arm of the Y chromosome that has been called AZF (azoospermia factor). Because these deletions present varying relative frequencies in different populations, we decided to ascertain whether their presence was correlated with specific Y-chromosome haplotypes. For that, we evaluated 51 infertile Israeli men, 9 of whom had microdeletions in AZF. Haplotypes were identified using a hierarchical system with eight biallelic DNA markers. We also checked for the presence of the deletion marker 50f2/C, which was absent in all seven patients with isolated AZFc deletion and also in the one patient with isolated AZFb deletion, suggesting that these microdeletions overlap. As expected, haplogroup J was the most common (47%), followed by equal frequencies of haplogroups Y* (xDE, J, K), P* (xR1a, R1b8), K* (xP), and E. In six patients with AZFc deficiencies of comparable size, three belonged to haplogroup J, two belonged to haplogroup P* (xR1a, R1b8), and one belonged to haplogroup R1a. Also, there were no significant differences in the haplotype frequencies between the groups with and without microdeletions. Thus we did not identify any association of a specific haplogroup with predisposition to de novo deletion of the AZF region in the Israeli population.

Chromosomes, Human, Y↗

Clinical and immunological spectrum of partial DiGeorge syndrome.

We present four cases of DiGeorge syndrome diagnosed at our center. Onset occurred during the neonatal period and was associated with severe congenital heart disease. In case 1, the patient had heart disease and absence of thymus. Total T-lymphocytes were 34%; total T4-lymphocytes were 27%. Stimulation test with phytohemagglutinin (PHA), concanavalin A (conA) and pokeweed mitogen were negative. Microdeletion was found in the chromosome 22q11 region. The second case involved heart disease, microstomia, round and rotated ears and branchial cyst. Total T-lymphocytes were 38% and total T4-lymphocytes 27%. Thymus was absent. Microdeletion in the chromosome 22q11 region. Case 3 showed heart disease, renal malformation, absence of thymus and parathyroid gland. The patient died 5 days postsurgery. Microdeletion was seen at chromosome 22q11. In the fourth case there was heart disease, microretrognathia, hypertelorism, short neck, absence of thymus and parathyroid glands. Total T-lymphocytes were 22%, total T4-lymphocytes 15%, and total T lymphocytes for pokeweed mitogen were negative. Microdeletion was found at chromosome 22q11. At the age of 13 days the patient died. The cases were recorded during a 2-year period, between 1997 and 1998. The prevalence of DiGeorge syndrome in the number of admissions for congenital heart disease among the neonates at our hospital was 3.14%. Presentation in the form of repeated infections is rare, since most cases of DiGeorge syndrome are partial, and functional cellular immunity is preserved.

Adult↗

[Molecular genetic analysis of Y-chromosome micro deletions in men with severe spermatogenic defects].

Microdeletions of the Y-chromosomal AZF loci were revealed in 10 (12%) of 82 patients with severe idiopathic spermatogenetic defects. Deletions involved AZFc in six patients, AZFa in one patient, AZFb + c in two patients, and AZFa + b + c in one patient. Microdeletion analysis employed multiplex PCR with 22 pairs of primers directed to Y-specific STS of deletion intervals 5, 6, and 7 (Yq11). Spermatogenesis in men with AZF microdeletions was assessed with semen analysis, microscopic examination of testicular aspirate, and quantitative karyotypic analysis of immature germline cells in ejaculate or aspirate. The character of spermatogenetic defects was correlated with the size and location of microdeletions in order to study the genotype-phenotype relationship.

Adult↗

[Analysis of an AZFc deletion family with natural transmission].

OBJECTIVE: To report a rare family of AZFc deletion with natural transmission and explore the potential mechanism by which identical microdeletions cause different phenotypes. METHODS: Chromosomal quantity and construction were detected by G-band, Y-chromosomal microdeletions by multiple PCR amplification for 12 sequence tagged sites (STSs, and the single-nucleotide polymorphisms (SNPs) of the DAZL gene, the autosomal homologue of deleted-in-azoospermia (DAZ) gene by DNA sequencing. RESULTS: Chromosome analysis revealed a normal karyotype 46, XY in the father and both of his two sons and microdeletions of the full AZFc region were identical, including sY152, sY157, sY242, sY254, sY255, sY239 locus. However, the phenotypes of the affected patients were different: the father had normal fertility, but the sperm density of his two sons deteriorated age-dependently, and the younger one suffered from left cryptorchidism. SNP analysis demonstrated that two polymorphisms in exon 2 and 3 of the DAZL gene were identical in both the father and his sons. CONCLUSION: Identical Y-chromosomal microdeletions causing different phenotypes in this family is not associated with the polymorphisms of DAZL gene and may be related to other genes or environmental factors.

Adult↗

Mosaicism for a full mutation, premutation, and deletion of the CGG repeats results in 22% FMRP and elevated FMR1 mRNA levels in a high-functioning fragile X male.

The molecular basis in the majority of fragile X patients results from expansion of the CGG repeats in the FMR1 gene causing its transcriptional silencing and deficiency of its encoded protein FMRP. In this communication, we report on a male patient who lacks the characteristic physical features of fragile X and carries a fully methylated mutation, a premutation, a non-methylated full mutation, and a microdeletion encompassing the entire CGG repeat region and 42 bp of upstream flanking sequence. Southern blot analysis revealed that the methylated full mutation accounted for only 10% of his genotype while the premutation/non-methylated full mutation and the microdeletion constituted 37% and 53%, respectively. Immunofluorescent staining of FMRP demonstrated the presence of 22% FMRP in his peripheral blood leukocytes and quantitative RT-PCR revealed a 3.6-fold elevation of FMR1 mRNA levels. Developmental assessments indicated that while he has a learning disability, he does not have mental retardation. Because previous reports had noted that 28% FMRP expression is associated with a characteristic fragile X phenotype, we propose that in our patient the association of 22% FMRP levels with normal physical features and a high-functioning status may have resulted from increased FMRP stability by a mechanism that takes into account the CGG microdeletion and elevated mRNA levels.

Adolescent↗

Comprehensive NF1 screening on cultured Schwann cells from neurofibromas.

Neurofibromatosis type 1 (NF1) is mainly characterized by the occurrence of benign peripheral nerve sheath tumors or neurofibromas. Thorough investigation of the somatic mutation spectrum has thus far been hampered by the large size of the NF1 gene and the considerable proportion of NF1 heterozygous cells within the tumors. We developed an improved somatic mutation detection strategy on cultured Schwann cells derived from neurofibromas and investigated 38 tumors from nine NF1 patients. Twenty-nine somatic NF1 lesions were detected which represents the highest NF1 somatic mutation detection rate described so far (76%). Furthermore, our data strongly suggest that the acquired second hit underlies reduced NF1 expression in Schwann cell cultures. Together, these data clearly illustrate that two inactivating NF1 mutations, in a subpopulation of the Schwann cells, are required for neurofibroma formation in NF1 tumorigenesis. The observed somatic mutation spectrum shows that intragenic NF1 mutations (26/29) are most prevalent, particularly frameshift mutations (12/29, 41%). We hypothesize that this mutation signature might reflect slightly reduced DNA repair efficiency as a trigger for NF1 somatic inactivation preceding tumorigenesis. Joint analysis of the current and previously published NF1 mutation data revealed a significant difference in the somatic mutation spectrum in patients with a NF1 microdeletion vs. non-microdeletion patients with respect to the prevalence of loss of heterozygosity events (0/15 vs. 41/81). Differences in somatic inactivation mechanism might therefore exist between NF1 microdeletion patients and the general NF1 population.

Adaptor Proteins, Signal Transducing↗

Characteristics, associations and outcome of absent pulmonary valve syndrome in the fetus.

OBJECTIVES: To assess in a population of 21 fetuses diagnosed with absent pulmonary valve syndrome (APVS) the accuracy of prenatal diagnosis, the incidence of extracardiac and chromosomal anomalies and the perinatal outcome. METHODS: This was a retrospective observational study of 21 fetuses with a confirmed diagnosis of APVS. All of them underwent fetal echocardiography and a detailed anatomical scan. Karyotyping was performed in 20/21 cases, with fluorescent in-situ hybridization analysis to detect the 22q11 microdeletion performed in 16/21 cases. The following variables were retrieved from databases and evaluated: indication for referral, gestational age at diagnosis, presence of cardiomegaly, branch pulmonary dilatation, associated anomalies or intrauterine growth restriction, and fetal/neonatal outcome. Autopsy reports and postnatal surgical/medical files were available for confirmation in all cases. RESULTS: Prenatal diagnosis of APVS proved correct in all cases, with only three cases occurring not in association with tetralogy of Fallot. Additional cardiovascular anomalies were present in five cases (24%). Extracardiac anomalies were found in nine cases (42.8%), and were associated with chromosomal anomalies in five cases (24%). The 22q11 microdeletion was present in 4/16 cases (25%). Fetal/neonatal outcome was as follows: nine terminations of pregnancy, three intrauterine deaths, six postnatal deaths. The remaining three (14.3%) neonates were alive after surgery. Cardiomegaly and marked branch pulmonary dilatation were present in 16 and 15 cases, respectively, and were associated with bronchomalacia in virtually all cases. CONCLUSIONS: APVS can be reliably diagnosed and characterized prenatally. The association with major chromosomal anomalies or 22q11 microdeletion is consistent with previous findings. The relatively poor survival rate is due to the high rate of terminations, associated genetic anomalies and bronchomalacia. Bronchomalacia is present in the overwhelming majority of cases featuring cardiomegaly and marked branch pulmonary dilatation.

Chromosome Disorders↗

Cloning, genomic organization, and chromosomal localization of human citrate transport protein to the DiGeorge/velocardiofacial syndrome minimal critical region.

DiGeorge syndrome (DGS) and velocardiofacial syndrome have been shown to be associated with microdeletions of chromosomal regions 22q11. More recently, patients with conotruncal anomaly face syndrome and some nonsyndromic patients with isolated forms of conotruncal cardiac defects have been found to have 22q11 microdeletions as well. The commonly deleted region, called the DiGeorge chromosomal region (DGCR), spans approximately 1.2 Mb and is estimated to contain at least 30 genes. We report a computational approach for gene identification that makes use of large-scale sequencing of cosmids from a contig spanning the DGCR. Using this methodology, we have mapped the human homolog of a rodent citrate transport protein to the DGCR. We have isolated a partial cDNA containing the complete open reading frame and have determined the genomic structure by comparing the genomic sequence from the cosmid to the sequence of the cDNA clone. Whether the citrate transport protein can be implicated in the biological etiology of DGS or other 22q11 microdeletion syndromes remains to be defined.

Animals↗

Diagnosis of DiGeorge and Williams syndromes using FISH analysis of peripheral blood smears.

We describe the use of a FISH protocol for detecting chromosome microdeletions in peripheral blood smear leukocytes. This method has the advantage of a smaller sample requirement than classical metaphase chromosome analysis and the potential for analysis of a larger number of chromosome microdeletions using a routine blood smear. A selected series of 10 DiGeorge syndrome (DGS) and 12 Williams-Beuren syndrome (WBS) patients were correctly diagnosed by this method confirming results obtained by molecular cytogenetic metaphases. These results support effectiveness of interphase FISH analysis on peripheral blood smears as a focused, single-step method for the detection of chromosome microdeletions.

Adolescent↗

Lack of evidence of a genetic origin in the impaired spermatogenesis of a patient cohort with low-grade varicocele.

Varicocele is the most common clinical finding in infertile men but controversy continues to surround the utility of its treatment. An increased response of FSH to gonadotrophin-releasing hormone testing has been described in patients with varicocele, while the co-influence of Yq chromosome microdeletions in the infertility associated to this pathology is still under investigation. We studied 30 patients with first- and second-grade varicocele, 15 idiopathic oligozoospermic men and 21 age-matched healthy controls. All subjects underwent testicular Doppler ultrasonography, semen analysis, gonadotrophin-releasing hormone testing and baseline blood sampling for total and free testosterone, PRL, 17beta-estradiol, SHBG evaluation and Yq chromosome analysis. Apart from FSH, no difference in baseline hormonal levels was found between the groups. The patients with varicocele showed both an increased basal (p=0.007) and GnRH-induced FSH response (peak and AUC) (p=0.004) in comparison with the controls, while the idiopathic oligozoospermic men had only higher GnRH-induced FSH AUC (p=0.04). In the varicocele group, FSH peaks after GnRH testing correlated positively with the grade of disease (r=0.42, p=0.02) and negatively with sperm count (r=-0.50, p=0.005) and bilateral testis volume (r=-0.52, p=0.005). Sperm count and sperm motility were similarly significantly reduced both in patients with varicocele and in patients with idiopathic oligozoospermia in comparison with healthy controls. Yq chromosome analysis by sequence-tagged site PCR revealed no microdeletion in the AZF regions in any subject studied. Given the quite small number of subjects studied, our overall findings can only prompt us to suggest a possible causal role of varicocele in the impairment of spermatogenesis in our patients. Furthermore, although a genetic co-influence (i.e. Yq microdeletions) does not seem to be involved in the pathogenesis of infertility in men with varicocele and mild to moderate oligozoospermia, genetic screening seems to be advisable, especially in those patients who present a severe impairment of sperm count, as has been suggested by recent literature data.

Adult↗

Molecular characterization of tetralogy of fallot within Digeorge critical region of the chromosome 22.

The purpose of this study was to determine whether the levels of heterozygosity and microdeletion of specific loci within the DiGeorge critical region (del22q11) are associated with different phenotypes of tetralogy of Fallot (TF). Examinations were conducted on 84 sporadic TF patients and their unaffected parents for del22q11, using the following 9 simple tandem repeat polymorphic microsatellite markers: D22S420, D22S427, D22S941, D22S944, D22S264, D22S311, D22S425, D22S303, D22S257. The microdeletions were confirmed using quantitative PCR with markers TUPLE1, exon 2 of the UFD1L gene, and D22S264; the boundaries of these microdeletions were estimated using genotypic analyses of the unaffected family members. The del22q11 was identified in 14 patients (16.6%). The boundary of the shortest region of deletion overlap (SRO) in these 14 TF patients was identified, proximally using D22S427 and distally using the TUPLE 1 gene. The deletion of exon 2 of the UFD1L gene and TUPLE1 gene was identified in 13 patients (13/14 cases; 93%). The SRO in TF patients with del22q11 was at or close to the ADU breakpoint and centromeric to the UFD1L gene. The level of heterozygosity for the marker D22S944 in TF patients without del22q11 (n = 70) was found to be significantly lower than expected. Overall, this study demonstrated the significantly low level of heterozygosity within DiGeorge critical region in TF patients with or without del22q11. Our results suggest that the genetic factors leading to DiGeorge/velocardiofacial syndrome might also be partly responsible for TF phenotypes.

Adolescent↗

Auto-immune pancytopenia in a child with DiGeorge syndrome.

UNLABELLED: We report on the development of auto-immune pancytopenia in a child with DiGeorge syndrome carrying the 22q11 microdeletion. She had congenital heart disease, dysmorphic facies, thymic hypoplasia, immunodeficiency, velopharyngeal insufficiency, scoliosis, and a hearing deficit. She had a low T-cell count with a normal CD4/CD8 ratio, IgA deficiency and a normal lymphoblastic response to mitogens. She has presented with pancytopenia since 10 years of age (leucocytes 3,300/mm(3), haemoglobin 107 g/l, platelets 80,000/mm(3)). Platelet-associated antibodies, anti-neutrophil antibodies and Coombs' positive red cells were present. At 14 years of age, she presented with a severe episode of haemolysis with pancytopenia. Steroids were effective in treating the pancytopenia at a dose of 2 mg/kg per day for 6 weeks. Since 15 years of age, she has had episodes of acrocyanosis. At 16 years of age, she still had mild pancytopenia without any treatment. CONCLUSION: the clinical spectrum of the 22q11 microdeletion syndrome is very broad. This case suggests that auto-immune disease such as pancytopenia is part of the 22q11 microdeletion syndrome.

Adolescent↗

Clinical relevance of monosomy 22q11.2 in children with pulmonary atresia and ventricular septal defect.

UNLABELLED: The purpose of our study was to describe the prevalence and the clinical spectrum of monosomy 22q11.2 in a population of patients with pulmonary atresia and ventricular septal defect. We examined all 44 patients with this conotruncal cardiac malformation who presented to our institution from January 1994 until December 1997. The type of collateral lung perfusion was recorded including anomalies of the pulmonary arteries as well as facial and immunological abnormalities. Molecular-cytogenetic testing for a 22q11.2 microdeletion was performed using the probes D22S75 and cHKAD26. Statistical differences were evaluated with the Fisher's Exact Test. Monosomy 22q11.2 was present in ten children (23%) with major aortopulmonary collateral arteries (group 1). The remaining 13 children (29%) with major aortopulmonary collateral arteries (group 2) and all 21 children (48%) with ductus arteriosus (group 3) were negative for this microdeletion. All children in group 1 had facial anomalies, six had mild immunological abnormalities including decreased CD 4 + or CD 8 + cells. Anomalies of the pulmonary vascular bed were significantly more frequent in children of group 1 (9/10) than in children of group 2 (4/13) or group 3 (0/21). Due to these pulmonary vascular anomalies, corrective surgery had been accomplished in fewer children with monosomy 22q11.2 (none in group 1) as compared to 7/13 children in group 2 and 14/21 children in group 3. CONCLUSION: In children with pulmonary atresia and ventricular septal defect, monosomy 22q11.2 is preferentially associated with major aortopulmonary collateral arteries. Due to the higher incidence of pulmonary arterial abnormalities, successful surgical repair will require a different therapeutic approach in most patients with this microdeletion.

Adolescent↗

A search for chromosome 22q11.2 deletions in a series of 176 consecutively catheterized patients with congenital heart disease: no evidence for deletions in non-syndromic patients.

Microdeletions in chromosome 22q11.2 are associated with DiGeorge syndrome (DGS), velo-cardio-facial syndrome (VCFS), and several other syndromes, collectively referred to as DG/VCF. Non-dysmorphic patients with cardiac defects have also been attributed to deletions in this chromosomal region. In this study 157 consecutively catheterized patients with isolated, non-syndromic cardiac defects, and 25 patients with cardiac defects and additional stigmata (10 of whom were clinically diagnosed as DG/VCF cases prior to chromosome analysis) were analysed by fluorescence in situ hybridization with the DGS-specific probe D0832. Chromosome 22q11.2 deletions were observed only in the ten patients with the clinical diagnosis of DG/VCF. Conclusion In a large unselected cohort of patients with congenital heart disease no association between isolated or non-syndromic heart defects and the 22q11.2 microdeletion was observed. One can conclude that testing for the 22q11.2 microdeletion is clearly indicated in cases when even mild extracardiac abnormalities are present, particularly in very young infants.

Adolescent↗