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PubMed2001

Molecular characterization and gene content of breakpoint boundaries in patients with neurofibromatosis type 1 with 17q11.2 microdeletions.

Homologous recombination between poorly characterized regions flanking the NF1 locus causes the constitutional loss of approximately 1.5 Mb from 17q11.2 covering > or =11 genes in 5%-20% of patients with neurofibromatosis type 1 (NF1). To elucidate the extent of microheterogeneity at the deletion boundaries, we used single-copy DNA fragments from the extreme ends of the deleted segment to perform FISH on metaphase chromosomes from eight patients with NF1 who had large deletions. In six patients, these probes were deleted, suggesting that breakage and fusions occurred within the adjacent highly homologous sequences. Reexamination of the deleted region revealed two novel functional genes FLJ12735 (AK022797) and KIAA0653-related (WI-12393 and AJ314647), the latter of which is located closest to the distal boundary and is partially duplicated. We defined the complete reading frames for these genes and two expressed-sequence tag (EST) clusters that were reported elsewhere and are associated with the markers SHGC-2390 and WI-9521. Hybrid cell lines carrying only the deleted chromosome 17 were generated from two patients and used to identify the fusion sequences by junction-specific PCRs. The proximal breakpoints were found between positions 125279 and 125479 in one patient and within 4 kb of position 143000 on BAC R-271K11 (AC005562) in three patients, and the distal breakpoints were found at the precise homologous position on R-640N20 (AC023278). The interstitial 17q11.2 microdeletion arises from unequal crossover between two highly homologous WI-12393-derived 60-kb duplicons separated by approximately 1.5 Mb. Since patients with the NF1 large-deletion syndrome have a significantly increased risk of neurofibroma development and mental retardation, hemizygosity for genes from the deleted region around the neurofibromin locus (CYTOR4, FLJ12735, FLJ22729, HSA272195 (centaurin-alpha2), NF1, OMGP, EVI2A, EVI2B, WI-9521, HSA272196, HCA66, KIAA0160, and WI-12393) may contribute to the severe phenotype of these patients.

Base Sequence↗
PubMed2004

Microdeletion of LIT1 in familial Beckwith-Wiedemann syndrome.

Beckwith-Wiedemann syndrome (BWS), which causes prenatal overgrowth, midline abdominal wall defects, macroglossia, and embryonal tumors, is a model for understanding the relationship between genomic imprinting, human development, and cancer. The causes are heterogeneous, involving multiple genes on 11p15 and including infrequent mutation of p57(KIP2) or loss of imprinting of either of two imprinted gene domains on 11p15: LIT1, which is near p57(KIP2), or H19/IGF2. Unlike Prader-Willi and Angelman syndromes, no chromosomal deletions have yet been identified. Here we report a microdeletion including the entire LIT1 gene, providing genetic confirmation of the importance of this gene region in BWS. When inherited maternally, the deletion causes BWS with silencing of p57(KIP2), indicating deletion of an element important for the regulation of p57(KIP2) expression. When inherited paternally, there is no phenotype, suggesting that the LIT1 RNA itself is not necessary for normal development in humans.

Beckwith-Wiedemann Syndrome↗
PubMed2004

Y chromosome microdeletions in infertile males from Andhra Pradesh, South India.

Studies on the frequency of Y chromosome microdeletions were carried out in 70 idiopathic infertile males with normal karyotypes. Genomic DNA was isolated from blood and PCR analysis was carried out with AZFa, AZFb, and AZFc STS markers SY 84, SY 87, SY 127, SY 254, and SY 158 to detect the deletions. In 9/70 (12.8%) subjects AZF deletions were observed. In 4/9 (44.4%) subjects were azoospermic, 4/9 (44.4%) of cases were severe oligozoospermic, and 1/9 (11.1%) cases was oligozoospermic.

Chromosome Deletion↗
PubMed1994

Evidence for a microdeletion in 1q32-41 involving the gene responsible for Van der Woude syndrome.

Van der Woude syndrome (VWS) is an autosomal dominant craniofacial disorder representing the most frequent form of syndromic cleft lip and palate. Other characteristic features are pits of the lower lip and hypodontia. The gene shows high penetrance and seems to play an important role in orofacial development determined by the tissues involved and their formation during different periods of craniofacial development. Although most individuals affected with VWS show Mendelian inheritance, one patient with a macroscopic deletion and multiple malformations including two primary features of VWS has been described in the literature, indicating hemizygosity is compatible with the VWS phenotype. We report here the allelic loss of a stable and highly polymorphic microsatellite (D1S205) from region 1q32-41 in one family with VWS. Classical manifestations of the syndrome superimposed on developmental delay in all affected members of the family, the absence of cytogenetic abnormalities, the reproducibility of the null allele with a new set of primers and close linkage of this marker in a total of 15 VWS families provide strong evidence that the first microdeletion involving the gene for VWS has been identified. Assuming 1 Mb of DNA per cM of genetic distance, the upper bound of the deletion size would amount to 4 Mb.

Abnormalities, Multiple↗
PubMed1994

X-linked mixed deafness (DFN3): cloning and characterization of the critical region allows the identification of novel microdeletions.

We have found that the microsatellite marker AFM207zg5 (DXS995) maps to all previously described deletions which are associated with X-linked mixed deafness (DFN3) with or without choroideremia and mental retardation. Employing this marker and pHU16 (DXS26) we have identified two partially overlapping yeast artificial chromosome clones which were used to construct a complete 850 kb cosmid contig. Cosmids from this contig have been tested by Southern blot analysis on DNA from 16 unrelated males with X-linked deafness. Two novel microdeletions were detected in patients which exhibit the characteristic DFN3 phenotype. Both deletions are completely contained within one of the known DFN3-deletions, but one of them does not overlap with two previously described deletions in patients with contiguous gene syndromes consisting of DFN3, choroideremia, and mental retardation. Assuming that only a single gene is involved, this suggests that the DFN3 gene spans a chromosomal region of at least 400 kb.

Chromosome Walking↗
PubMed1995

Genetic mapping of cleidocranial dysplasia and evidence of a microdeletion in one family.

Cleidocranial dysplasia (CCD) is an autosomal, dominantly inherited disorder of high penetrance affecting skeletal ossification and tooth development. Typically, affected individuals have hypoplastic/aplastic clavicles, patent fontanelles and sutures, supernumerary teeth, and short stature. We have used a candidate locus approach to map the responsible gene in two families with typical features of CCD. Linkage was established between CCD and four loci (D6S426, D6S451, D6S459, TCTE1) that span a region of 10 cM on chromosome 6p. A maximum lod score, Zmax, of 4.1 at a recombination fraction of zero was obtained at D6S451. One highly polymorphic microsatellite from this region (D6S459) showed allelic loss in all affected members of one family with two different sets of primers. The presence of a deletion in this area was confirmed by Southern blot analysis using a probe derived from the amplification product of the D6S459 marker. The data assign a gene for CCD to chromosome 6p21 and suggest that a microdeletion within an area of tight linkage to the CCD-phenotype has been identified.

Base Sequence↗
PubMed1996

Identification by STS PCR screening of a microdeletion in Xp21.3-22.1 associated with non-specific mental retardation.

X-linked non-specific mental retardation (MRX) is a heterogeneous condition in which mental retardation (MR) appears to be the only consistent manifestation. The genetic and phenotypic heterogeneity exclude any possibility of pooling families and, therefore, of fine-mapping the related disease genes. In order to identify genomic critical regions involved in the MRX condition assigned to Xp21.3-22.1 region, we have implemented the PCR screening of non fragile X MR patients for the presence of deletions in this region. The amplification by PCR of 12 markers located between POLA and DXS704 using genomic DNA from 192 MR males led to the identification, in a 9 year old mentally retarded boy, of a microdeletion which extends from DXS1202 to DXS1065. None of the known genes, POLA, MAGE genes cluster, DAX1, GK and DMD, that map in the Xp21.3-22.1 region is affected by this deletion. This approach, which could easily be applied to several other MRX loci, allowed not only a confirmation of the presence of a potential locus in Xp21.3-22.1 involved in non-specific mental retardation, but also a better definition of the genomic critical region corresponding to this locus.

Child↗
PubMed1999

The chromosome 15 imprinting centre (IC) region has undergone multiple duplication events and contains an upstream exon of SNRPN that is deleted in all Angelman syndrome patients with an IC microdeletion.

Imprinting of the Prader-Willi/Angelman syndrome region on human chromosome 15 is regulated by an imprinting centre (IC), which spans 5' exons of the gene encoding the small nuclear ribonucleoprotein N ( SNRPN ). The IC/ SNRPN transcripts are initiated at two alternative start sites, which share a high degree of sequence similarity with each other and with two newly identified sites 63 and >700 kb further upstream. Three of these sites are hypermethylated on the maternal chromosome, whereas one displays an oppositemethylation pattern. We have also identified novel splice variants of the IC/ SNRPN transcripts and hitherto undetected exons. One of these exons, which we designate u5, is deleted in all Angelman syndromepatients with a microdeletion of the IC. We conclude that elements of the IC region have undergone multiple duplication events and that u5 or a sequence close by may play a role in maternal imprinting.

Angelman Syndrome↗
PubMed2003

Investigation of a pathogenic mtDNA microdeletion reveals a translation-dependent deadenylation decay pathway in human mitochondria.

Human mtDNA is transcribed from both strands, producing polycistronic RNA species that are immediately processed. Discrete RNA units are matured by the addition of nucleotides at their 3' termini: -CCA trinucleotide is added to mt-tRNAs, whilst mt-rRNAs and mt-mRNAs are oligo- or polyadenylated, respectively. The cis-acting elements, enzymes and indeed the mechanisms involved in these processes are still largely uncharacterized. Further, the function of polyadenylation in promoting stability, translation or decay of human mt-mRNA is unclear. A microdeletion has been identified in a patient presenting with mtDNA disease. Loss of these two residues removes the termination codon for MTATP6 and sets MTCO3 immediately in frame. Accurate processing at this site still occurs, but there is a markedly decreased steady-state level of RNA14, the ATPase 8- and 6-encoding bi-cistronic mRNA unit, establishing that an mtDNA mutation can cause dysregulation of mRNA stability. Analysis of the polyadenylation profile of the processed RNA14 at steady state revealed substantial abnormalities. The majority of mutated RNA14 terminated with short poly (A) extensions and a second, partially truncated population, was also present. Initial maturation of mutated RNA14 was unaffected, but deadenylation occurred rapidly. Inhibition of mitochondrial protein synthesis showed that the deadenylation was dependent on translation. Finally, deadenylation was shown to enhance mRNA decay, explaining the decrease in steady-state RNA14. An hypothesis is presented to describe how an mtDNA mutation that results in the loss of a termination codon causes enhanced mt-mRNA decay by translation-dependent deadenylation.

Adenosine Triphosphatases↗
PubMed2004

Cloning of a new familial t(3;8) translocation associated with conventional renal cell carcinoma reveals a 5 kb microdeletion and no gene involved in the rearrangement.

This study describes the molecular cloning of a familial translocation, t(3;8)(p14.2;q24.2), that segregates with the conventional renal cell carcinoma (conventional RCC). We had previously reported the family history and, through loss of heterozygosity and comparative genomic hybridization, detected the loss of the 3p chromosome arm and somatic mutation in the retained von Hippel-Lindau gene in some members of the family. With the help of array painting and sequence tagged site-PCR on flow-sorted derivative chromosomes, we have cloned the breakpoints of the translocation. We have studied the junctions on both derivative chromosomes at the genomic and expression levels. The analysis of the sequence revealed a 5 kb microdeletion at the chromosome 3 breakpoint together with a high density of repetitive motifs (Alu, short interspersed nuclear element) and an AT-rich region. Both chromosome 3 and 8 rearranged regions were very poor in gene content. We tested an expressed sequence tag, two predicted genes, one novel gene and LRIG1, a gene located more than 200 kb apart from the breakpoint on chromosome 3. None of these genes, except LRIG1, showed expression in any of the tested tissues (including normal adult and fetal kidney, sporadic kidney tumours and tumour samples from the proband's family). Taken together, all these data suggest that, rather than deregulation of specific genes that may be rearranged by the translocation, the proposed three-step model of tumour development (translocation, loss of the 3p chromosome, and mutation in a tumour suppressor gene located within that region) could be the biological mechanism that takes place in this familial form of conventional RCC.

Carcinoma, Renal Cell↗
PubMed1998

Chromosome anomalies and Y chromosome microdeletions as causal factors in male infertility.

Among the 10% or so of men who are diagnosed as oligo- or azoospermic in the absence of any physical obstruction, research is now showing that between 8 and 15% carry a microdeletion in the long arm of the Y chromosome which, by loss of specific DNA segments, leads to loss of vital genes for sperm production. Chromosomal anomalies account for approximately 2% of all men who attend infertility clinics, rising to 15% among those with azoospermia. There are serious implications for couples seeking help by intracytoplasmic sperm injection (ICSI), since chromosomal or gene defects which might normally be lost or eliminated by natural means could be transmitted in offspring. The need for genetic testing of ICSI donors and their offspring is raised, and a requirement for counselling is recommended.

Chromosome Aberrations↗
PubMed2002

Clinical characterization of 42 oligospermic or azoospermic men with microdeletion of the AZFc region of the Y chromosome, and of 18 children conceived via ICSI.

BACKGROUND: Severe spermatogenic compromise may be the result of a Y-chromosomal deletion of the AZFc region. Prior studies are limited to relatively small numbers of AZFc-deleted men. In this study, we have fully characterized 42 infertile men with a Y chromosome microdeletion strictly confined to the AZFc region, and we report on 18 children conceived through the use of ICSI. METHODS: A total of 42 oligospermic or azoospermic men had AZFc deletions. History, physical examination, karyotype, FSH, LH, testosterone, testis histology and results of ICSI using ejaculated or testis sperm were retrospectively accumulated in two academic clinical practices. RESULTS: All men were somatically healthy. Karyotypes were 46,XY in all but two men. FSH, LH, testosterone and testis histology could not differentiate those with oligospermia or azoospermia, nor could they predict whether sperm could be found in harvested testis tissue. Paternal age was not increased. Sperm production appeared stable over time. The results of ICSI were not affected by the AZFc deletion. All but one of the offspring were healthy. The sons inherited the AZFc deletion with no increase in length. CONCLUSIONS: AZFc-deleted men are somatically healthy, will most likely have useable sperm, will have stable sperm production over time and will have a good chance to experience biological paternity, but their sons will also be AZFc-deleted.

Adult↗
PubMed2003

A simple, low cost and non-invasive method for screening Y-chromosome microdeletions in infertile men.

BACKGROUND: Recent investigations emphasized a high prevalence of Y-chromosome microdeletions in men having severely impaired spermatogenesis. Screening of these men is recommended prior to assisted reproduction techniques. METHODS: The aim of this study was to define a reliable and efficient method to detect Y-chromosome deletions in infertile men. At first the feasibility of using a cytobrush to collect buccal cells as a source of DNA was tested. Then, a multiplex PCR in accordance with European recommendations (European Andrology Academia: EAA) was compared with a commercial kit. The test population consisted of 18 infertile male patients (with a known Y-deletion). Both buccal and blood cells were used for DNA extraction. A specific DNA extraction protocol was carried out on the buccal cells. RESULTS: Between 4-10 micro g of DNA were retrieved per brush, allowing for several PCR attempts. The commercial kit failed to detect an AZFa deletion. Furthermore, markers sY130, sY133 and sY153, included in the kit, are not reliable. Both false negative and false positive results were generated by the commercial kit. CONCLUSION: A multiplex PCR performed pursuant to EAA recommendations is proposed. When the testing is conducted with DNA extracted from buccal cells, this protocol is simple, accurate and affordable.

Blood Cells↗
PubMed2000

Y chromosome microdeletions and germinal mosaicism in infertile males.

Molecular deletions of the Y chromosome long arm are a frequent cause of male infertility. Because these deletions are thought to be inherited from fathers without Y chromosome deletions, the question arises as to whether their relatively high incidence in the male population could be due to the existence of a mosaicism in somatic and/or germinal paternal cells. This study included a total of 181 infertile men, among whom 18 were found to have an abnormal karyotype. In the other 163, polymerase chain reaction (PCR) analysis detected nine (5.5%) Y chromosome microdeletions. Blood, spermatozoa or testicular cells from 47 men (27 oligozoospermia, 20 azoospermia), including six Y-deleted patients, were screened for mosaicism using double target fluorescence in-situ hybridization (FISH) with Y centromeric and deleted in azoospermia (DAZ) gene-specific probes. Results indicated that: (i) percentages of double (intact Y chromosome) or single (deleted Y chromosome) fluorescent signals by FISH were in agreement with PCR data, thus demonstrating the reliability of the method; and (ii) a weak germ cell mosaicism was found in only two oligozoospermic patients, carrying 1.97 and 4.13% respectively of spermatozoa with a deleted Y chromosome. Further studies on larger populations are needed to evaluate precisely the incidence of Y deletion mosaicisms in infertile men.

Chromosome Aberrations↗
PubMed1988

Microdeletion associated with the integration process of hepatitis B virus DNA.

Hepatitis B virus (HBV) DNA is often found in integrated form in hepatocellular carcinomas (HCC) and in non-cancerous liver cells of chronic carriers of HBV. However, the process of integration has not been well understood. Analyses of integrant DNA was expected to give clues. However, the majority of the integrants are products of multistep rearrangements following integrations, and analysis of randomly selected samples do not give clues for understanding the process of primary integrant formation. Therefore, one must select an appropriate integrant(s) that has a simple structure. We surveyed a collection of integrants prepared from many HCC's, and found one integrant that has the simplest structure so far studied: The viral genome is almost complete, is joined to cellular DNA using the cohesive end of the viral DNA, and furthermore, the "left" and "right" flanking cellular DNA's are almost contiguous. Analysis of the unoccupied sites in cellular DNA showed that, although almost contiguous, it has generated a microdeletion (15 base pairs) in the target sequence. This target sequence has a short region of homology to the sequence in the viral genome located close to the junction. One integrant with strikingly similar features has been reported independently. Two similar, but not identical cases from literatures could be added to this category. Therefore, the integrants with these properties may represent a unique category among those prepared from hepatocellular carcinomas. Based on these findings, we propose that this integrant represents the primary product of integration, and discuss the intermediate acting in the process of integration.

Base Sequence↗
PubMed1999

Chromosomal abnormalities: trisomy 18, trisomy 13, deletions, and microdeletions.

The birth of an infant with a chromosomal abnormality such as trisomy 18, 13, Wolf-Hirschhorn (4p-) syndrome, Cri-du-chat (5p-) syndrome, and the microdeletion syndromes creates a stressful and devastating experience for families. Many of these disorders have severe consequences encompassing major malformations and mental retardation. With increasing diagnostic accuracy, clinicians can now appreciate the wide variability and natural history of these disorders. Although many of these infants do not survive the neonatal period, others do. Neonatal nurses have the opportunity to assist families in these situations by providing anticipatory guidance and care.

Chromosome Aberrations↗
PubMed2002

Microdeletion 22q11.2, Kousseff syndrome and spina bifida.

A fetus was diagnosed on ultrasound scan as having sacral spina bifida and a ventricular septal defect in the heart. At postmortem examination the cardiac defect was found to be a conotruncal abnormality, and there was a cleft palate, some facial dysmorphism as well as the spina bifida. A diagnosis of Kousseff syndrome was made, but detailed cytogenetics subsequently revealed a 22q11.2 deletion. In the light of these findings, and on review of the literature, we suggest that spina bifida is recognized as a feature of the variable phenotype associated with this microdeletion.

Abnormalities, Multiple↗
PubMed2006

A case of 3q29 microdeletion with novel features and a review of cytogenetically visible terminal 3q deletions.

A further case of 3q29 deletion, in a 13-year-old boy, is described and compared with previous reports. Our case shares a number of dysmorphic and neurodevelopmental features with previously reported individuals with 3q29 microdeletion and is the second reported case with deceleration in head growth--which may be a useful diagnostic clue. Novel features, which may expand the phenotype, include nasal voice, six lumbar vertebrae, lower limb contractures and cerebral sigmoid venous thrombosis. Additionally, cases with cytogenetically visible terminal 3q deletions are reviewed.

Abnormalities, Multiple↗