Multiple congenital abnormalities in a newborn with two supernumerary marker chromosomes derived from chromosome 14.

Pure partial duplication or triplication of the proximal part of chromosome 14 has been reported in only 4 patients. Other individuals with a duplication or triplication of this region have additional chromosome imbalances. We present a new case with a supernumerary marker chromosome in all blood cells and in 35% of the cells an additional smaller marker chromosome. Both markers appeared to be derived from chromosome 14 (del(14)(q21.2) in all cells and del(14)(q11.2) in 35% of the cells). This results in a partial duplication of the proximal region of chromosome 14, combined with a mosaic partial triplication of a smaller segment of the same region. In this paper, we compare the clinical features of this case to those of cases from the literature. Although most of the patients from literature were unbalanced translocation carriers, their clinical features were comparable, except from renal abnormalities.

Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA).

BACKGROUND: Subtelomeric rearrangements contribute to idiopathic mental retardation and human malformations, sometimes as distinct mental retardation syndromes. However, for most subtelomeric defects a characteristic clinical phenotype remains to be elucidated. OBJECTIVE: To screen for submicroscopic subtelomeric aberrations using multiplex ligation dependent probe amplification (MLPA). METHODS: 210 individuals with unexplained mental retardation were studied. A new set of subtelomeric probes, the SALSA P036 human telomere test kit, was used. RESULTS: A subtelomeric aberration was identified in 14 patients (6.7%) (10 deletions and four duplications). Five deletions were de novo; four were inherited from phenotypically normal parents, suggesting that these were polymorphisms. For one deletion, DNA samples of the parents were not available. Two de novo submicroscopic duplications were detected (dup 5qter, dup 12pter), while the other duplications (dup 18qter and dup 22qter) were inherited from phenotypically similarly affected parents. All clinically relevant aberrations (de novo or inherited from similarly affected parents) occurred in patients with a clinical score of >or=3 using an established checklist for subtelomeric rearrangements. Testing of patients with a clinical score of >or=3 increased the diagnostic yield twofold to 12.4%. Abnormalities with clinical relevance occurred in 6.3%, 5.1%, and 1.7% of mildly, moderately, and severely retarded patients, respectively, indicating that testing for subtelomeric aberrations among mildly retarded individuals is necessary. CONCLUSIONS: The value of MLPA is confirmed. Subtelomeric screening can be offered to all mentally retarded patients, although clinical preselection increases the percentage of chromosomal aberrations detected. Duplications may be a more common cause of mental retardation than has been appreciated.

Identification of an unbalanced cryptic translocation between the chromosomes 8 and 13 in two sisters with mild mental retardation accompanied by mild dysmorphic features.

Recently, much attention has been given to subtelomeric chromosomal rearrangements as important aetiological factors leading to idiopathic mental retardation. However, detection of these aberrations is difficult, mostly due to technical limitations and lack of genotype-phenotype relationships. We report on a family with a history suggestive of segregation of a chromosomal anomaly. In two mildly mentally retarded sisters with a similar phenotype consisting of obesitas, skin atrophy of the lower limbs and mild facial dysmorphisms, a subtle unbalanced cryptic translocation (46,XX,der(13)t(8;13)(q24.3;q34)) was detected on routine cytogenetic investigation followed by additional FISH studies. The translocation originated from the mother.

Towards the isolation of a human malignant extragonadal germ cell tumour-associated breakpoint in chromosome 11q13.

In a previous study we have defined a subgroup of human malignant extragonadal germ cell tumours that is characterized by complex translocations involving chromosomes 6 and 11 (Echten et al. 1995). Here we report (i) the use of fluorescent in situ hybridization, pulsed field gel electrophoresis and direct visual hybridization techniques to localize the tumour-associated breakpoint within band 11q13, and (ii) the construction of a phage library enriched for this region to facilitate genomic walks towards the breakpoint. Extensive breakpoint-flanking contigs were generated and within these contigs six candidate genes could be identified.

Fine mapping of the human renal oncocytoma-associated translocation (5;11)(q35;q13) breakpoint.

Recent cytogenetic analysis of a series of human renal oncocytomas revealed the presence of a recurring chromosomal translocation (5;11)(q35;q13) as sole anomaly in a subset of the tumors. The molecular characterization of this translocation was initiated using two primary t(5;11)-positive renal oncocytomas and a panel of somatic cell hybrids derived from one of these tumors, in conjunction with fluorescence in situ hybridization (FISH) and Southern blot analysis. The breakpoint in chromosome band 11q13 could be located within a genomic interval of at maximum 400 Kb immediately centromeric to the BCL1 locus.

Severe Progressive Autism Associated with Two de novo Changes: A 2.6-Mb 2q31.1 Deletion and a Balanced t(14;21)(q21.1;p11.2) Translocation with Long-Range Epigenetic Silencing of LRFN5 Expression.

In a 19-year-old severely autistic and mentally retarded girl, a balanced de novo t(14;21)(q21.1;p11.2) translocation was found in addition to a de novo 2.6-Mb 2q31.1 deletion containing 15 protein-encoding genes. To investigate if the translocation might contribute to developmental stagnation at the age of 2 years with later regression of skills, i.e. a more severe phenotype than expected from the 2q31.1 deletion, the epigenetic status and expression of genes proximal and distal to the 14q21.1 breakpoint were investigated in Ebstein Barr Virus-transformed lymphoblast and primary skin fibroblast cells. The 14q21.1 breakpoint was found to be located between a cluster of 7 genes 0.1 Mb upstream, starting with FBXO33, and the single and isolated LRFN5 gene 2.1 Mb downstream. Only expression of LRFN5 appeared to be affected by its novel genomic context. In patient fibroblasts, LRFN5 expression was 10-fold reduced compared to LRFN5 expressed in control fibroblasts. In addition, a relative increase in trimethylated histone H3 lysine 9 (H3K9M3)-associated DNA starting exactly at the translocation breakpoint and going 2.5 Mb beyond the LRFN5 gene was found. At the LRFN5 promoter, there was a distinct peak of trimethylated histone H3 lysine 27 (H3K27M3)-associated DNA in addition to a diminished trimethylated histone H3 lysine 4 (H3K4M3) level. We speculate that dysregulation of LRFN5, a postsynaptic density-associated gene, may contribute to the patient's autism, even though 2 other patients with 14q13.2q21.3 deletions that included LRFN5 were not autistic. More significantly, we have shown that translocations may influence gene expression more than 2 Mb away from the translocation breakpoint.

Banding of human chromosomes with basic fuchsin.

In this paper a technique is described for the banding of human metaphase chromosomes with basic fuchsin. The main characteristics of the G-banding pattern obtained with this cationic triphenylmethane dye are: the secondary constriction regions of chromosomes Nos. 1 and 16 are strongly stained, especially in the latter one; the heterochromatic area of chromosome No. 9, usually negative with most other G-banding techniques, is clearly visible as an intensely stained band adjacent to the centromere; the chromosomal outline is often very distinct, facilitating the study of the telomeres; a number of chromosomal regions with bright Q fluorescence such as the polymorphic regions of the chromosomes Nos. 3, 4, and Y also stain strongly with basic fuchsin. The basic fuchsin technique combines therefore properties of G-, C-, and Q-banding methods and seems very suitable for use in e.g., family and linkage studies. Several triphenylmethanes closely related to basic fuchsin produce similar banding patterns. The band-producing ability is, however, diminished in those dyes which contain methylated amino groups. If the methyl groups are attached to the carbon atoms at the 3-positions in the phenyl rings, band formation seems unaffected. The way in which basic fuchsin and chromatin may interact as well as the possible mechanism(s) of band formation with this dye are discussed.

Neither age nor sex influence the expression of folate sensitive common fragile sites on human chromosomes.

The expression of folate sensitive common fragile sites was investigated in 82 normal healthy males and females of various ages. In 100 studied metaphases of each of these controls, between 0 and 56 lesions were detected (mean 18.3 +/- 10.3 SD). No significant difference was found between the mean number of expressed lesions in females and males. No age-effects were observed. Two "new" common fragile sites were discovered at 6p21 and 17q21. Their fragile site status, however, needs to be confirmed.

Frequent occurrence of translocations of the short arm of chromosome 15 to other D-group chromosomes.

The presence of DA/DAPI (distamycin A/4,6-diamino-2-phenyl-indole) heteromorphism on the short arm of human acrocentric chromosomes was investigated in 127 individuals. In 7 cases, a DA/DAPI signal was observed on an acrocentric chromosome other than 15. Subsequently, in situ hybridization (ISH) with a pericentromeric probe specific for chromosome 15 was carried out. In all 7 cases, three ISH signals were present in every metaphase, i.e., on both chromosomes 15 and on the third DA/DAPI-fluorescence-positive acrocentric chromosome (a chromosome 13 or 14), indicating that a chromosome 15 short arm was also present on these chromosomes. Therefore, we conclude that translocations of short arm sequences from chromosome 15 onto other D-group chromosomes occur frequently. Moreover, it appears that DA/DAPI staining remains specific for the short arm of chromosome 15, despite a number of recent papers suggesting otherwise.

Prometaphase banding of human chromosomes with basic fuchsin.

A technique is described for the production of detailed and richly contrasting G-band patterns in human prometaphase chromosomes with the aid of the triphenylmethane dye basic fuchsin. The usefulness of this method is illustrated by its application for the precise analysis of two chromosome 11 rearrangements. It is also demonstrated that high-resolution banding with basic fuchsin can reveal bands not present in the international standard idiogram of human prophase chromosomes (ISCN 1981). The technique described can also be used for easy recognition of the late replicating X chromosome, which stains darker than its early replicating homologue. A preliminary analysis of the late replicating X chromosomes in a 49,XXXXY individual suggests that the three supernumerary X chromosomes do not necessarily replicate synchronously.

Nomarski-optical studies of human chromosomes R-banded with barium hydroxide.

The morphologic changes occurring in human chromosomes during R-banding by Ba(OH)2 treatment were followed with the aid of bright-field and Nomarski interference contrast microscopy. It was found that the hot Ba(OH)2 pretreatment alone, i.e., without staining, caused a pattern of transverse ridges in the chromosomes that clearly corresponded to positive R-band regions. No chromosomal collapse could be seen during any stage of the R-banding procedure. Thus these events contrast with those observed in G-band formation with trypsin, where complete chromosomal collapse occurs after pretreatment and where staining is necessary to induce G-band ridges. The possible mechanism of R-band induction by Ba(OH)2 is discussed. It is proposed that the R-band ridges arise as a result of chromatin loss from the interband regions during the hot alkaline pretreatment.

Structure and chromosome location of Smtn, the mouse smoothelin gene.

Smoothelins are cytoskeleton-associated proteins that are found in contractile smooth muscle. Two isoforms have been identified: smoothelin-A, expressed in visceral tissues and smoothelin-B, found in vascular tissues. The mouse smoothelin gene (Smtn) was isolated and characterized. It was assigned to chromosome 11 band A2-A3 by fluorescence in situ hybridization. The gene consists of 20 exons and spans 23 kb. Its structure is conserved between mouse and human. The proximal promoter of both smoothelin-A and smoothelin-B contains several transcription factor-binding sites but lacks a consensus TATA box.

Analysis of chromosome aberrations and sister chromatid exchanges in peripheral blood lymphocytes of newborns after vitamin K prophylaxis at birth.

In many countries vitamin K prophylaxis at birth is recommended to prevent bleeding in infants due to vitamin K deficiency. Because the incidence of clinical vitamin K deficiency is very low, such a vitamin K administration should be completely safe. However, an increase in sister chromatid exchanges in lymphocytes of fetal sheep 24 h after injection of vitamin K1 has been reported. Therefore, a study concerning genotoxicity of vitamin K1 in man was conducted. Sister chromatid exchanges and chromosome aberrations were analyzed in peripheral blood lymphocytes of six newborns 24 h after intramuscular administration of 1 mg vitamin K1 and in six control neonates. The mean number of sister chromatid exchanges per metaphase in the vitamin K group was 8.88 +/- 1.22 as compared with 9.05 +/- 1.14 in the control group (NS). The mean number of chromosome aberrations per 100 mitoses was 3.00 +/- 2.61 in the vitamin K group and 2.50 +/- 1.87 in the control group (NS). Vitamin K1 plasma concentrations ranged from 115 to 1150 ng/mL (255 to 2555 x 10(-9) M) in the supplemented group, a 5000-fold rise as compared with the control group (p less than 0.01). We did not find any evidence for genetic toxicity due to the administration of 1 mg vitamin K1 intramuscularly to the newborn child.

Pathogenesis of axonal dystrophy and demyelination in alphaA-crystallin-expressing transgenic mice.

We recently described a transgenic mouse strain overexpressing hamster alphaA-crystallin, a small heat shock protein, under direction of the hamster vimentin promoter. As a result myelin was degraded and axonal dystrophy in both central nervous system (especially spinal cord) and peripheral nervous system occurred. Homozygous transgenic mice developed hind limb paralysis after 8 weeks of age and displayed progressive loss of myelin and axonal dystrophy in both the central and peripheral nervous system with ongoing age. Pathologically the phenotype resembled, to a certain extent, neuroaxonal dystrophy. The biochemical findings presented in this paper (activity of the enzymes superoxide dismutase, catalase and transglutamase, myelin protein zero expression levels and blood sugar levels) confirm this pathology and exclude other putative pathologies like Amyothrophic Lateral Sclerosis and Hereditary Motor and Sensory Neuropathy. Consequently, an excessive cytoplasmic accumulation of the transgenic protein or a disturbance of the normal metabolism are considered to cause the observed neuropathology. Therefore, extra-ocular alphaA-crystallin-expressing transgenic mice may serve as a useful animal model to study neuroaxonal dystrophy.

Mapping and characterization of the mouse and human SS18 genes, two human SS18-like genes and a mouse Ss18 pseudogene.

We have previously isolated and characterized a mouse cDNA orthologous to the human synovial sarcoma associated SS18 (formerly named SSXT and SYT) cDNA. Here, we report the characterization of the genomic structure of the mouse Ss18 gene. Through in silico methods with sequence information contained in the public databases, we did the same for the human SS18 gene and two human SS18 homologous genes, SS18L1 and SS18L2. In addition, we identified a mouse Ss18 processed pseudogene and mapped it to chromosome 1, band A2-3. The mouse Ss18 gene, which is subject to extensive alternative splicing, is made up of 11 exons, spread out over approximately 45 kb of genomic sequence. The human SS18 gene is also composed of 11 exons with similar intron-exon boundaries, spreading out over about 70 kb of genomic sequence. One alternatively spliced exon, which is not included in the published SS18 cDNA, corresponds to a stretch of sequence which we previously identified in the mouse Ss18 cDNA. The human SS18L1 gene, which is also made up of 11 exons with similar intron-exon boundaries, was mapped to chromosome 20 band q13.3. The smaller SS18L2 gene, which is composed of three exons with similar boundaries as the first three exons of the other three genes, was mapped to chromosome 3 band p21. Through sequence and mutation analyses this gene could be excluded as a candidate gene for 3p21-associated renal cell cancer. In addition, we created a detailed BAC map around the human SS18 gene, placing it unequivocally between the CA-repeat marker AFMc014wf9 and the dihydrofolate reductase pseudogene DHFRP1. The next gene in this map, located distal to SS18, was found to be the TBP associated factor TAFII-105 (TAF2C2). Further analogies between the mouse Ss18 gene, the human SS18 gene and its two homologous genes were found in the putative promoter fragments. All four promoters resemble the promoters of housekeeping genes in that they are TATA-less and embedded in canonical CpG islands, thus explaining the high and widespread expression of the SS18 genes.

Gene structure and chromosomal mapping of human epithelial calcium channel.

The epithelial Ca(2+) channel, ECaC, represents the rate-limiting step of vitamin D(3)-regulated Ca(2+) (re)absorption in kidney and intestine, and provides, therefore, a new candidate gene for Ca(2+)-related disorders. To supply the basis for direct mutation analysis, we report here the structure of the human ECaC gene (ECAC1(2)). It consists of 16 exons spanning 25 kb with introns ranging from 98 to 8500 bp. The 5'-flanking region of ECAC1 contains four putative vitamin D(3)-responsive elements. At positions -92 and -13 transcription initiation sites were identified, but the former lacks the canonical TATA or CAAT boxes. ECAC1 was mapped to chromosome 7q35 by fluorescent in situ hybridization, reassigning a previous radiation hybrid mapping to 7q31.1-2. The gene of a recently identified rat intestine homologue of ECaC, named Ca(2+) transporter 1, was found juxtaposed to the ECaC gene, indicating that both genes are the products of evolutionary local gene duplication.

Construction of a 350-kb sequence-ready 11q13 cosmid contig encompassing the markers D11S4933 and D11S546: mapping of 11 genes and 3 tumor-associated translocation breakpoints.

Previously, we located three novel human tumor-associated translocation breakpoints in the chromosome 11q13 region between the markers D11S4933 and D11S546. To facilitate the molecular analysis of these breakpoints, we have constructed a continuous sequence-ready cosmid and PAC contig of approximately 350 kb, including the markers D11S4933 and D11S546. In addition, a detailed transcript map was generated. This resulted in the precise positioning of 11 genes and ESTs within the contig, including 4 genes already known to map in the 11q13 region. Three other genes that we positioned within the contig showed homologies to unmapped genes from human and/or other species. Three ESTs were novel. Partial cosmid sequencing resulted in the establishment of the direction of transcription of several of the reported genes. This contig will be instrumental for the detailed characterization of the tumor-associated chromosomal breakpoints and the identification of other 11q13-associated disease genes.

cDNA cloning and chromosomal localization of the genes encoding the alpha- and beta-subunits of human Rab geranylgeranyl transferase: the 3' end of the alpha-subunit gene overlaps with the transglutaminase 1 gene promoter.

We have isolated and sequenced the complete coding sequences of the human genes for the alpha- and beta-subunits of Rab geranylgeranyl transferase (Rab GGTase). The alpha- and beta-subunit genes code for proteins of 567 and 331 amino acids, respectively, showing 91 and 95% amino acid identity to their rat counterparts. We employed fluorescence in situ hybridization to map the beta-subunit gene to human chromosome 1p31. The alpha-subunit gene could be assigned to 14q11.2, less than 2 kb upstream of the transcription initiation site of the gene for transglutaminase 1 (TGM1). The two genes are arranged in tandem in a head-to-tail orientation. The short intergenic sequence between the two loci contains several promoter elements that are involved in the induction of TGM1 gene expression in squamous cells. These results suggest that cis-acting factors for cell-type-specific transcription of one gene are located within the transcribed region of a functionally unrelated gene.

Genomic organization and chromosomal localization of three members of the UDP-N-acetylgalactosamine: polypeptide N-acetylgalactosaminyltransferase family.

A homologous family of UDP- N -acetylgalactosamine: polypeptide N -acetylgalactosaminyltransferases (GalNAc-transferases) initiate O-glycosylation. These transferases share overall amino acid sequence similarities of approximately 45-50%, but segments with higher similarities of approximately 80% are found in the putative catalytic domain. Here we have characterized the genomic organization of the coding regions of three GalNAc-transferase genes and determined their chromosomal localization. The coding regions of GALNT1 , -T2 , and -T3 were found to span 11, 16, and 10 exons, respectively. Several intron/exon boundaries were conserved within the three genes. One conserved boundary was shared in a homologous C. elegans GalNAc-transferase gene. Fluorescence in situ hybridization showed that GALNT1 , -T2 , and -T3 are localized at chromosomes 18q12-q21, 1q41-q42, and 2q24-q31, respectively. These results suggest that the members of the polypeptide GalNAc-transferase family diverged early in evolution from a common ancestral gene through gene duplication.

Genomic structure, chromosomal localization, and embryonic expression of the mouse homolog of PRCC, a gene associated with papillary renal cell carcinoma.

In a subset of papillary renal cell carcinomas a t(X;1)(p11;q21) chromosome translocation has repeatedly been reported. Positional cloning has demonstrated that, as a result of this translocation, the transcription factor TFE3 gene on the X-chromosome becomes fused to a novel gene, PRCC, on chromosome 1. Since as yet little is known about the function of PRCC, we sought to identify the mouse counterpart of the PRCC gene. Isolation and sequence analysis of a mouse Prcc cDNA revealed a high level of conservation between man and mouse, both at the nucleotide and protein level. As the human PRCC gene, the mouse Prcc gene is ubiquitously expressed. It shows low expression in all mouse fetal tissues examined. In addition, we identified a genomic cosmid clone containing the complete Prcc gene. The mouse Prcc gene consists of seven exons, all of which contain coding sequences. The small second exon, which was found to be located adjacent to the t(X;1) breakpoint in the human gene on chromosome 1, is also conserved between man and mouse. In mouse, Prcc is located on chromosome 3. These cDNA and genomic clones will be instrumental in the creation of mouse models for a further elucidation of the function of PRCC.