Detailed molecular and clinical characterization of three patients with 21q deletions.

We have investigated three patients with 21q deletions, two with developmental delay, dysmorphic features and internal organ malformations, and one with cognitive function within the normal range but with some deficits in gross and fine motor development. All aberrations were characterized by array-comparative genomic hybridization (array-CGH). In addition, extensive fluorescence in situ hybridization (FISH) mapping on metaphase chromosomes and mechanically stretched chromosomes was performed on patient 1 who had an extremely complex intrachromosomal rearrangement with 16 breakpoints, four deletions and four duplications. Patients 2 and 3 had interstitial deletions comprising 21q21.1-21q22.11 and 21q11.2-21q21.3, respectively. Partial deletions of 21q are rare and these patients display a highly variable phenotype depending on the size and position of the deletion. A review of the literature identified 38 cases with pure 21q deletions. Twenty-three of these had reliable mapping data. The combined information of present and previous cases suggests that the ITSN1 gene is involved in severe mental retardation in patients with 21q deletion. In addition, a critical region of 0.56 Mb containing four genes, KCNE1, DSCR1, CLIC6 and RUNX1, is associated with severe congenital heart defects, and deletions of the most proximal 15-17 Mb of 21q is associated with mild or no cognitive impairment, but may lead to problems with balance and motor function.

Concurrent microdeletion and duplication of 22q11.2.

Microduplication of 22q11.2 has been reported in fewer than 40 cases, all of them including the DiGeorge critical region (DGCR). We here present the characterization of a new duplication that does not include the DGCR. The duplication was initially found by multiplex ligation-dependent probe amplification analysis of 22q11.2 in a young girl with a concurrent deletion of the DGCR in 70% of her peripheral blood lymphocytes. Her phenotype included many of the features of the velocardiofacial syndrome, with velopharyngeal insufficiency, recurrent infections, learning and concentration problems as well as difficulties in social interactions. However, there were no congenital malformations, and her facial appearance was not typical for the syndrome. Further investigations included array comparative genomic hybridization (CGH) to size map the deletion/duplication and interphase fluorescent in situ hybridization to investigate mosaicism and the structure of the rearrangement. An identical duplication of this part of 22q11.2 has not been reported before, and the duplication itself seems to be associated with very mild or no symptoms. This study contributes to the growing knowledge regarding new deletions and duplications of 22q11.2, most of them mediated by the pre-disposing high number of low-copy repeats in the region.

Molecular cytogenetic characterization of an insertional translocation, ins(6;7)(p25;q33q34): deletion/duplication of 7q33-34 and clinical correlations.

A balanced insertional translocation between chromosomes 6 and 7, ins(6;7)(p25;q33q34) has been extensively investigated. The insertional translocation was found in several members of a three-generation family, where some were healthy balanced carriers while others had clinical symptoms due to deletion or duplication of 7q33-34. The deleted/duplicated segment could only be detected using high resolution banding and fluorescent in situ hybridization. A number of BAC/PAC clones located on chromosome 6 and 7 were used to characterize the breakpoint regions in detail and to determine the size of the deletion, which was 7.6 Mb, containing up to 68 genes. However, the insert on chromosome 6 was only 7.4 Mb, due to a deletion of 227 kb at the distal breakpoint on 7q. This small deletion was also found in the "balanced" carriers, and although the chromosome segment contains at least eight genes, none of the carriers seem to be affected by haploinsufficiency, since the phenotype is apparently normal. This is the first detailed characterization and phenotype correlation of such a deletion/duplication of distal 7q.

Comparative genomic hybridization and karyotyping of human embryonic stem cells reveals the occurrence of an isodicentric X chromosome after long-term cultivation.

Human embryonic stem (hES) cells are important research tools in studies of the physiology of early tissue differentiation. In addition, prospects are high regarding the use of these cells for successful cell transplantation. However, one concern has been that cultivation of these cells over many passages might induce chromosomal changes. It is thus important to investigate these cell lines, and check that a normal chromosomal content is retained even during long-term in vitro culture. Comparative genomic hybridization (CGH) was used to analyse three hES cell lines derived in our laboratory and cultured continuously for 30-42 weeks, comprising 35-39 cell passages. CGH could be successfully performed in 48 out of a total of 50 isolated single cells (96%). All three lines (HS181, HS235 and HS237) were shown to have a normal chromosomal content when analysed by both single cell CGH and by karyotyping up to passages 39, 39 and 35 respectively. No aneuploidies or larger deletions or amplifications were detected, and they were female (46,XX). However, HS237 was reanalysed at passage 61, and at that point an aberrant X chromosome was detected by karyotyping. The aberration was confirmed and characterized by single cell CGH and fluorescence in situ hybridization analysis, 46,X,idic(X)(q21). Thus, chromosomal aberrations may occur over time in stem cell lines, and continuous analysis of these cells during cultivation is crucial. Single cell CGH is a method that can be used for continuous analysis of the hES cell lines during cultivation, in order to detect chromosome imbalance.

Single cell CGH analysis reveals a high degree of mosaicism in human embryos from patients with balanced structural chromosome aberrations.

We have performed comparative genomic hybridization (CGH) analysis of single blastomeres from human preimplantation embryos of patients undergoing preimplantation genetic diagnosis (PGD) for inherited structural chromosome aberrations and from embryos of IVF couples without known chromosomal aberrations. The aim was to verify the PGD results for the specific translocation, reveal the overall genetic balance in each cell and visualize the degree of mosaicism regarding all the chromosomes within the embryo. We successfully analysed 94 blastomeres from 28 human embryos generated from 13 couples. The single cell CGH could verify most of the unbalanced translocations detected by PGD. Some of the embryos exhibited a mosaic pattern regarding the chromosomes involved in the translocation, and different segregation could be seen within an embryo. In addition to the translocations, we found a high degree of numerical aberrations including monosomies, trisomies and duplications or deletions of parts of chromosomes. All of the embryos (100%) were mosaic, containing more than one chromosomally uniform cell line, or even chaotic with a different chromosomal content in each blastomere.

Detailed characterization of 12 supernumerary ring chromosomes using micro-FISH and search for uniparental disomy.

Twelve patients with varying degrees of mosaicism for a supernumerary ring chromosome were studied. The ring chromosomes were characterized using microdissection in combination with degenerate nucleotide-primed polymerase chain reaction (PCR) and reverse painting (micro-FISH). This method made it possible to determine the chromosomal origin of the ring chromosomes in detail, and thus to compare the phenotypes of similar cases. Eleven of the marker chromosomes were derived from the most proximal part of 1p, 3p, 3q, 5p, 7q, 8p, 8q, 9p, 10p and 20p. One marker chromosome had a complex origin, including the proximal and the most distal part of 20q. Eight of the families were also investigated for uniparental disomy (UPD) using microsatellite analysis. One case with maternal UPD 9 was found in a child with a ring chromosome derived from chromosome 9, r(9)(p10p12).

High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH.

Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder whose hallmark is bilateral vestibular schwannoma. It displays a pronounced clinical heterogeneity with mild to severe forms. The NF2 tumor suppressor (merlin/schwannomin) has been cloned and extensively analyzed for mutations in patients with different clinical variants of the disease. Correlation between the type of the NF2 gene mutation and the patient phenotype has been suggested to exist. However, several independent studies have shown that a fraction of NF2 patients with various phenotypes have constitutional deletions that partly or entirely remove one copy of the NF2 gene. The purpose of this study was to examine a 7 Mb interval in the vicinity of the NF2 gene in a large series of NF2 patients in order to determine the frequency and extent of deletions. A total of 116 NF2 patients were analyzed using high-resolution array-comparative genomic hybridization (CGH) on an array covering at least 90% of this region of 22q around the NF2 locus. Deletions, which remove one copy of the entire gene or are predicted to truncate the schwannomin protein, were detected in 8 severe, 10 moderate and 6 mild patients. This result does not support the correlation between the type of mutation affecting the NF2 gene and the disease phenotype. This work also demonstrates the general usefulness of the array-CGH methodology for rapid and comprehensive detection of small (down to 40 kb) heterozygous and/or homozygous deletions occurring in constitutional or tumor-derived DNA.

Fine mapping of the constitutional translocation t(11;22)(q23;q11).

Translocation t(11;22)(q23;q11) is the most common constitutional reciprocal translocation in man. Balanced carriers are phenotypically normal, except for decreased fertility, an increased spontaneous abortion rate and a possible predisposition to breast cancer in some families. Here, we report the high resolution mapping of the t(11;22)(q23;q11) breakpoint. We have localised the breakpoint, by using fluorescence in situ hybidisation (FISH) walking, to a region between D11S1340 and WI-8564 on chromosome 11, and D22S134 and D22S264 on chromosome 22. We report the isolation of a bacterial artificial chromosome (BAC) clone spanning the breakpoint in 11q23. We have narrowed down the breakpoint to an 80-kb sequenced region on chromosome 11 and FISH analysis has revealed a variation of the breakpoint position between patients. In 22q11, we have sequenced two BACs (BAC2280L11 and BAC41C4) apparently mapping to the region; these contain low copy repeats (LCRs). Southern blot analysis with probes from BAC2280L11 has revealed different patterns between normal controls and translocation carriers, indicating that sequences similar/identical to these probes flank the translocation breakpoint. The occurrence of LCRs has previously been associated with genomic instability and "unclonable" regions. Hence, the presence of such repeats renders standard translocation breakpoint cloning techniques ineffective. Thus, we have used high resolution fiber-FISH to study this region in normal and translocation cases by using probes from 22q11, LCRs and 11q23. We demonstrate that the LCR containing the gap in 22q11 is probably substantially larger than the previous estimates of 100 kb. Using fiber-FISH, we have localised the breakpoint in 22q11 to approximately 20-40 kb from the centromeric border of the LCR (i.e. the telomeric end of AC006547) and have confirmed the breakpoint position on 11q23.

Molecular cytogenetic characterization and origin of two de novo duplication 9p cases.

We report on two additional cases with duplication of 9p, minor with facial anomalies and developmental delay. Using fluorescence in situ hybridization and single-copy probes, we showed that the first case was a direct duplication, whereas the second case was inverted. The extent of the direct duplication was defined as 9p12 --> p24 by microdissection and microcloning of the aberrant chromosome and subsequent chromosome-specific comparative genomic hybridization. DNA polymorphism analysis with eight microsatellite markers revealed that the origin of the dup(9p) was maternal in the first case, whereas it was paternal in the second.

Detailed characterization of a complex karyotype in a patient with primary plasma cell leukaemia using multicolour spectral karyotyping and micro-FISH.

INTRODUCTION: Plasma cell leukaemia is a rare disorder that usually carries an aggressive course with a rapidly fatal outcome. A variety of chromosomal abnormalities have been reported in plasma cell leukaemia but the clinical significance of an abnormal karyotype is still unclear. MATERIALS AND METHODS: We have applied the molecular cytogenetic techniques multicolour spectral karyotyping and microdissection in combination with fluorescence in situ hybridization on metaphases from a patient with primary plasma cell leukaemia and a fatal outcome. RESULTS AND CONCLUSION: The chromosome analysis showed severe hypodiploidy and 12 marker chromosomes. Identification of the structural rearrangements was not possible using routine cytogenetic methods. Utilizing the methods above, all marker chromosomes could be identified in detail and the karyotype was shown to be very complex. Forty-three breakpoints were found, and 25 could be identified at the band level, among others 14q32 where the immunoglobulin heavy chain locus is situated. Thus, these techniques provide the opportunity to resolve very complex chromosomal changes in a way that has not been previously possible and will consequently be of great importance in the search for hot spots that may harbour new cancer genes.

Cloning, expression pattern, and chromosomal assignment to 16q23 of the human gamma-adaptin gene (ADTG).

Adaptins are important components of clathrin-coated vesicles transporting ligand-receptor complexes from the plasma membrane or from the trans-Golgi network to lysosomes. Adaptins, together with medium and small subunits, form a heterotetrameric complex called an adaptor, whose role is to promote the formation of clathrin-coated pits and vesicles. We present the cloning and sequencing of the human gamma-adaptin cDNA (HGMW-approved symbol ADTG) consisting of 3723 bp with an open reading frame capable of encoding a protein of 825 amino acids, 98.9% identical to the mouse protein. Northern blot analysis of the mouse and human gamma-adaptin genes revealed a ubiquitous and abundant expression, except in human adult lung. Using a monochromosomal somatic cell hybrid panel and fluorescence in situ hybridization, we mapped this gene to human chromosome 16q23, which is syntenic with mouse chromosome 8, band D. In addition, we localized genes for two other components of the AP-1 adaptor, i.e., the medium (AP47) and small (AP19) subunits, to chromosomes 19 and 7, respectively. Expression analysis of these genes in human tissues revealed ubiquitously expressed transcripts of approximately 2.5 and 1.5 kb, respectively.

Bilateral multiple renal oncocytomas and cysts associated with a constitutional translocation (8;9)(q24.1;q34.3) and a rare constitutional VHL missense substitution.

We report here on a patient with bilateral multifocal renal oncocytomas and cysts. Cytogenetic analysis of the patient's lymphocytes revealed a constitutional 46,XY,add (9)(q34.3) karyotype. The rearrangement was further resolved as a constitutional reciprocal t(8;9)(q24.1;q34.3) by microdissection and FISH. Because the 9q breakpoint was located in the same region as the tuberous sclerosis type I locus (TSC1), which is associated with renal tumors, we performed FISH with two TSC1 flanking cosmids that were mapped proximal to the 9q breakpoint, thus excluding its involvement. Loss of heterozygosity (LOH) studies of the tumors revealed LOH in chromosome I, further strengthening the molecular diagnosis of oncocytoma. A previously unreported germline missense substitution, Pro40Arg, in exon I of the VHL gene was also found in the patient's constitutional DNA, adding to the complexity of the genetic profile.

The human RAD51/RecA homologue gene is not a candidate gene for Bloom's syndrome.

The human gene HSRAD51/RecA homologue has been investigated as a possible candidate gene involved in Bloom's syndrome. No mutations were found in the cDNA isolated from three different Bloom's syndrome cell lines, thus excluding the possibility that HSRAD51 is directly involved in the syndrome. Other possible candidates are discussed.

A missense mutation in the hypoxanthine phosphoribosyltransferase gene in a pediatric patient with hyperuricemia.

We have identified a mutation in the gene coding for the enzyme hypoxanthine phosphoribosyltransferase in a pediatric patient with hyperuricemia and nephrolithiasis. The mutation is a nucleotide substitution causing an amino acid substitution in the hypoxanthine phosphoribosyltransferase protein. In this patient, fibroblasts but not lymphocytes showed resistance to 6-thioguanine, and reduced enzyme activity was detected in lymphocytes. These results are consistent with the intermediary phenotype associated with partial hypoxanthine phosphoribosyltransferase enzyme deficiency. Altogether, six males in this family suffered from hyperuricemic symptoms, and small differences in phenotype were seen.

Hprt activities and RNA phenotypes in 6-thioguanine resistant human T-lymphocytes.

The phenotypic effects of mutation in the hypoxanthine phosphoribosyltransferase (hprt) gene on hprt enzyme activity and hprt mRNA levels were studied in 6-thioguanine (TG) resistant human T-cell clones with various types of hprt mutation. The mean enzyme activity in 16 TG selected clones was less than 1% of the mean in unselected clones. The hprt mRNA levels, measured by a quantitative RNA/RNA solution hybridization assay, were within the normal range in 38% of the mutant clones. Reduced hprt mRNA levels were found in all of three nonsense mutations, four out of five splicing mutations, both of two clones with genomic alterations, three out of five missense mutations and one out of four frameshift mutations caused by 1-4-bp deletions. Intermediate and high enzyme activity and normal hprt mRNA levels were found in two TG selected clones where no hprt mutation was detected. Several clones with very low hprt mRNA levels were found to yield hprt cDNA by PCR amplification. These results show that hprt mutation leads to decreased steady state levels of hprt mRNA in a majority of TG resistant T-cell clones, and that many different types of hprt mutation can have this effect.

The fragile X mutation does not have any major effect on the expression of the hypoxanthine phosphoribosyltransferase (HPRT) locus in human fibroblasts.

The possible influence of the fragile X mutation at Xq27 on the expression of the neighbouring gene (at Xq26) for hypoxanthine phosphoribosyl transferase (HPRT) was studied by determination of the levels of HPRT-RNA and HPRT enzyme activity in fibroblast cell cultures from 7 fragile X patients. These levels were lower (although not statistically significantly lower) than in normal fibroblast cultures. Hence, these data do not support the notion of a major effect of the fragile X mutation on the expression of the HPRT gene.

Expression of the hypoxanthine phosphoribosyl transferase gene in resting and growth-stimulated human lymphocytes.

Expression of the hypoxanthine phosphoribosyl transferase (hprt) gene was studied in resting and growth stimulated human lymphocytes by determinations of hprt-RNA and enzyme activity levels in cell extracts. Hprt-RNA was determined by quantitative solution hybridization and enzyme activity by measuring the rate of conversion of [14C]hypoxanthine to inosine 5'-monophosphate. In resting Go-lymphocytes, the hprt activity (5 nmol/h per 10(6) cells) was twice as high as in human fibroblasts, whereas the hprt-RNA level was very low (0.3 pg per 10(6) cells, or approx. one mRNA molecule per cell). Both RNA and enzyme activity remained at these levels in cells that were incubated in the presence of cycloheximide (CHX, 20 micrograms/ml) for up to 48 h, which suggests that hprt gene expression in resting lymphocytes depends mainly on a stable protein with a half-life of more than 48 h. In phytohemagglutinin (PHA) stimulated lymphocytes, the hprt-RNA levels increased 10-20-fold, while the enzyme activity increased 5-fold. The addition of hydroxyurea (0.01 M) to the culture medium did not prevent the increase of hrpt-RNA, whereas the increase of both RNA and enzyme activity was abrogated in the presence of CHX. Thus, the induction of hprt expression in growth stimulated lymphocytes requires new protein synthesis, and is not coupled to DNA replication. In long-term lymphocyte cultures, both hprt-RNA and enzyme activities showed high steady-state levels. After removal of PHA and growth factors from the culture medium the hprt-RNA levels decreased by over 80% within 24 h, while the enzyme activity was unaffected. Inhibition of transcription by actinomycin D (5 micrograms/ml) caused a rapid decay of the hprt-RNA, with an estimated half-time of 5.1 h. When CHX was added to actinomycin D inhibited cells, the rate of hprt-RNA breakdown was reduced. The hprt enzyme activity declined by approx. 50% during 24 in the presence of CHX. Thus, the enhanced expression of hprt-RNA in proliferating lymphocytes depends on continuous growth stimulation and seems to be associated with a high transcriptional activity and turnover of the RNA. In contrast, the enzyme activity is relatively stable, and less sensitive to alterations of growth conditions.

Unequal SCE is a rare event in homologous recombination between duplicated neo gene fragments in CHO cells.

The frequency of sister-chromatid exchange (SCE) was studied in Chinese hamster ovary (CHO) cell lines with stable insertions of the vector pIII-14gpt which contains 2 truncated neomycin resistance (neo) gene fragments. Recombination between regions of homology in the 2 fragments can restore a functional neo gene and make the cell resistant to the antibiotic G418, a neomycin analogue. Unequal SCE would be one of several possible mechanisms for this event. The observed spontaneous rate of formation of G418-resistant subclones was approximately 6.4 x 10(-6) per cell per generation, as compared to the estimated spontaneous frequency of 3 SCE per cell per generation. Given this SCE frequency, the probability of an SCE occurring in a target site of about 1600 bp (the distance separating the homologous regions in the neo fragments) would be about 8 x 10(-7) per cell per generation, or approximately one tenth of the estimated rate of recombination. Treatment of the cells with methyl methanesulfonate (MMS, 50 x 10(-6) M) induced about 80-90 SCE per cell, corresponding to a probability of 2 x 10(-5) SCE per 1600-bp target per cell. In the same cell culture, MMS treatment induced 4-8 x 10(-4) recombination events per cell giving rise to G418 resistance. Cells treated with HN2 (up to 4 x 10(-6) M) showed a significant increase in SCEs, but no change in the frequency of G418-resistant revertants. These results suggest that the 2 pathways leading to SCE and recombination respectively are uncoupled, and only a small fraction of the recombination events, if any, are due to unequal SCE in this system.