Analysis of marker or complex chromosomal rearrangements present in pre- and post-natal karyotypes utilizing a combination of G-banding, spectral karyotyping and fluorescence in situ hybridization.

The significance of complex chromosomal rearrangements presents a diagnostic dilemma. In the past, the use of G-banding coupled with fluorescence in situ hybridization (FISH) has been the standard approach. The recent development of spectral karyotyping (SKY) and multicolor FISH (M-FISH) has resulted in an increased accuracy of identification of marker or other complex chromosomal rearrangements. However, owing to the additional cost and time associated with SKY or M-FISH, and the restricted availability of such imaging facilities in many centers, it is not feasible to perform these procedures routinely on every sample. In addition, the identification of an aberration by SKY or M-FISH will often require confirmation by FISH. A practical approach is needed to take advantage of the complementary strengths of each method. In our center we utilize an algorithm that dictates the use of routine G-banding for the initial preliminary evaluation of a patient, followed by SKY characterization if marker chromosomes or complex translocations are detected by the G-banding analysis. According to this algorithm, FISH is used to verify the results once the origin of the abnormal chromosome has been determined by SKY. To demonstrate the effectiveness of this algorithm, we have analyzed both amniocyte and lymphocyte slides, using a combination of G-banding, SKY, and FISH. Our results confirm that an algorithm which selectively uses SKY or M-FISH will provide an efficient and improved method for pre- and post-natal chromosomal analysis.

The origin of four squirrel monkey cell lines established by karyotype analysis.

The squirrel monkey is a neotropical primate genus which is widely used in biomedical research but includes individual species and subspecies that respond differently to experimental perturbations. GTG-banding patterns of chromosomes 15 and 16, which are distinct among different squirrel monkey species and subspecies, were used to determine the origin of three lung fibroblast cell lines from squirrel monkeys of unknown genetic background (DPSO 114/74, SqMkLu/68, and 7603830) and to confirm the origin of a lymphoblast cell line (GSML) recently established from Guyanese squirrel monkey. DPSO 114/74 cells are from Peruvian squirrel monkey, SqMkLu/68 cells are Bolivian squirrel monkey, and 7603830 cells are from a Peruvian/Bolivian hybrid. Chromosome analysis of GSML cells confirmed that they are from Guyanese squirrel monkey.

Partial trisomy 7p defined by analysis of a complex chromosome rearrangement using a BAC clone panel.

PURPOSE: To illustrate the use of bacterial artificial chromosome (BAC) clone panels for molecular cytogenetic analysis of complex chromosome rearrangements (CCRs). METHODS: High resolution cytogenetics followed by fluorescence in situ hybridization (FISH) analysis using chromosome band-specific BAC probes, in addition to commercially available probes. RESULTS: High resolution cytogenetics in conjunction with FISH using commercially available probes proved inadequate to resolve problems in characterizing a balanced CCR in the mother of a patient who had inherited an unbalanced form of the CCR. Accurate interpretation of the CCR and the unbalanced rearrangement in the patient as trisomy 7p12.2-->p21.3 was accomplished only through use of the BAC clone panel. CONCLUSION: Use of BAC clone panels can enhance the power of FISH analysis in defining chromosome rearrangements that cannot be resolved by high resolution chromosome analysis.

Hypersensitivity to radiation-induced non-apoptotic and apoptotic death in cell lines from patients with the ICF chromosome instability syndrome.

Immunodeficiency, centromeric region instability, and facial anomalies (ICF), a rare recessive chromosome instability syndrome, involves the loss of DNA methyltransferase 3B activity and the consequent hypomethylation of a small portion of the genome. We demonstrate for the first time that ICF cells are strongly hypersensitive to a genotoxic agent, namely, ionizing radiation. However, unlike cell lines from patients with ataxia telangiectasia or Nijmegen breakage syndrome, chromosome instability syndromes also associated with unusual sensitivity to ionizing radiation, ICF cells did not show any deficiencies in their cell cycle checkpoints. ICF lymphoblastoid cell lines demonstrated increased apoptosis, long-term cell cycle arrest, and loss of viability in clonogenicity assays after irradiation compared to analogous normal cell lines. Also, the ICF cell lines were subject to high frequencies of rapid non-apoptotic cell death upon irradiation but not to abnormally high levels of radiation-induced, cytogenetically detectable chromosome abnormalities. ICF-associated undermethylation of some regulatory gene(s) might lead to an exaggerated response to radiation-induced breaks in DNA yielding increased rates of cell death and irreversible cell cycle arrest. As a defense against their frequent spontaneous breaks in chromosomes 1 and 16, ICF patients may be abnormally prone to chromosome break-induced apoptosis, non-apoptotic cell death, and permanent cell cycle arrest so as to minimize the number of cycling cells with spontaneous rearrangements. A similarly increased cell death and cycle-arrest response to chromosome breaks due to cancer-linked DNA hypomethylation might occur during carcinogenesis.

FGFR3 gene mutation (Gly380Arg) with achondroplasia and i(21q) Down syndrome: phenotype-genotype correlation.

We report the case of a boy with achondroplasia and i(21q) Down syndrome. Besides craniofacial features typical in Down syndrome, the skeletal findings of achondroplasia dominate the clinical picture. The diagnosis of Down syndrome was based on clinical features and the cytogenetic finding of i(21q) trisomy 21. The diagnosis of achondroplasia was based on the presence of clinical and radiographic findings and confirmed by the presence of a common FGFR3 gene mutation (Gly380Arg) detected by restriction enzyme analysis and sequencing of the polymerase chain reaction products. This is the first report of achondroplasia associated with i(21q) Down syndrome.

DNA hypomethylation and unusual chromosome instability in cell lines from ICF syndrome patients.

The ICF syndrome (immunodeficiency, centromeric region instability, facial anomalies) is a unique DNA methylation deficiency disease diagnosed by an extraordinary collection of chromosomal anomalies specifically in the vicinity of the centromeres of chromosomes 1 and 16 (Chr1 and Chr16) in mitogen-stimulated lymphocytes. These aberrations include decondensation of centromere-adjacent (qh) heterochromatin, multiradial chromosomes with up to 12 arms, and whole-arm deletions. We demonstrate that lymphoblastoid cell lines from two ICF patients exhibit these Chr1 and Chr16 anomalies in 61% of the cells and continuously generate 1qh or 16qh breaks. No other consistent chromosomal abnormality was seen except for various telomeric associations, which had not been previously noted in ICF cells. Surprisingly, multiradials composed of arms of both Chr1 and Chr16 were favored over homologous associations and cells containing multiradials with 3 or >4 arms almost always displayed losses or gains of Chr1 or Chr16 arms from the metaphase. Our results suggest that decondensation of 1qh and 16qh often leads to unresolved Holliday junctions, chromosome breakage, arm missegregation, and the formation of multiradials that may yield more stable chromosomal abnormalities, such as translocations. These cell lines maintained the abnormal hypomethylation in 1qh and 16qh seen in ICF tissues. The ICF-specific hypomethylation occurs in only a small percentage of the genome, e.g., ICF brain DNA had 7% less 5-methylcytosine than normal brain DNA. The ICF lymphoblastoid cell lines, therefore, retain not only the ICF-specific pattern of chromosome rearrangements, but also of targeted DNA hypomethylation. This hypomethylation of heterochromatic DNA sequences is seen in many cancers and may predispose to chromosome rearrangements in cancer as well as in ICF.

Adrenal insufficiency in Smith-Lemli-Opitz syndrome.

We describe three unrelated patients with adrenal insufficiency and RSH or Smith-Lemli-Opitz syndrome (SLOS), a disorder due to deficient synthesis of cholesterol. These patients presented with hyponatremia, hyperkalemia, and decreased aldosterone-to-renin ratio, which is a sensitive measure of the renin-aldosterone axis. All patients had profound serum total cholesterol deficiency (14-31 mg/dl) and marked elevation of 7-dehydrocholesterol (10-45 mg/ dl). Two patients were newborn infants with 46, XY karyotypes and complete failure to masculinize; one of these patients also had cortisol deficiency. Both patients died within 10 days of birth of cardiopulmonary complications while on adrenal replacement therapy. The third patient diagnosed with SLOS at birth presented at age 7months with fever and diarrhea and was noted to have profound hyponatremia. This patient is maintaining normal serum electrolytes on mineralocorticoid replacement. We conclude that adrenal insufficiency may be a previously undetected and treatable manifestation in SLOS. We hypothesize that deficiency of cholesterol, an adrenal hormone precursor, may lead to insufficient synthesis of adrenal steroid hormones.

1p microdeletion in sibs with minimal phenotypic manifestations.

We report on two sibs with a paracentric inversion of chromosome 1 [inv(1)(p22.3p34.1)] and a small deletion of the same chromosome (p34.1-->p34.3). They presented with learning disabilities and disturbed conduct but lacked the more severe manifestations usually associated with autosomal chromosome deletion. Born to an alcoholic mother and later placed in foster care because of abuse and neglect, the behavior abnormalities they present are likely to be associated with their traumatic postnatal experience. Microscopic deletions without significant morphological phenotypic expression have been described but are rarely reported. Most reported cases of interstitial deletion of 1p had associated malformations and psychomotor retardation. These sibs may represent the first evidence that deletion of 1p34.1-->1p34.3 may have little impact on the phenotype.

Prenatal detection of de novo duplication of the short arm of chromosome 18 confirmed by fluorescence in situ hybridization (FISH).

We present a patient with developmental delay, minor anomalies, and duplication 18p confirmed by fluorescence in situ hybridization with whole chromosome 18 painting probe (Oncor p5218). Our observation confirms the findings of other investigators that duplication 18p is not associated with major malformations.

Hyperlipidemia, insulin-dependent diabetes mellitus, and rapidly progressive diabetic retinopathy and nephropathy in Prader-Willi syndrome with del(15)(q11.2q13).

We report on a white man with Prader-Willi syndrome (PWS) and del(15)(q11.2q13), confirmed by fluorescence in situ hybridization (FISH), who had hyperlipidemia, insulin-dependent diabetes, and the early onset and rapid progression of diabetic retinopathy and nephropathy within 4 years after diagnosis of diabetes. The spectrum of glucose intolerance in patients with PWS is discussed, as well as those references which suggest that the prevalence of hyperlipoproteinemia in this condition may be greater than previously recognized. We suggest the need for clarification of both the prevalence and types of hyperlipoproteinemia, as well as the pathophysiology of glucose intolerance and correlation with molecular cytogenetic findings. We also encourage careful monitoring for diabetic complications to further clarify the prevalence and possible accelerated course of microvascular lesions.

A complex five breakpoint intrachromosomal rearrangement ascertained through two recombinant offspring.

Intrachromosomal rearrangements usually result from three of fewer breaks. We report a complex intrachromosomal rearrangement resulting from five breaks in one chromosome 10 of a phenotypically normal father of two developmentally delayed children. GTG-banding analysis of the father's rearranged chromosome 10 suggested in initial pericentric inversion followed by an insertion from the short arm into the terminal band of the long arm [der(10) (pter-->p13::q21.2-->p12.2::q22.1::-->q26.3::q22.1-->q 21.2::p12.2-->p13::q26.3-->qter)]. To our knowledge, this rearrangement is the most complex ever reported in a single chromosome. Both children inherited a recombinant chromosome 10 with loss of the insertion and the segment distal to it [rec(10)der(pter-->p13: :q21.2-->p12.2::q22.1-->q26.3:)]. Mechanisms for both rearrangements are proposed.

Isodicentric Y chromosome: cytogenetic, molecular and clinical studies and review of the literature.

Dicentrics are among the most common structural abnormalities of the human Y chromosome. Predicting the phenotypic consequences of different duplications and deletions of dicentric Y chromosomes is usually complicated by varying degrees of mosaicism (45,X cell lines), which may, in some cases, remain undetected. Molecular studies in patients with dicentric Y chromosomes have been few, and only two studies have attempted to determine the presence of SRY (the putative testis-determining factor gene). We report an 18-year-old female with short stature, amenorrhea, hirsutism, hypoplastic labia minora, and clitoromegaly who has a 45,X/46,X,idic(Y)(p11.32)/47,X,idic(Y)(p11.32),idic(Y) (p11.32) karyotype. Southern analysis using Y-specific probes (Y97, 2D6, 1F5, pY3.4) and polymerase chain reaction (PCR) analysis using primers for ZFY and SRY were positive for all loci tested, indicating that almost all of the Y chromosome was present. Our findings and an extensive review of the literature emphasize the importance of molecular analyses of abnormal Y chromosomes before any general conclusions can be reached concerning the relative effects of the Y-chromosome abnormality and mosaicism on sexual differentiation.

Translocation 10;18 in a patient with juvenile neuronal ceroid-lipofuscinosis (Batten disease).

We report the first observation of a chromosome abnormality in a patient with typical juvenile ceroid-lipofuscinosis (NCL), who was found to have an apparently balanced translocation between chromosomes 10 and 18 [t(10;18)(q22.1;q21.1)]. Since juvenile NCL was previously mapped to 16p12, this report raises the possibility of heterogeneity in this form of NCL.

Identification of supernumerary ring chromosome 1 mosaicism using fluorescence in situ hybridization.

We report on a 15-year-old black boy with severe mental retardation, multiple congenital anomalies, and a supernumerary ring chromosome mosaicism. Fluorescence in situ hybridization with a chromosome 1 painting probe (pBS1) identified the ring as derived from chromosome 1. The karyotype was 46,XY/47,XY,+r(1)(p13q23). A review showed 8 reports of ring chromosome 1. In 5 cases, the patients had a non-supernumerary ring chromosome 1 resulting in partial monosomies of the short and/or long arm of chromosome 1. In 3 cases, the presence of a supernumerary ring resulted in partial trisomy of different segments of chromosome 1. In one of these cases the supernumerary ring was composed primarily of the centromere and the heterochromatic region of chromosome 1, resulting in normal phenotype. Our patient represents the third report of a supernumerary ring chromosome 1 resulting in abnormal phenotype.

Molecular characterization of a deleted X chromosome (Xq13.3-Xq21.31) exhibiting random X inactivation.

As a result of selection following random X chromosome inactivation in human females, X chromosomes with visible deletions are usually inactive in every somatic cell. We have studied a female with mental retardation and dysmorphic features whose karyotype includes an X chromosome with a visible interstitial deletion in the proximal long arm. Based on cytogenetic analysis, the proximal breakpoint appeared to be in band Xq13.1, and the distal one in band q21.3. However, molecular analyses show that less of the q13 band is missing than cytogenetic studies indicated, as the deletion includes only loci from the region Xq13.3 to Xq21.31. Unexpectedly, studies of chromosome replication show that the pattern of X inactivation is random. Whereas the deleted X chromosome is late replicating in some cells from all tissues studied, it is early replicating in the majority of blood lymphocytes and skin fibroblasts, and is the active X chromosome in many of the hybrids derived from skin fibroblasts. As this chromosome is able to inactivate, it must include those DNA sequences from the X-inactivation center (XIC) that are essential for cis X inactivation. Molecular studies show that the XIC region, at Xq13.2, is present, so it is unlikely that the lack of consistent inactivation of this chromosome is attributable to close proximity of the breakpoint to the XIC. Supporting this conclusion is the similarity of the breakpoints to those of the other chromosomes we studied, whose deletions clearly do not interfere with the ability to inactivate. Our results show that deletions distal to DXS441 in Xq13.2 do not interfere with cis X inactivation. We attribute the random pattern of X inactivation reported here to the fact that in the tissues studied, cells with this interstitial deletion are not at a selective disadvantage.

De novo dup (5p) in a patient with congenital hypoplasia of the adrenal gland.

We report on a black male child with congenital hypoplasia of the adrenal gland (CHA) with a de novo duplication of 5p [dir dup(5) (p13.3-->p15.1)], confirmed by fluorescence in situ hybridization (FISH). In addition to a characteristic clinical course, the patient has hyperpigmentation (melanoderma) since birth, normal external genitalia, marked elevation of ACTH, and absent response to an IV ACTH challenge. To the best of our knowledge, this is the first case of congenital hypoplasia of the adrenal gland associated with a chromosome abnormality. Reviews of dup (5p) and of our patient suggest that duplication of 5p13.3-pter has only minor phenotypic effect, while duplication of the relatively small critical segment p11-p13.2 apparently causes far more deleterious changes. The concurrence of CHA and dup(5p) in our patient may indicate the possible gene localization of an autosomal form of CHA to either at or near 5p13.3 or 5p15.1.

A rapid method for PCR amplification of DNA directly from cells fixed in Carnoy's fixative.

We describe a method for rapid and efficient polymerase chain reaction (PCR) amplification of specific target DNA sequences directly from cells fixed in 3:1 methanol-acetic acid (Carnoy's fixative) for routine cytogenetic analysis. The fixed cells used had been stored at -20 degrees C from a few weeks up to 6 years. Primer sets used correspond to loci on an autosome (retinoblastoma, RB1), as well as the X (Duchenne muscular dystrophy, DMD) and Y (sex-determining region of the Y, SRY) chromosomes. Sizes of amplified products were the expected 400, 251 and 609 bps, respectively. No differences in quality of amplification products were found between PCR templates obtained from fresh tissues or from cells fixed for varying lengths of time in Carnoy's fixative. This technique has the following advantages: (1) it allows retrospective studies of genetic disorders from archived specimens; (2) it requires only a limited number of cells; (3) it is rapid and simple; and (4) it avoids multistep procedures required in extraction of the DNA.

Lysosomal chitobiase (CTB) and the G-protein gamma 5 subunit (GNG5) genes co-localize to human chromosome 1p22.

Previously isolated human placental cDNA clones represent a fusion of specific RNA sequences encoded by two genes: lysosomal chitobiase (CTB) and G-protein gamma 5 subunit (GNG5, Fisher and Aronson, 1992a, 1992b). Both genes have now been mapped to 1p by PCR analysis of somatic cell hybrids and further refined to 1p22 by fluorescence in situ hybridization (FISH) using a YAC clone that contains both the chitobiase and gamma 5 genes.