Refining the 22q11.2 deletion breakpoints in DiGeorge syndrome by aCGH.

Hemizygous deletions of the chromosome 22q11.2 region result in the 22q11.2 deletion syndrome also referred to as DiGeorge, Velocardiofacial or Shprintzen syndromes. The phenotype is variable but commonly includes conotruncal cardiac defects, palatal abnormalities, learning and behavioral problems, immune deficiency, and facial anomalies. Four distinct highly homologous blocks of low copy number repeat sequences (LCRs) flank the deletion region. Mispairing of LCRs during meiosis with unequal meiotic exchange is assumed to cause the recurrent and consistent deletions. The proximal LCR is reportedly located at 22q11.2 from 17.037 to 17.083 Mb while the distal LCR is located from 19.835 to 19.880 Mb. Although the chromosome breakpoints are thought to localize to the LCRs, the positions of the breakpoints have been investigated in only a few individuals. Therefore, we used high resolution oligonucleotide-based 244K microarray comparative genomic hybridization (aCGH) to resolve the breakpoints in a cohort of 20 subjects with known 22q11.2 deletions. We also investigated copy number variation (CNV) in the rest of the genome. The 22q11.2 breaks occurred on either side of the LCR in our subjects, although more commonly on the distal side of the reported proximal LCR. The proximal breakpoints in our subjects spanned the region from 17.036 to 17.398 Mb. This region includes the genes DGCR6 (DiGeorge syndrome critical region protein 6) and PRODH (proline dehydrogenase 1), along with three open reading frames that may encode proteins of unknown function. The distal breakpoints spanned the region from 19.788 to 20.122 Mb. This region includes the genes GGT2 (gamma-glutamyltransferase-like protein 2), HIC2 (hypermethylated in cancer 2), and multiple transcripts of unknown function. The genes in these two breakpoint regions are variably hemizygous depending on the location of the breakpoints. Our 20 subjects had 254 CNVs throughout the genome, 94 duplications and 160 deletions, ranging in size from 1 kb to 2.4 Mb. The presence or absence of genes at the breakpoints depending on the size of the deletion plus variation in the rest of the genome due to CNVs likely contribute to the variable phenotype associated with the 22q11.2 deletion or DiGeorge syndrome.

Accumulation of methotrexate and methotrexate polyglutamates in lymphoblasts and treatment outcome in children with B-progenitor-cell acute lymphoblastic leukemia: a Pediatric Oncology Group study.

We reported that children with B-progenitor-cell acute lymphoblastic leukemia (BpALL) treated in the early 1980s whose lymphoblasts accumulated high levels of methotrexate (MTX) and of methotrexate polyglutamates (MTXPGs) in vitro had an improved 5-year event-free survival (EFS) (65% (standard error (s.e.) 12%) vs 22% (s.e. 9%)). We repeated this study in children with BpALL treated in the early 1990s. The major change in treatment was the addition of 12 24-h infusions of 1 g/M2 MTX with leucovorin rescue (IDMTX). In 87 children treated on Pediatric Oncology Group (POG) study 9005 and POG 9006, the 5-year EFS for those whose lymphoblasts accumulated high levels of MTX and MTXPGs (79.2%, s.e. 8.3%) was not significantly different from that of patients with lesser accumulation of MTX and MTXPGs (77.7%, s.e. 5.4%). These findings support the notion that higher dose MTX therapy has contributed to increased cure, particularly for patients whose lymphoblasts accumulate the drug less well.

Immunohistochemical determination of HER-2/neu expression in invasive breast carcinoma.

Numerous methods exist for HER-2/neu assessment; however, technical and interpretive standardization is virtually absent. We evaluated 2 commercially available antibodies on routinely fixed paraffin-embedded tissue sections to establish our own guidelines. Thirty-three cases of infiltrating breast carcinoma were evaluated simultaneously with monoclonal and polyclonal antibodies. Only membranous staining, no matter how focal, was considered positive. An additional 32 tumors were studied subsequently using only the polyclonal antibody. Of all carcinomas, 13.0% showed immunohistochemical evidence of HER-2/neu overexpression. High-grade tumors were more often positive. There was no HER-2/neu gene expression in the benign epithelium that generally was present in the tissue section or in any of the well-differentiated tumors tested. The polyclonal antibody proved more sensitive than the monoclonal antibody. While true cytoplasmic staining was present occasionally, it did not create substantial difficulty in interpretation. The polyclonal antibody cost substantially less than the monoclonal antibody. Fluorescence in situ hybridization assay for HER-2/neu gene amplification performed on 32 of 65 cases showed concordant results in 31 cases. The immunohistochemical assay for HER-2/neu gene overexpression, using our methods, is accurate, economic, and easily integrated into the laboratory.

Cytogenetic analysis of 120 primary pediatric brain tumors and literature review.

We report chromosome results from 108 pediatric central nervous system (CNS) tumors. From our data and those in the literature we found that (1) cerebellar and low-grade astrocytic tumors, including gangliogliomas, are most often karyotypically normal; (2) supratentorial tumors were more frequently high-grade tumors that demonstrated a complex karyotype. Chromosome abnormalities were similar to those described in adult astrocytic tumors, namely, +7, 9p abnormalities, and -10; (3) primitive neuroectodermal tumors (PNETs) were virtually always karyotypically abnormal with a high frequency of +7, -8, i(17q), and -22. PNETs with -22 may represent a subset of tumors; (4) typical choroid plexus papillomas showed a normal karyotype, atypical papillomas showed a hyperdiploid karyotype (with +7, +12, and +20), choroid plexus carcinomas showed a hyperhaploid karyotype; (5) a few ependymomas showed hyperdiploidy or hypertetraploidy; (6) germ cell tumors showed complicated karyotypes; (7) monosomy 22 or 22q abnormalities appear to be a recurring finding in the malignant rhabdoid tumors; and (8) meningiomas showed -22 or 22q abnormalities associated with a complex karyotype. In general, in pediatric CNS tumors the least differentiated neoplasms have the greatest number of cytogenetic abnormalities. However, our present morphologic criteria for tumor diagnosis do not always correlate with a consistent karyotype, and further study of pediatric brain tumor morphology, site, behavior, and karyotype is required.

Cytogenetic characterization of three human and three rat medullary thyroid carcinoma cell lines.

Medullary thyroid carcinoma (MTC) is a neuroendocrine tumor of the thyroid C-cells. MTC may arise as a sporadic tumor or as a component of one of three autosomal dominant familial cancer syndromes, MEN 2A, MEN 2B, or familial MTC. Recent studies have identified mutations of the RET proto-oncogene in the proximal long arm of chromosome 10, which are thought to be causative for these syndromes. To facilitate the search for other genes involved in the development of MTC, we characterized cytogenetically three human MTC cell lines and three rat MTC cell lines. The human cell lines studied were TT and RO-H85-1, previously reported, and an uncharacterized cell line, MZ-CRC-1, derived from a malignant pleural effusion from a patient with metastatic MTC. The rat MTC cell lines characterized were CA-77, 6-23C6, and 44-2. Cytogenetic abnormalities present in the human and rat cell lines were compared with 13 reported cytogenetic studies of human MTC tumors and three other cytogenetically analyzed MTC cell lines. The human 9q/rat 3 and human 3p/rat 15 chromosomes were affected in six of the comparable cell lines and tumors. These findings suggest human chromosome regions 9q and 3p may contain genes involved in the pathogenesis of MTC.

Infant cardiac fibroma with clonal t(1;9)(q32;q22) and review of benign fibrous tissue cytogenetics.

Cardiac fibromas are rare lesions which occur more frequently in infants and children than in the adult population. These tumors are nonmalignant proliferations of connective tissue most often found in the left ventricular myocardium or septal myocardium. No cytogenetic studies of cardiac fibromas have been reported. We report a case of an infant with a subepicardial tumor in whom the cytogenetic analysis showed a clonal reciprocal translocation, 46,XY,t(1;9)(q32;q22),inv(9)(p11q12)c. We review the literature regarding cardiac fibromas and briefly discuss the cytogenetics of benign fibrous neoplasias.

Cytogenetic analysis of a scapular chondromyxoid fibroma.

Chondromyxoid fibroma (CMF) is a rare cartilaginous tumor of bone. It typically presents in the lower extremities of young males. Cytogenetic analysis of two chondromyxoid fibromas has been previously reported. We studied a scapular CMF from an 11-year-old female by cytogenetic and molecular cytogenetic methods and found an unbalanced reciprocal translocation between the short arm of chromosome 3 and the long arm of chromosome 6. In this translocation, several bands from chromosome 3 (3p12, 3p13, 3p14, 3p21) are lost and several bands on chromosome 6 (6q21, 6q22, 6q23) appear rearranged. Two known cartilage-related genes are located in the regions affected by this unbalanced rearrangement: the type X collagen gene (COL10A1) located at 6q21-q22 and the parathyroid hormone/parathyroid hormone-related peptide receptor gene (PTH/PTHrP) located at 3p21.1-p22. These genes function to control growth and maturation of endochondral bone, the site of origin of cartilaginous tumors.

Detection of double minute chromosomes in a child with acute lymphoblastic leukemia.

A child with acute lymphoblastic leukemia (ALL) whose predominant leukemic clone demonstrated double minute chromosomes (dmin) is presented. The patient had no history of mutagen or carcinogen exposure and responded well to combination chemotherapy. Although dmin have been described in acute myelogenous leukemia and various solid tumors in adults, their presence in childhood neoplasms is less frequent and limited primarily to neurogenic tumors. This is the first documentation of dmin in childhood ALL, suggesting that there may be an unrecognized subgroup of ALL patients with gene amplification.

Accumulation of methotrexate polyglutamates, ploidy and trisomies of both chromosomes 4 and 10 in lymphoblasts from children with B-progenitor cell acute lymphoblastic leukemia: a Pediatric Oncology Group Study.

Levels of accumulation of methotrexate polyglutamates were measured in vitro in lymphoblasts obtained at diagnosis from children with B-progenitor cell acute lymphoblastic leukemia (pro-B ALL). They were compared to numerical and structural chromosomal abnormalities present in these leukemic cells. In a series of 95 patients, the percent with high lymphoblast methotrexate polyglutamate levels increased with the increase in modal number of total chromosomes (p<0.001). Thus, lymphoblast methotrexate polyglutamate accumulation appeared to be closely linked to the extent of hyperdiploidy in childhood pro-B ALL. Lymphoblasts from 35 (88%) of the 40 children with hyperdiploid (>50 chromosomes) and 23 (88%) of 26 with hyperdiploid (DNA Index >1.16) pro-B ALL accumulated high levels of methotrexate polyglutamate, suggesting that they were more sensitive to methotrexate cytotoxicity. While children with hyperdiploid (DNA Index >1.16) pro-B ALL have a good prognosis, those with trisomies of both chromosomes 4 and 10, almost all of whom are hyperdiploid, have an even better outcome. There was no significant difference in methotrexate polyglutamate levels in lymphoblasts from 19 children with and 21 without trisomies of both chromosomes 4 and 10 (p = 0.25). The improved response to multi-agent chemotherapy conferred by the presence of trisomies of both chromosomes 4 and 10 in such patients may be due to increased sensitivity of their lymphoblasts to one or more anti-leukemic agents in addition to methotrexate.

Malignant meningioma in Gorlin's syndrome: cytogenetic and p53 gene analysis. Case report.

Gorlin's syndrome, also known as multiple basal cell carcinoma syndrome, is a familial tumor condition with autosomal-dominant inheritance. Patients develop multiple basal cell carcinomas beginning in childhood. They also have a typical dysmorphic facies, skeletal malformations, and a particular type of epithelial cyst of the jaws. Recent evidence localizes a Gorlin's syndrome locus on chromosome 9 at band q31. Both tumors and malformations of the central nervous system occur with Gorlin's syndrome. Medulloblastoma is the primary brain tumor most frequently associated with this syndrome; over 40 such cases have been reported. However, only seven cases of meningioma associated with Gorlin's syndrome have been described. The authors report the case of a woman with Gorlin's syndrome whose mother and maternal grandfather also had the condition. The patient was found to have a medulloblastoma at 4 years of age and presented with a large bifrontal meningioma at 19 years of age. The meningioma was histologically malignant and had a complex karyotype with multiple translocations including a t(5;9) with the breakpoint on chromosome 9 located at 9q32. The constitutional karyotype of the mother was normal. No mutations of exons 5 to 9 of the p53 gene were detected using single-stranded conformational polymorphism analysis.

Isotretinoin therapy for recurrent respiratory papillomatosis.

Retinoic acid has been advocated for use in several premalignant and malignant epithelial lesions of the head and neck, including benign recurrent respiratory papillomatosis, with varying results. We describe a 24-year-old man with extensive tracheoesophageal and bronchoalveolar papillomatosis that degenerated into squamous cell carcinoma. Multiple endoscopic carbon dioxide laser excisions, at one point performed on a weekly basis, as well as a prolonged trial of interferon, failed to control the progression of his disease. Isotretinoin (13-cis-retinoic acid) therapy (1 mg/kg per day) was instituted, with dramatic clinical, radiographic, and functional improvement. The patient experienced no significant toxic effects and required no endoscopic procedures over a 6-month period. We propose that isotretinoin may be an effective adjuvant therapy for aggressive respiratory papillomatosis.

Malignant peripheral nerve sheath tumor with a t(X;18).

We describe an ankle tumor arising in a 16-year-old girl. The tumor demonstrated histology typical of a malignant peripheral nerve sheath tumor (MPNST), but exhibited a variant form of the (X;18) translocation associated with synovial sarcoma. Immunohistochemical stains were positive for vimentin, CD57, collagen type IV, and Bcl-2. Routine and molecular cytogenetic studies showed an unbalanced 3-way chromosomal translocation that involved chromosomes X, 18, and 1. Electron microscopic findings were noncontributory. This unusual tumor raises the following questions and possibilities: (1) As the t(X;18) suggests, could this tumor be a monophasic synovial sarcoma with the histologic features of an MPNST? (2) Or, as the histology suggests, is this tumor an MPNST that has a t(X;18)? (3) Finally, could MPNST histology, a t(X;18), and no defining immunohistochemical or electron microscopic features represent an as yet unrecognized part of a spectrum that spans from synovial sarcoma to MPNST or other spindle cell tumors?

Pilot studies for proficiency testing using fluorescence in situ hybridization with chromosome-specific DNA probes: a College of American Pathologists/American College of Medical Genetics Program.

Fluorescence in situ hybridization using chromosome-specific DNA probes is rapidly becoming part of clinical laboratory practice for certain congenital and neoplastic disorders. Current legislation requires proficiency testing for clinical laboratory studies. To evaluate the efficacy of fluorescence in situ hybridization proficiency testing, we invited 19 representative institutions to participate in three pilot studies. One study used probes for the X and Y chromosomes to evaluate metaphase spreads and interphase nuclei. Another study used probes for bcr and abl to detect bcr/abl fusion in interphase nuclei in chronic myelogenous leukemia. The third study used a D22S75 probe to detect microdeletions in metaphase spreads from a patient with velocardiofacial syndrome. The results of these studies demonstrate that proficiency testing with fluorescence in situ hybridization is attainable using either metaphase or interphase preparations, and that either microscope slides or fixed cell pellets are suitable.

Extensive analysis of mosaicism in a case of Turner syndrome: the experience of 287 cytogenetic laboratories. College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee.

OBJECTIVE: To assemble and interpret karyotype data provided as part of the College of American Pathologists/American College of Medical Genetics Cytogenetics Proficiency Testing Program. DATA SOURCES, EXTRACTION, AND SYNTHESIS: The Cytogenetics Resource Committee requested data on all cells analyzed in a 1994 whole-blood specimen challenge. In that study, 287 participating laboratories analyzed a total of 14297 cells derived from a sample drawn from an adult donor with Turner syndrome. This individual had previously been found to have mosaicism, including cell lines with X structural anomalies along with monosomy X, making this an excellent challenge for a multicenter cytogenetic survey. RESULTS AND CONCLUSIONS: Analysis of the data from this extensive study revealed mosaicism of up to 10 different sex chromosome complements involving the X chromosome with and without a small ring X or a derivative X chromosome. In the routine cytogenetic analysis performed by the participating laboratories, cell lines observed, in decreasing order of prevalence, included 45,X (n = 8357 cells), 46,X,r(X) (n = 3597), 46,X,der(X)t(X;X) (n = 2237), 46,XX (n = 93), 47,X,r(X),r(X) (n = 5), 47,X,der (X)t(X;X),der(X)t(X;X) (n = 3), 47,XX,r(X) (n = 2), and one observation each of 47,XX,der(X)t(X;X), 47,X,der(X)t (X;X),r(X), and 47,XXX. Our molecular cytogenetic data, as well as detailed analysis of G-banded chromosomes, suggest the nomenclature for these 2 abnormal X chromosomes as r(X)(p11.3q21.3) and der(X)t(X;X)(p11.3;q21.3), and we discuss models for the concomitant formation of these 2 entities. Both the degree of analysis and the extensive mosaicism that was discovered in this study are exceptional, and similar reported cases as well as possible mechanisms for the observed X chromosome instability are reviewed.

Inversion of two-band superconductivity at the critical electron doping of (Mg, Al)B2.

Electron energy-loss spectroscopy (EELS) was combined with heat capacity measurements to probe changes of electronic structure and superconductivity in Mg(1-x)Al(x)B(2). A simultaneous decrease of EELS intensity from sigma-band hole states and the magnitude of the sigma gap was observed with increasing x, thus verifying that band filling results in the loss of strong superconductivity. These quantities extrapolated to zero at x approximately 0.33 as inferred from the unit cell volume. However, superconductivity was not quenched completely, but persisted with T(c) < 7 K up to about x approximately 55. Only the pi band had detectable density of states for 0.33 < or =x < or = 0.55, implying an inversion of the two-band hierarchy of MgB(2) in that regime. Since pi-band superconductivity is active in other materials such as intercalated graphite, implications for new materials with high T(c) are discussed.

"PCR karyotype" of monochromosomal somatic cell hybrids.

Following fusion of human diploid fibroblast-derived microcells with mouse A9 cells, we isolated seven monochromosomal hybrids containing a single human chromosome 2, 3, 5, 12, 15, 20, or 22. Cytogenetic analysis as well as PCR karyotyping (chromosome-specific banding pattern generated by Alu-PCR) was performed on all the hybrids. We here present, for the first time, the specific PCR karyotypes of human chromosomes 2 and 20.

Cytogenetic demonstration of gene amplification in a primary intracranial germ cell tumor.

We report the cytogenetic analysis of a primary pineal germinoma. The modal chromosome number was 81. Multiple numerical and structural chromosome abnormalities were noted along with a large homogeneously staining region (HSR). No isochromosome 12p was identified.

Pancytopenia with chromosomal fragility: vitamin B12 deficiency.

PURPOSE: Pancytopenia in children may have many etiologies. Chromosomal abnormalities with pancytopenia is of particular concern because clonal abnormalities indicate a neoplastic process. We describe three children who had vitamin B12 deficiency and who displayed pancytopenia with multiple chromosomal breaks, rearrangements, and deletions consistent with chromosomal fragility. Severe vitamin B12 deficiency is rare in children and should be considered in the differential diagnosis of a child with pancytopenia, dyserythropoiesis, and multiple chromosomal abnormalities. PATIENTS AND METHODS: Three children displayed pancytopenia with dyserythropoiesis in the bone marrow. Routine cytogenetic analyses in all three patients were performed and chromosome breakage study was performed on the peripheral blood of one patient after vitamin B12 supplementation. RESULTS: All three patients had severe vitamin B12 deficiency. Spontaneous chromosomal fragility was seen in routine cytogenetic analyses in all three patients. Vitamin B12 supplementation resolved the pancytopenia in all three patients and spontaneous and diepoxybutane-induced breakage rates in chromosomes were well within normal rates after therapy in one patient. CONCLUSION: The presence of pancytopenia with cytogenetic abnormalities in a child is worrisome. However, careful interpretation of dyserythropoiesis and megaloblastic changes in bone marrow in the aforementioned clinical situation would result in the correct diagnosis of a disorder that is easily cured.

The first recurring chromosome translocation in hepatoblastoma: der(4)t(1;4)(q12;q34).

We report four cases of hepatoblastoma with a derivative chromosome 4 from an unbalanced translocation between the long arms of chromosomes 1 and 4, an aberration reported only rarely in isolated cases of other types of neoplasms. The abnormality in three hepatoblastomas was der(4)t(1;4)(q12;q34), whereas the fourth case appeared to have a der(4)t(q25;q32). All had hyperdiploid tumor karyotypes; however, in the case with t(q25;q32), the der(4) was the only abnormality in the stemline. We speculate that the oncogenetic event in our cases may be the loss of a gene on distal 4q or their alteration by juxtaposition to 1q12 heterochromatin.