Neocentromere marker chromosome of distal 3q mimicking dup(3q) syndrome phenotype.

Supernumerary marker chromosomes (SMCs) lacking alpha-satellite sequences and possessing a newly derived functional centromere are referred to as neocentromere marker chromosomes (NMCs). Although the delineation of the chromosome content of these NMCs would be helpful for genetic counseling, such fine mapping has been difficult because of the limited sizes of the involved segments. We report on a female patient with mosaic NMC involving 3q26.3-3qter, the content of which was determined using an array CGH analysis. Our results support the validity of an array CGH-based approach to investigating the origins of SMCs. Further FISH analyses revealed that the NMC is characterized by an asymmetric inv-dup structure separated by a single-copy region. The present case had many manifestations of dup(3q) syndrome, the critical interval of which is considered to be 3q26.3-q27. Common features included mental and growth retardation, hirsutism, synophrys, a broad nasal root, anteverted nares, downturned corners of the mouth, and malformed ears. The observation gives further credence to the concept that the critical region responsible for the dup(3q) phenotype to 3q26.3-q27.

A case of acute myeloblastic leukemia with a novel variant of t(8;21)(q22;q22).

We encountered a case of acute myeloblastic leukemia (AML), with extramedullary leukemia (EML) and a masked type of the variant translocation t(8;21)(q22;q22). Morphologically, the AML M2 subtype according to the French-American-British (FAB) classification was present. Phenotypically, leukemic cells were negative for CD19 and positive for CD56. Clinically, the case showed chemo-refractoriness and a poor outcome. The initial karyotypic interpretation was t(8;9)(q22;q34) on G-banding. Multiplex-fluorescence in situ hybridization (multiplex-FISH) analysis revealed a three-way translocation involving chromosomes 8, 9, and 21, and identified a masked type of variant t(8;21)q22;q22) translocation. The karyotype was finally determined as 45,X,-Y,der(8)t(8;21)(q22;q22), der(9)(8;9)(q22;q34), and der(21)t(9;21)(q34;q22). Results of FISH using the AML1/ETO probe and detection of the AML1/ETO fusion transcripts by reverse transcriptase-polymerase chain reaction (RT-PCR) support the karyotype as well as the sequence of the PCR product. Additionally, C-KIT mutation was detected.

Detection of the CBFB/MYH11 fusion gene in de novo acute myeloid leukemia (AML): a single-institution study of 224 Japanese AML patients.

The cytogenetic findings in acute myeloid leukemia (AML) are a powerful prognostic indicator. Among these abnormalities, the World Health Organization has classified inv(16)(p13q22), which is closely associated with the M4E classification in the French-American-British system, as indicating a good-risk AML. However, this chromosomal abnormality can often be difficult to detect. In this study, we used RT-PCR and FISH analysis to examine 224 Japanese adult de novo AML patients for the presence of the CBFB/MYH11 fusion transcript at the time of diagnosis. The CBFB/MYH11 fusion gene was detected in 17 patients (7.6%): eight patients had the inv(16) chromosome and in all of them it was M4E; nine patients did not have abnormalities in chromosome 16. AML with the CBFB/MYH11 fusion gene but without inv(16) was found in M2, M4, and M5, but not in M4E patients. There were no statistically significant differences in the clinical features of patients with the inv(16) and those with the cryptic inv(16) chromosome. These results indicate that even if eosinophilia is not found, molecular screening for CBFB/MYH11 fusion gene should be performed in all AML patients at the time of diagnosis to help guide disease management.

22q13 Microduplication in two patients with common clinical manifestations: a recognizable syndrome?

We report here on two unrelated patients (Patients 1 and 2) with a cryptic microduplication involving a 22q13 segment. Both patients manifested infantile hypotonia, developmental delay, and growth deficiency. In addition, an abnormal signal intensity area was detected in the frontal white matter of Patient 2 by brain MRI. Whole-genome microarray comparative genomic hybridization for Patient 1 and fluorescence in situ hybridization analysis with 22q-subtelomeric probes performed in both patients showed a submicroscopic 22q13 duplication that involved the SHANK3 gene. The duplication in Patient 1 was de novo type, while that in Patient 2 was derived from a familial 17;22 translocation. The presence of common clinical manifestations in the two patients with the common duplicated region led to a conclusion that 22q terminal duplication is a recognizable clinical entity, that is, the 22q13 microduplication syndrome.

FISH 1p/19q deletion/imbalance for molecular subclassification of glioblastoma.

Glioblastoma is the most malignant and frequent of the glial tumors. A minor fraction of glioblastoma may contain areas showing oligodendroglioma-like tumor cell differentiation. Several authors have described such tumors as glioblastoma with oligodendroglial component (GBMO). GBMO may represent the ultimate level of malignancy in the oligodendroglial lineage. The oligodendroglial component and combined loss of chromosomal arm 1p and 19q in glioblastoma indicate increased survival. In our study, we analyzed 1p and 19q status in a series of 12 glioblastoma and 8 oligodendroglial tumors using fluorescence in situ hybridization (FISH) on paraffin-embedded tissues. In each case, hybridization status was classified as deletion, imbalance, polysomy, amplification, or normal pattern. Other genetic alterations such as CDKN2A (p16), RB, and EGFR were also assessed. On histological review, 2 of 12 glioblastoma (16.7%) were classified as GBMO. Chromosome 1p/19q deletion was detected in 3 of 12 glioblastomas (25%). In contrast, all 8 oligodendroglial tumors showed 1p/19q deletion. All GBMO had 19q deletion with imbalance, whereas 1 of 10 ordinary glioblastoma (10%) demonstrated 19q deletion with imbalance. All but 1 ordinary glioblastoma (90%) showed CDKN2A (p16) deletion, but no GBMO displayed this alteration. Our results indicate that GBMO may be a distinct subtype of glioblastoma harboring a characteristic molecular profile. FISH on paraffin-embedded specimens is a useful method for subclassification of glioblastoma.

Screening for partial deletions in the CREBBP gene in Rubinstein-Taybi syndrome patients using multiplex PCR/liquid chromatography.

Rubinstein-Taybi syndrome (RTS, MIM 180849) is a multiple malformation syndrome characterized by growth retardation, developmental delay, and dysmorphic features, including down-slanting palpebral fissures, a beaked nose, broad thumbs, and halluces. Mutations in the gene encoding the CREB-binding protein gene (CREBBP, also known as CBP) on chromosome 16p13.3 were identified in 1995. Recently, we developed a mutation analysis protocol using denaturing high-performance liquid chromatography (DHPLC) and identified heterozygous CREBBP mutations in 12 of 21 RTS patients. To test whether exonic deletions represent a common pathogenic mechanism, we assessed the copy number of all the coding exons using a recently developed method, the multiplex PCR/liquid chromatography assay (MP/LC). By using MP/LC, we performed screening for CREBBP exonic deletions among 25 RTS patients in whom no point mutations or small insertions/deletions were identified by DHPLC screening. We identified four classic RTS patients with deletions encompassing multiple exons (14-16, 5-31, 1-16, and 4-26). We conclude that large deletions including several exons are a relatively frequent cause of RTS, and that MP/LC is an effective method for detecting these deletions.

Fluorescent in situ hybridization analysis of Philadelphia chromosome-negative chronic myeloid leukemia with the bcr/abl fusion gene.

This report describes a patient with Philadelphia chromosome-negative (Ph-) but bcr/abl fusion gene-positive chronic myeloid leukemia (CML) and a molecular analysis of the mechanisms behind the Ph status. Spectral karyotyping-fluorescent in situ hybridization (SKY-FISH) analysis showed no abnormal translocation; however, a bcr/abl fusion gene was detected by reverse transcriptase-polymerase chain reaction analysis. FISH analysis showed that signals from the 9q and 22q subtelomere probes were detected on the der(9) and der(22) chromosomes, respectively. On the other hand, FISH analysis of the abl and bcr genes with dual fusion probes, which can detect the bcr/abl fusion gene on both the der(9) and der(22) chromosomes, showed the signal for bcr/abl fusion on the der(22) chromosome but not on the der(9) chromosome. These results indicate that insertion of the abl gene into the bcr region on the der(22) chromosome or retranslocation between the der(9) chromosome and the der(22) chromosome may have caused the Ph CML in this case.

Fluorescent in situ hybridization 1p/19q deletion/imbalance analysis of low-grade and atypical meningiomas.

The chromosomal 1p/19q state was analyzed in 16 low-grade meningiomas and 7 atypical meningiomas using fluorescent in situ hybridization (FISH) analysis. Chromosome 1p aberrations were observed in all atypical meningiomas, but in only one low-grade meningioma. Atypical meningiomas showed 19q deletion or imbalance, suggesting chromosomal instability of 19q. A small group of low-grade meningioma showed 19q aberrations. FISH 1p/19q deletion/imbalance analysis is a sensitive method for detecting chromosome aberrations of meningiomas and provides useful information for grading of meningiomas. Patients with low-grade meningioma with chromosomal instability of 1p/19q should be followed up carefully. Assessment of the chromosomal state by FISH might be of crucial importance in the clinical management of meningiomas.

An Alu retrotransposition-mediated deletion of CHD7 in a patient with CHARGE syndrome.

CHD7 mutations account for about 60-65% among more than 200 CHARGE syndrome cases. When rare whole gene deletion cases associated with chromosomal abnormalities are excluded, all mutations of CHD7 reported to date have been point mutations and small deletions and insertions, rather than exonic deletions. To test whether exonic deletions represent a common pathogenic mechanism, we assessed exon copy number by using a recently developed method, the multiplex PCR/liquid chromatography assay (MP/LC). Multiple exons were amplified using unlabeled primers, then separated by ion-pair reversed-phase high-performance liquid chromatography, and quantitated by fluorescence detection using a post-column intercalation dye under the premise that the relative peak intensities for each target directly reflect exon copy number. By using MP/LC, we identified one CHARGE syndrome patient who had a de novo deletion encompassing exons 8-12 among 13 classic CHARGE patients in whom screening by denaturing high-performance liquid chromatography (DHPLC) failed to identify point mutations and small insertions/deletions in CHD7. This is the first CHARGE patient who was documented to have exonic deletion of CHD7. The deletion closely recapitulated the Alu-mediated inactivation of the human CMP-N-acetylneuraminic acid hydroxylase gene (CMP-Neu5Ac hydroxylase), which is regarded as a novel molecular mechanism in the evolution from non-human primates to humans. As demonstrated in this study, MP/LC is a promising method for characterizing exonic deletions, which are largely left unexamined in most routine mutation analysis.