Chromosome 15q11-q13 copy number gain detected by array-CGH in two cases with a maternal methylation pattern

Background

The 15q11-q13 region contains many low copy repeats and is well known for its genomic instability. Several syndromes are associated with genomic imbalance or copy-number-neutral uniparental disomy. We report on two patients: Patient 1 is a boy with developmental delay and autism; and Patient 2 is a girl with developmental delay, hypotonia and dysmorphism. We performed analyses to delineate their dosage in the 15q region, determine whether the patients’ dosage correlates with phenotypic severity, and whether genes in the amplified regions are significantly associated with identified functional networks.

Results

For the proximal region of 15q, molecular cytogenetic analysis with Agilent oligonucleotide array showed a copy number of 3 for Patient 1 and a copy number of 4 for Patient 2. Fluorescent in situ hybridization analysis of Patient 2 showed two different populations of cells with different marker chromosomes. Methylation analysis of the amplified region showed that the extra copies of small nuclear ribonucleoprotein polypeptide N gene were of maternal origin. Phenotypic severity did not correlate with the size and dosage of 15q, or whether the amplification is interstitial or in the form of a supernumerary marker. Pathway analysis showed that in Patient 2, the main functional networks that are affected by the genes from the duplicated/triplicated regions are developmental disorder, neurological disease and hereditary disease.

Conclusions

The 15q11-q13 gains that were found in both patients could explain their phenotypic presentations. This report expands the cohort of patients for which 15q11-q13 duplications are molecularly characterized.

Molecular Cytogenetic Characterization of an inv(Y)(p11.2q11.221∼q11.222) in a Syrian Family

Constitutional chromosomal abnormalities are an important cause of miscarriage, infertility, congenital anomalies and mental retardation in humans. Pericentric inversions of the human Y-chromosome [inv(Y)] are rather common and show an estimated incidence of 0.6–1:1,000 in males in the general population. Most of the reported cases with inv(Y) are familial. For carriers of pericentric inversions the risk of mental retardation or multiple abortions is not apparently increased and there is no relation with abnormal phenotypic features. Polymerase chain reaction (PCR) analysis to detect microdeletions along the Y-chromosome as well as cytogenetic and fluorescence in situ hybridization (FISH) analysis were done to delineate the characteristics of an inv(Y) in a Syrian family. Thus, we present a detailed molecular-cytogenetic characterization of a father and his two sons having an inv(Y)(p11. 2q11.221∼q11.222) with varying mental retardation features but otherwise normal phenotype.

Do novo del(9)(p13) in a childhood T-cell prolymphocytic leukemia as sole abnormality

T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive subtype of chronic lymphocytic leukemia. Usually it presents in older people with a median age of 61 years. T-PLL is characterized by elevated white blood cell (WBC) count with anemia and thrombocytopenia, hepatosplenomegaly, and lymphadenopathy; less common findings are skin infiltration and pleural effusions. The most frequent chromosomal abnormalities in T-PLL include 14q11.2, chromosome 8, and 11q rearrangements. Also deletions in the short arm of a chromosome 9 are reported in ~30% of T-PLL together with other aberrations. Here we report a childhood T-PLL case with a de novo del(9)(p13) as sole acquired anomaly leading to monosomy of the tumor suppressor gene CDKN2A (cyclin-dependent kinase inhibitor 2A). Also, to the best of our knowledge this is the first case of a childhood T-PLL with this aberration.

Diagnostic method for the detection of KIF5B-RET transformation in lung adenocarcinoma

KIF5B-RET fusions have recently been reported to occur in pulmonary adenocarcinomas, thereby being proposed as a novel genetic alteration in adenocarcinoma of the lung. However, clinically useful methods to detect RET-rearrangement in pulmonary adenocarcinoma have not been well established. 53 cases of lung adenocarcinomas harbored "triple (EGFR, KRAS and ALK)-negative" were tested for KIF5B-RET fusions using whole-transcriptome sequencing, fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and long-range PCR. Dual color break-apart probes and KIF5B-RET fusion probes were used for FISH. Three different commercial antibodies against C-terminal RET protein were tested for IHC. Primers designed for 3 different variants of KIF5B-RET fusions were used for long-range PCR. Three patients (5.6%) showed RET rearrangement in whole-transcriptome sequencing, which were used as a gold standard. All those three patients were also positive in FISH for both KIF5B-RET fusion and RET break-apart probes. None of remaining patients showed positive result, resulting in 100% concordance rate of FISH and transcriptome sequencing methods. However, fused RET proteins were not detected by IHC in none of true positive patients. Moreover, 6 patients without RET fusions showed gain of gene copy number of both KIF5B and RET. All those three true positive cases were detected by long-range PCR methods and none with true negative cases were positive. Both FISH and PCR may be useful methods to detect novel KIF5B-RET rearrangements in pulmonary adenocarcinomas rather than IHC. However, as there may be additional variant of fusion mutation, FISH may be better than PCR method in terms of sensitivity.

Anaplastic lymphoma kinase (ALK) gene rearrangement in non-small cell lung cancer (NSCLC): results of a multi-centre ALK-testing

BACKGROUND

The reliable identification of non-small cell lung cancers (NSCLC) with chromosomal breaks in the gene of the anaplastic lymphoma kinase (ALK) is crucial for the induction of therapy with ALK-inhibitors. In order to ensure a reliable detection of ALK-breaks by means of fluorescence in situ hybridization (FISH) testing, round robin tests are essential. In preparation of a nation (German)-wide round robin test we initiated a pre-testing phase involving 8 experts in FISH-diagnostics to identify NSCLC cases (n = 10) with a pre-tested ALK-status. In addition, ALK immunohistochemistry (IHC) was performed to assess ALK protein expression.

MATERIAL AND METHODS

Sections derived from a tissue microarray, each consisting of 3 cores from 10 NSCLC cases, were independently tested for ALK protein expression by IHC and genomic ALK-breaks by FISH involving 8 institutes of pathology. Based on a pre-screening, 5 cases were identified to be clearly ALK-break negative, whereas the remaining 5 cases were ALK-break positive including one case with low percentage (20%) of positive cells. The latter had been additionally tested by RT-PCR.

RESULTS

The 5 unequivocal ALK-break negative NSCLC were almost consistently scored negative by means of FISH and IHC by all 8 experts. Interestingly, 4 of the 5 cases with pre-defined ALK-breaks revealed homogenous FISH results whereas IHC for the detection of ALK protein expression showed heterogeneous results. The remaining case (low number of ALK-break positive cells) was scored negative by 3 experts and positive by the other 5. RT-PCR revealed the expression of an EML4-ALK fusion gene variant 1.

CONCLUSION

ALK-break negative NSCLC cases revealed concordant homogeneous results by means of FISH and IHC (score 0-1) by all 8 experts. Discordant FISH results were raised in one ALK-break positive case with a low number of affected tumor cells. The remaining 4 ALK-break positive cases revealed concordant FISH data whereas the ALK-IHC revealed very diverse results. The cases with concordant FISH results provide an excellent basis for round robin ALK-FISH testing. As long as standardized ALK-IHC protocols are missing, ALK protein expression cannot by regarded as the method of choice for identification of patients eligible for treatment with ALK inhibitors.

Comprehensive characterization of genomic instability in pluripotent stem cells and their derived neuroprogenitor cell lines

The genomic integrity of two human pluripotent stem cells and their derived neuroprogenitor cell lines was studied, applying a combination of high-resolution genetic methodologies. The usefulness of combining array-comparative genomic hybridization (aCGH) and multiplex fluorescence in situ hybridization (M-FISH) techniques should be delineated to exclude/detect a maximum of possible genomic structural aberrations. Interestingly, in parts different genomic imbalances at chromosomal and subchromosomal levels were detected in pluripotent stem cells and their derivatives. Some of the copy number variations were inherited from the original cell line, whereas other modifications were presumably acquired during the differentiation and manipulation procedures. These results underline the necessity to study both pluripotent stem cells and their differentiated progeny by as many approaches as possible in order to assess their genomic stability before using them in clinical therapies.