Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization to detect chromosomal abnormalities in chronic lymphocytic leukemia: a comparative study

Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease characterized by recurrent chromosomal aberrations of prognostic significance. We aimed to evaluate the potential of the multiplex ligation-dependent probe amplification (MLPA) assay to detect genomic alterations in CLL. Highly purified (>90%) peripheral mononuclear CD19+ cell populations from 100 untreated CLL patients (pts) in early stage disease (Binet stage A) were included in this study. All samples were investigated by fluorescence in situ hybridization (FISH) for the presence of trisomy 12 and 17p13.1, 11q22.3, and 13q14.3 deletions. For MPLA analysis, DNA was amplified by means of two commercially available probes sets allowing the simultaneous screening of 56 genomic sequences. Overall, a high degree of concordance (95%) between MPLA and FISH results was found, if the abnormal clone was present in more than 30% of the leukemic cell population. The use of multiple MPLA probes allowed the fine-mapping of the 13q14 deletion and the identification of intragenic or small alterations undetected by FISH. Moreover, additional alterations in 2p24 (MYCN) (3 pts), 8q24 (MYC) (1 pt), 9p21 (CDKN2A2B) (1 pt), 1q21 (LMNA) (1 pt), and 6q25-26 (1 pt) regions not covered by a standard FISH assay were detected and all confirmed by FISH. Our data extend previously limited evidence that MLPA may represent a useful technique for the characterization of well-known lesions as well as the investigation of additional genomic changes in CLL.     

Clonal profiling of mixed lobular and ductal carcinoma revealed by multiplex ligation‐dependent probe amplification and fluorescence in situ hybridization

A needle biopsy of a mass in the right breast of a 36‐year‐old woman revealed invasive ductal carcinoma (IDC), and approximately 20% of cancer cells showed unequivocal membranous staining with the HercepTest. After systemic therapy with trastuzumab and paclitaxel followed by FEC (fluorouracil + epirubicin + cyclophosphamide), a right mastectomy was performed. By histological and immunohistochemical examinations, the resected tumor consisted mainly of E‐cadherin‐negative invasive lobular carcinoma (ILC), and the rest was ERBB2‐positive IDC; thus, the diagnosis was mixed ductal and lobular carcinoma. Multiplex ligation‐dependent probe amplification and fluorescence in situ hybridization (FISH) analyses revealed that ILC and IDC shared high‐level amplification of CCND1 in homogeneously staining regions (HSR) and that IDC had an additional HSR‐type amplicon of ERBB2. These findings strongly indicate that IDC and ILC had a common precursor cell with CCND1 amplification. Review of the biopsy specimen with FISH showed IDC with gene amplifications of CCND1 and ERBB2 as a minor component, IDC without amplification of CCND1 or ERBB2 as a major component, and a minute portion of ILC with CCND1 amplification. We speculate that chemotherapy and trastuzumab caused a marked reduction in IDC; however, ILC with CCND1 amplification was resistant to chemotherapy and grew.     

Overexpression and gene amplification of both ERBB2 and EGFR in an esophageal squamous cell carcinoma revealed by fluorescence in situ hybridization,multiplex ligation‐dependent probe amplification and immunohistochemistry

EGFR and ERBB2 belong to the EGFR gene family. In esophageal squamous cell carcinomas (SCCs), amplification of EGFR or ERBB2 is usually mutually exclusive. EGFR amplification occurs in approximately 15% of SCCs, ERBB2 occurs in less than 5%. Here, we report the co‐amplification of EGFR and ERBB2 in an ulcerative and infiltrating‐type SCC that measured approximately 4.2 × 2.7 × 1.2 cm with a superficial lesion occurring in the thoracic esophagus of a 72‐year‐old man. Multiplex ligation‐dependent probe amplification using representative tumor sections showed gain of CCND1 and coincident amplification of ERBB2 or EGFR or neither. Immunohistochemistry and fluorescence in situ hybridization revealed that the tumor comprised three cancer‐cell populations: well‐differentiated SCC with high‐level ERBB2 amplification and ERBB2 overexpression, more infiltrative poorly‐differentiated SCC with high‐level EGFR amplification and EGFR overexpression, and poorly‐differentiated SCC lacking any ERBB2 or EGFR abnormality. These three populations each had low‐level CCND1 amplification and nuclear cyclin D1 overexpression. This histological topology and gene amplification combinations suggested that genetic instability first produced CCND1 amplification, and then ERBB2 or EGFR gene amplification occurred. It is further speculated that during cancer progression and clonal selection indecisive predominance of either clone caused the rare co‐amplification of ERBB2 and EGFR in a single chimeric tumor.     

First‐trimester spontaneous pregnancy loss – molecular analysis using multiplex ligation‐dependent probe amplification

Spontaneous miscarriages are the most frequent complications of pregnancy and, in at least half of cases, are caused by chromosomal abnormalities, mainly aneuploidies. We present the preliminary results of the implementation of multiplex ligation‐dependent probe amplification (MLPA) in the detection of chromosomal aberrations in the tissue derived from first‐trimester miscarriage and evaluate the limitations and requirements of the method. We studied 181 MLPA analyses with subtelomeric and subcentromeric probe kits for all chromosomes (SALSA P070 and SALSA P181) performed on the first‐trimester spontaneous miscarriage products in our Department of Genetics between September 2012 and December 2014. Conclusive MLPA results were obtained in 97.2% of samples. Chromosomal aberrations were detected in 40.3% of samples: 61.8% samples of good quality and 12.6% samples of poor quality (p < 0.001). The normal female karyotype was detected in 14.7% of good quality samples and 84.8% of poor quality samples (p < 0.001). MLPA is a useful tool for the detection of chromosomal aberrations in first‐trimester miscarriage products. However, the tissue has to be well prepared before testing and the results 46,XX should be interpreted with caution.     

Combined cytogenetic testing and fluorescence in situ hybridization analysis in the study of chronic lymphocytic leukemia and multiple myeloma

We investigated the usefulness of fluorescence in situ hybridization (FISH) panels when testing for chromosomal aberrations of known prognostic significance in chronic lymphocytic leukemia (CLL) and multiple myeloma (MM). Our CLL panel included probes for 11q, 12 centromere, 13q, 14, and 17p. Karyotype and FISH were abnormal in 13 of 60 (21.6%) cases, two (3.3%) abnormal by karyotype alone, and 25 (41.6%) by FISH alone. Karyotype and FISH were normal in 16 (27%) patients, and 4 samples were unsuitable for karyotype analysis. One patient had an abnormality not included in the panel (20q deletion). FISH was abnormal in 19 cases (31.6%) with a normal karyotype and in 6 cases with no analyzable metaphases. Thirteen CLL cases with abnormal karyotypes were either confirmed or clarified by FISH. The MM panel probes were 11q, 13q, 17p, and t(11;14). Karyotype and FISH were abnormal in 18 of 139 (13%) MM cases. Twenty patients (14.4%) had a normal karyotype and abnormal FISH. Two samples not suitable for metaphase analysis were abnormal by interphase FISH. Karyotype and FISH were normal in 94 (68%) patients. Five patients (3.6%) had chromosomal abnormalities not included in the panel. Compared to karyotyping alone, the FISH panels improved the detection rate of recurrent chromosomal aberrations in CLL from 22-63% and in MM from 15-29%.     

Multiplex ligation-dependent probe amplification to detect subtelomeric rearrangements in routine diagnostics

Subtelomeric rearrangements are believed to be responsible for 5-7% of idiopathic mental retardation cases. Due to the relative complexity and high cost of the screening methods used till now, only preselected patient populations including mostly the more severely affected cases have been screened. Recently, multiplex ligation-dependent probe amplification (MLPA) has been adapted for use in subtelomeric screening, and we have incorporated this technique into routine diagnostics of our laboratory. Since the evaluation of MLPA as a screening method, we tested 275 unselected patients with idiopathic mental retardation and detected 12 possible subtelomeric aberrations: a der(11)t(11;20)(qter;qter), a 19pter duplication, a der(18)t(18;10)(qter; pter), a 15qter deletion, a 8pter deletion, a 6qter deletion, a der(X)t(X;1)(pter;qter), a der(X)t(X;3)(pter;pter), a 5qter duplication, a 3pter deletion, and two 3qter duplications. The patients can be subdivided into two groups: the first containing de novo rearrangements that are likely related to the clinical presentation of the patient and the second including aberrations also present in one of the parents that may or may not be causative of the mental retardation. In our patient cohort, five (1.8%) subtelomeric rearrangements were de novo, three (1.1%) rearrangements were familial and suggestively disease causing, and four (1.5%) were possible polymorphisms. This high frequency of subtelomeric abnormalities detected in an unselected population warrants further investigation about the feasibility of routine screening for subtelomeric aberrations in mentally retarded patients.     

Molecular cytogenetic abnormalities in patients with concurrent chronic lymphocytic leukemia and multiple myeloma shown by interphase fluorescence in situ hybridization: evidence of distinct clonal origin

The coexistence of chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) is rare, and there is no consensus about the clonal relationship of the two disorders when they occur in the same individual. We investigated chromosomal abnormalities in two patients with concurrent CLL and MM using interphase fluorescence in situ hybridization (FISH) with a panel of region-specific DNA probes. In patient 1, the clonal plasma cells harbored IgH translocations (14q32); however, FISH with probes for the four most frequent IgH partner genes in MM (CCND1, FGFR3, MAF, and MYC) did not detect translocations involving any of them. The CLL cells were characterized by deletions of 13q14, 11q23, and 17p13, as well as trisomy 12, none of which were found in the MM cells. In patient 2, deletions of 13q14 and 17p13 were detected in CLL cells, but no cytogenetic abnormalities were found in the MM cells. Both patients had relapsed MM following chemotherapy and had autologous stem-cell transplant, whereas their CLL has been stable and not requiring treatment. Our results show that the cytogenetic profiles differ between CLL and MM within the same patients, and provide evidence for two distinct malignant clones in both patients.     

Evaluation of multiplex ligation‐dependent probe amplification as a method for the detection of copy number abnormalities in B‐cell precursor acute lymphoblastic leukemia

Recent genomic studies have shown that copy number abnormalities (CNA) of genes involved in lymphoid differentiation and cell cycle control are common in B‐cell precursor acute lymphoblastic leukemia (BCP‐ALL). We have evaluated Multiplex Ligation‐dependent Probe Amplification (MLPA) on 43 BCP‐ALL patients for the detection of the most common deletions among these genes and compared the results to those obtained by fluorescence in situ hybridization (FISH) and genomic quantitative PCR (qPCR). There was good correlation between methods for CDKN2A/B, IKZF1, and PAX5 deletions in the majority of cases and MLPA confirmed the presence of deletions within the PAR1 region in two of three cases identified by FISH. Small intragenic aberrations detected by MLPA, which were below the resolution of FISH for CDKN2A/B (n = 7), IKZF1 (n = 3), and PAX5 (n = 3) were confirmed by qPCR. MLPA and qPCR were unable to detect populations present at a low level (<20%) by FISH. In addition, although MLPA identified the presence of a deletion, it was unable to discern the presence of mixed cell populations which had been identified by FISH: CDKN2A/B (n = 3), IKZF1 (n = 1), PAX5 (n = 2), and PAR1 deletion (n = 1). Nevertheless, this study has demonstrated that MLPA is a robust technique for the reliable detection of CNA involving multiple targets in a single test and thus is ideal for rapid high throughput testing of large cohorts with a view to establishing incidence and prognostic significance. © 2010 Wiley‐Liss, Inc.     

Utility of fluorescence in situ hybridization to detect MDM2 amplification in liposarcomas and their morphological mimics

The atypical lipomatous tumor (ALT)/well-differentiated liposarcoma (WDLS) and the de-differentiated liposarcoma (DDLS) represent the most common category of liposarcomas. ALT/WDLSs and DDLSs are often difficult to distinguish from other tumors with similar morphological characteristics. In this study, we investigated whether the detection of amplified or overexpressed murine double-minute 2 (MDM2) can be a useful diagnostic ancillary aid. We used fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) to detect MDM2 amplification and protein overexpression, respectively, in 49 WDLSs, 5 DDLSs, 23 myxoid liposarcomas, 25 benign lipomatous tumors, and 75 spindle and pleomorphic sarcomas. MDM2 amplification was detected in 48 of 49 WDLSs, 5 of 5 DDLSs, 2 of 9 malignant peripheral nerve sheath tumors, and 2 of 10 myxofibrosarcomas. We did not detect MDM2 amplification in any of the benign lipomatous tumors. FISH-mediated detection of MDM2 amplification was the most valuable diagnostic aid for ALT/WDLS, as determined by using the Fisher exact test to compare two different diagnoses of 19 biopsies. On the contrary, unequivocal nuclear overexpression of MDM2 was found in only 10 of 50 ALT/WDLSs. The sensitivity and specificity of MDM2 amplification in distinguishing a DDLS from spindle and pleomorphic sarcomas were 100% and 95%, respectively, while those of MDM2 overexpression were 100% and 87%, respectively. In conclusion, our results indicate that FISH-mediated detection of MDM2 amplification is the most useful adjunct in the diagnosis of both ALT/WDLS and DDLS. However, IHC-mediated detection of MDM2 protein is useful only for the diagnosis of DDLS.     

Molecular cytogenetic abnormalities in multiple myeloma and plasma cell leukemia measured using comparative genomic hybridization

Comparative genomic hybridization (CGH) was used to identify recurrent regions of DNA sequence loss and gain in 21 multiple myeloma (MM) and plasma cell leukemia (PCL) primary tumor specimens and cell lines. Multiple regions of non-random sequence loss and gain were observed in 8/8 primary advanced stage tumors and 13/13 cell lines. Identification of sequence copy number changes was facilitated by statistical analyses that reduce subjectivity associated with identification of copy number changes and by requiring that sequence changes are visible using both red- and green-labeled tumor DNA. Loss of sequence on 13q and 14q and gain of sequence on 1q and chromosome 7 occurred in 50–60% of the population. In general, cell lines carry more and larger regions of sequence gain and loss than primary tumors. Regions of sequence copy number change that recur among MM cell lines and primary tumors include, in order of prevalence, enh(1q12qter), dim(13), enh(7), enh(3q22q29), enh(11q13.3qter), dim(14q11.2q31), enh(8q21qter), enh(3p25pter), dim(17p11.2p13), and dim(6q22.1q23). Population distributions of genome-wide changes in primary tumors reveal “hot-spots” of sequence loss from 13q12.1-q21, 13q32-q34, 14q11.2-q13, and 14q23-q31. Genomic changes detected using CGH are consistent with those identified using banding analyses, although recurrent involvement of additional regions of the genome are also evident. A higher prevalence of genomic changes is visible using CGH compared to banding. Identification of recurrent regions of sequence gain and loss provides opportunities to identify regions of the genome that may be involved in the malignant phenotype and/or disease progression. Genes Chromosom. Cancer 19:124–133, 1997. © 1997 Wiley-Liss, Inc.     

荧光原位杂交技术与细胞遗传学分析在慢性淋巴细胞白血病检测中的评价应用

目的比较常规细胞遗传学分析（CCA）及荧光原位杂交（FISH）两种技术在慢性淋巴细胞白血病（CLL）染色体异常检测中的灵敏度和特异性。方法CCA法采用骨髓短期培养法,核型分析采用R带技术。FISH法采用间期FISH。结果采用CCA法,CLL患者的染色体异常检出率为35．71％,而采用FISH技术染色体异常检出率为64．2％。结论采用组合探针的FISH更为敏感和特异。     

Use of fluorescence in situ hybridization for retrospective detection of aneuploidy in multiple myeloma

In malignancies with a low mitotic index such as multiple myeloma (MM), conventional cytogenetic studies may not be informative. This study's purpose was to assess specific numerical chromosomal aberrations in non-dividing MM cells by fluorescence in situ hybridization (FISH) of DNA chromosome probes on bone marrow smears. Old air-dried bone marrow smears from 18 MM patients were probed with alpha satellite DNA sequences for chromosomes 7, X, and Y, and a whole painting probe for chromosome 11. Plasma cells were identified by their morphologic characteristics so that counts of fluorescent signals in the nuclei of MM cells could be differentiated from those of normal marrow cells. Numerical chromosome aberrations were found in 66.7% of the cases (12 of 18), including 5 cases of trisomy 7, 2 cases of tetraploidy, 2 cases of monosomy X in females, 2 cases of disomy X in males, and 1 case of nullisomy Y. In addition, 2 of the 7 cases probed with chromosome 11 paint demonstrated 3 signals in about 15% of the cells. This study illustrates the advantages of FISH for interphase analysis of chromosome aberrations in slowly dividing cells, as well as the ability to use old slides for retrospective studies. © 1993 Wiley-Liss, Inc.     

多探针荧光原位杂交检测急性髓系白血病常见细胞遗传学异常

目的:评价多探针荧光原位杂交(FISH)在检测急性髓系白血病(AML)常见细胞遗传学异常中的价值,探讨细胞遗传学异常与临床诊断、治疗、预后的关系。方法:采用针对AML/MDS的FISH多探针诊断系统,即以针对AML1/ETO融合基因、PML-RARα融合基因、CBFβ/MYH11融合基因、MLL基因、P53基因、Del(5q)、Del(7q)、Del(20q)8种DNA探针对40例患者进行多探针FISH检测,同时联合染色体核型、临床资料进行研究。结果:40例AML中,共22例多探针FISH检出了细胞遗传学改变,包括:AML1/ETO、PML-RARα、MLL基因断裂重排、Del(5q)、Del(7q)、P53基因缺失、8号染色体三体7种细胞遗传学异常。而常规染色体核型分析仅检出11例遗传学异常。多探针FISH与染色体核型分析的总阳性率分别为57.50%及27.50%。AML1/ETO、PML/RARα阳性者首次诱导化疗效果较理想;而Del(7q)、MLL基因断裂重排阳性、伴复杂细胞遗传学改变者可能预示不良预后。结论:FISH多探针诊断系统检测AML患者常见遗传学异常更省时、准确、高效,有利于完善白血病的分层诊断及指导临床个体化治疗。     

Chromogenic in situ hybridization: a practical alternative for fluorescence in situ hybridization to detect HER-2/neu oncogene amplification in archival breast cancer samples

Determination of HER-2/neu oncogene amplification has become necessary for selection of breast cancer patients for trastuzumab (Herceptin) therapy. Fluorescence in situ hybridization (FISH) is currently regarded as a gold standard method for detecting HER-2/neu amplification, but it is not very practical for routine histopathological laboratories. We evaluated a new modification of in situ hybridization, the chromogenic in situ hybridization (CISH), which enables detection of HER-2/neu gene copies with conventional peroxidase reaction. Archival formalin-fixed paraffin-embedded tumor tissue sections were pretreated (by heating in a microwave oven and using enzyme digestion) and hybridized with a digoxigenin-labeled DNA probe. The probe was detected with anti-digoxigenin fluorescein, anti-fluorescein peroxidase, and diaminobenzidine. Gene copies visualized by CISH could be easily distinguished with a x40 objective in hematoxylin-stained tissue sections. HER-2/neu amplification typically appeared as large peroxidase-positive intranuclear gene copy clusters. CISH and FISH (according to Vysis, made from frozen pulverized tumor samples) correlated well in a series of 157 breast cancers (kappa coefficient, 0.81). The few different classifications were mostly because of low-level amplifications by FISH that were negative by CISH and immunohistochemistry with monoclonal antibody CB-11. We conclude that CISH, using conventional bright-field microscopy in evaluation, is a useful alternative for determination of HER-2/neu amplification in paraffin-embedded tumor samples, especially for confirming the immunohistochemical staining results.     

荧光原位杂交技术检测多发性骨髓瘤分子遗传学改变及其意义

目的 研究多发性骨髓瘤(multiple myeloma,MM)患者1q21扩增、13q14缺失、TP53基因缺失及IgH易位的发生率及预后意义.方法 应用CD138单克隆抗体磁珠分选结合间期荧光原位杂交技术检测43例MM患者上述各种核型异常.结果 43例患者中28例(65.1%)出现了1q21的扩增,30例(69.7%)出现了13q14的缺失,8例(18.6%)出现了TP53基因的缺失,29例(67.4%)出现了IgH易位.1q21扩增、13q14缺失和TP53基因缺失与MM高死亡率有密切相关性.结论 1q21扩增、13q14缺失、TP53基因缺失及IgH易位是MM常见的核型异常,1q21扩增、13q14缺失和TP53基因缺失是MM的预后不良因子.     

Cytogenetic and fluorescence in situ hybridization studies in 60 patients with multiple myeloma and plasma cell leukemia

We report cytogenetic results in a series of 60 patients affected with multiple myeloma (MM) and plasma cell leukemia (PCL) and compare the results with those previously reported. In our series, a total of 41% of MM patients and 71% of PCL patients displayed chromosome abnormalities. To evaluate the clinical value of monosomy 18, we obtained fluorescence in situ hybridization results (using centromeric probe for chromosome 18) of 22 MM patients who displayed a normal karyotype. Monosomy 18 was present in 3 of 22 patients (14%). Using conventional cytogenetics, we detected monosomy 18 in one patient affected with PCL. Two of four cases with monosomy 18 followed an aggressive course, with overall survival of 1 and 9 months. The remaining two are in follow-up and remain stable. The association of monosomy 18 with IgA subtype predominance and poor prognosis was not observed in this series of MMs and PCLs. Although these results do not confirm our previous hypothesis, further observations of this group of patients (with monosomy 18) regarding malignant transformation is warranted.     

多重荧光原位杂交技术检测多发性骨髓瘤复杂核型异常

目的 探讨多重荧光原位杂交(multiplex fluorescence in situ hybridization,M-FISH)技术在多发性骨髓瘤(multiple myeloma,MM)复杂核型异常(complex chromosomal aberrations,CCAs)检测中的价值.方法 对10例常规细胞遗传学(conventional cytogenetics,CC)方法检测具有复杂核型的MM患者应用M-FISH技术确定复杂染色体的重排及标记染色体的组成.结果 M-FISH证实了CC显示的29种结构异常,并进一步明确了1p-、6q-、9q-、9q+、+8q+×2、14q+、?14q、der(4)、der(22)、der(1)t(1;?)(q10;?)、der(3)、del(7)的具体来源;同时也发现CC分析没有发现或不能识别的21种异常,其中t(2;15)(q33;q22)、t(6;7)(q23;q34)、t(8;11)(q24;q23)、t(1;14)(q10;q32)和t(X;1)(q26;q25)是新发现的核型异常.这10例随访的MM患者病例资料中9例已死亡,中位生存期仅为23个月,较公认的MM患者的平均生存期34个月明显缩短.结论 对伴有CCAs的MM患者,M-FISH技术可以明确CC分析中复杂染色体异常,并发现和纠正CC分析中漏检及误检的异常,为MM的染色体异常研究提供了一种重要的方法,已经成为精确染色体核型分析所不可缺少的手段之一.