Comparative genomic hybridisation as a supportive tool in diagnostic pathology

Clonality assessment of multifocal lung adenocarcinoma by pathology evaluation and molecular analysis

The aim of this study was to explore morphologic and molecular features distinguishing between multifocal lung adenocarcinoma (MLA) and intrapulmonary metastases (IMs). Sixteen patients with MLAs, a total of 34 tumors, were reviewed. Four approaches were used: (1) array-comparative genomic hybridization (CGH) as a standard clonality assessment; (2) EGFR and KRAS mutational profiles as a supplementary method; (3) comprehensive histologic assessment (CHA) was method I in pathology evaluation; and (4) CHA combined with lepidic component analysis was method II. The lepidic component was divided into low grade and high grade according to extent of atypia; tumors with low-grade lepidic component were defined as primary. Eight patients were found to have IMs and 8 to have multiple primaries (MPs) by array-CGH; 7 had MPs and 9 had IMs by method I; 5 had MPs and 11 had IMs by method II. Compared with array-CGH, method I had a lower coincidence rate (65%) than method II (85%). Univariate analysis revealed that patients with MP had a better clinical outcome than those with IM only if the MPs were diagnosed by array-CGH (P = .034) or method II (P = .027) but not EGFR/KRAS mutation (P = .843) or method I (P = .493). Our results suggest that a low-grade lepidic component is a sign of a primary tumor. CHA combined with a low-grade lepidic component (method II) is more accurate clinically and more cost-effective in distinguishing MLAs from IMs. Also, EGFR mutation is not an appropriate molecular marker for clonality assessment.

Surgery in oligometastatic NSCLC patients in the targeted therapy era

More than 50% of NSCLC patients present with metastatic disease at first diagnosis, with a median survival of 8-11 months. However, selected patients with oligometastatic disease who receive appropriate local therapy for both the primary lesion and metastases enjoy long-term survival or are even cured. The new (eighth) edition of the tumor, node and metastasis classification of lung cancer suggests that patients with a single metastatic lesion in one distant organ should be placed into a new category, M1b, which will certainly lead to more applications of local therapy in such subpopulations. Moreover, as the applications of targeted therapy increase, surgery will play an evermore critical role in eliminating drug-resistant cancer clones of patients who exhibit mixed responses to tyrosine kinase inhibitors. The lung, brain and adrenal gland are the most common oligometastatic organs, and are reviewed separately.

Surgical treatment of oligometastatic non-small cell lung cancer

Patients with stage IV metastatic non-small cell lung cancer (NSCLC) are generally believed to have an incurable disease. Patients with oligometastatic disease represent a distinct subset of patients among those with metastatic disease. There is evidence that these patients have synchronous or metachronous satellite nodules in different pulmonary lobes or have solitary extrapulmonary metastases. In these cases, evidence has shown that surgical resection may provide patients with survival benefit. This article discusses the biology of the oligometastatic state in patients with lung cancer and the selection of patients for surgery, as well as the prognostic factors that influence survival of the patient. To properly select patients for an aggressive local treatment regime, accurate clinical staging is of prime importance. The use of FDG-PET should be considered for restaging if oligometastatic disease is suspected based on a patient's CT scan. A limitation of retrospective clinical studies for oligometastatic disease is that it is difficult to summarize and evaluate the available evidence for the effectiveness of surgical resection due to selection bias, and to a high degree of variability among different clinical studies. Nevertheless, we can certainly learn from the clinical experience acquired from retrospective case series to identify prognostic factors. Following surgical resection, the overall 5-year actuarial survival rate is about 28% for patients with satellite nodules and 21% for patients with ipsilateral nodules. Patients with resected brain metastasis achieve 5-year survival rates between 11% and 30%, and those with adrenalectomy for adrenal metastasis achieve 5-year survival rates of 26%.

A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data

When a cancer patient develops a new tumor it is necessary to determine if it is a recurrence (metastasis) of the original cancer, or an entirely new occurrence of the disease. This is accomplished by assessing the histo-pathology of the lesions. However, there are many clinical scenarios in which this pathological diagnosis is difficult. Since each tumor is characterized by a distinct pattern of somatic mutations, a more definitive diagnosis is possible in principle in these difficult clinical scenarios by comparing the two patterns. In this article we develop and evaluate a statistical strategy for this comparison when the data are derived from array copy number data, designed to identify all of the somatic allelic gains and losses across the genome. First a segmentation algorithm is used to estimate the regions of allelic gain and loss. The correlation in these patterns between the two tumors is assessed, and this is complemented with more precise quantitative comparisons of each plausibly clonal mutation within individual chromosome arms. The results are combined to determine a likelihood ratio to distinguish clonal tumor pairs (metastases) from independent second primaries. Our data analyses show that in many cases a strong clonal signal emerges. Sensitivity analyses show that most of the diagnoses are robust when the data are of high quality.

Testing clonal relatedness of tumors using array comparative genomic hybridization: a statistical challenge

In recent years several investigative groups have sought to use array technologies that characterize somatic alterations in tumors, such as array comparative genomic hybridization (ACGH), to classify pairs of tumors from the same patients as either independent primary cancers or metastases. A wide variety of strategies have been proposed. Several groups have endeavored to use hierarchical clustering for this purpose. This technique was popularized in genomics as a means of finding clusters of patients with similar gene expression patterns with a view to finding subcategories of tumors with distinct clinical characteristics. Unfortunately, this method is not well suited to the problem of classifying individual pairs of tumors as either clonal or independent. In this article we show why hierarchical clustering is unsuitable for this purpose, and why this method has the paradoxical property of producing a declining probability that clonal tumor pairs will be correctly identified as more information is accrued (i.e., more patients). We discuss alternative strategies that have been proposed, which are based on more conventional conceptual formulations for statistical testing and diagnosis, and point to the remaining challenges in constructing valid and robust techniques for this problem.

Comprehensive histologic assessment helps to differentiate multiple lung primary nonsmall cell carcinomas from metastases

The pathologic classification of nonsmall cell lung cancer (NSCLC) is evolving. Lung adenocarcinoma is morphologically heterogeneous, with mixtures of acinar, papillary, bronchioloalveolar, and solid patterns in more than 80% of cases. In case of synchronous or metachronous multiple NSCLC, the distinction of intrapulmonary metastases from independent primary tumors is of great clinical importance as it influences staging and potentially the therapeutic strategy. Here we took advantage of a cohort of 20 patients with 42 multiple NSCLC tumors (24 potential pair comparisons) that were annotated molecularly using genomic and mutational profiling to evaluate the value of comprehensive histologic assessment in this setting. Using the Martini-Melamed criteria, paired tumors were characterized as multiple primary NSCLCs in 21 cases and as intrapulmonary metastases in 3 cases. Genomic and mutational data led to a diagnosis of multiple primaries in 14 cases and of metastases in 8 cases; 2 cases could not be assessed. This molecular characterization contradicted the Martini-Melamed diagnosis in 7 (32%) of the 22 assessable comparisons. Adenocarcinoma was found in 32 (76%) of the 42 tumors. After review in a blinded fashion, semiquantitative comprehensive histologic assessment of paired tumors was different in 16 and similar in 8 paired tumors. We found that comparing adenocarcinomas is a complex issue that requires assessment not only of percentages of the histologic subtypes, but also the recording of additional histologic details such as cytologic features, patterns of stroma, necrosis, discrete nodularity versus miliary growth and variants such as clear cell, signet ring, mucinous, and fetal patterns. We also found that paired squamous cell carcinomas could be compared based on histologic subtyping in addition to cytologic and stromal characteristics. Considering histologically different tumors as multiple primaries, and similar tumors as metastases, comprehensive histologic subtyping was consistent with the molecular characterization in 20 (91%) of the 22 pairs comparisons. In summary, based on a well characterized cohort with detailed clinical, pathologic and molecular data, we found comprehensive histologic assessment is a powerful tool that seems to be a promising way to determine whether multiple lung adenocarcinomas or squamous cell carcinomas are metastatic or multiple primaries. This has great clinical implications for staging and therapeutic management of lung cancer patients with multiple tumors. Given its high correlation with molecular characterization of such tumors, it may provide a much cheaper and faster method to address this problem.

Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers

PURPOSE

In cases of multiple non-small cell lung cancer, clinicians must decide whether patients have independent tumors or metastases and tailor treatment accordingly. Decisions are currently made using the Martini and Melamed criteria, which are mostly based on tumor location and histologic type. New genomic tools could improve the ability to assess tumor clonality.

EXPERIMENTAL DESIGN

We obtained fresh-frozen tumors specimens from patients who underwent surgery on at least two occasions for presumptively independent NSCLC. We did array comparative genomic hybridization (aCGH), mutational profiling of select genes, and detailed clinicopathologic review.

RESULTS

We analyzed a total of 42 tumors from 20 patients (6 patients with synchronous tumors, 14 patients with metachronous tumors, 24 potential tumor pair comparisons); 22 tumor pairs were evaluable by aCGH. Surprisingly, classification based on genomic profiling contradicted the clinicopathologic diagnosis in four (18%) of the comparisons, identifying independent primaries in one case diagnosed as metastasis and metastases in three cases diagnosed as independent primaries. Matching somatic point mutations were observed in these latter three cases. Another four tumor pairings were assigned an "equivocal" result based on aCGH; however, matching somatic point mutations were also found in these tumor pairs. None of the tumor pairs deemed independent primaries by aCGH harbored matching mutations.

CONCLUSION

Genomic analysis can help distinguish clonal tumors from independent primaries. The development of rapid, inexpensive, and reliable molecular tools may allow for refinement of clinicopathologic criteria currently used in this setting.

The potential of comparative genomic hybridization as a tool in the differential diagnosis of matrix-producing bone lesions

Matrix-producing bone lesions consist of a wide variety of benign and malignant conditions. With respect to morphology, an overlap exists between benign and malignant bone tumors that causes difficulties in the final determination of the tumor. This study was conducted to show the potential of comparative genomic hybridization as a tool in the differential diagnosis of matrix-producing bone lesions. Thirty benign bone tumors were evaluated by conventional comparative genomic hybridization. To test its diagnostic reliability, 5 additional cases were analyzed, all with differential diagnostic difficulties related to morphology and radiology. All were ultimately diagnosed as malignant sarcomas, and unbalanced alterations were detected. In contrast benign tumors or tumor-like lesions did not reveal any chromosomal alterations. Comparative genomic hybridization is a useful adjunct in the complicated differential diagnostic algorithms of matrix-producing bone tumors.

Microarray-based comparative genomic hybridization and its applications in human genetics

Through the years, several techniques capable of detecting DNA copy number changes have been developed. A number of those, such as karyotyping and fluorescence in situ hybridization (FISH), have proven to be valuable tools in both research and diagnostics. Recently, a new technique, called microarray-based comparative genomic hybridization (array CGH), has been introduced. Array CGH has proven to be a specific, sensitive, and fast technique, with considerable advantages compared to other methods used for the analysis of DNA copy number changes. Array CGH enables analysis of the whole genome in a single experiment. Until now, its applications have been mainly directed at detecting genomic abnormalities in cancer. However, array CGH is also suitable for the analysis of DNA copy number aberrations that cause human genetic disorders. This review gives an overview of array CGH and its applications in human genetics. Advantages, limitations, and future perspectives of array CGH are discussed.

Molecular cytogenetics of ovarian granulosa cell tumors by comparative genomic hybridization

OBJECTIVE

Patients with stage I granulosa cell tumors (GCTs) may occasionally develop metastasis, which is hard to predict using pathologic criteria. It is interesting to elucidate whether certain chromosomal imbalances (CIs), detected by comparative genomic hybridization (CGH), could be useful prognostic markers.

METHODS

CGH was used to identify CI(s) in 37 adult-type GCTs from 36 women. Nonrandom CIs were compared with clinical and pathological features to evaluate their significance as a prognostic marker.

RESULTS

Twenty-two (61%) of the 36 primary tumors had CIs. One woman's tumor showed identical CIs to another tumor that occurred in contralateral ovary 2 years later, supporting a metastatic nature. The nonrandom CIs included losses of 22q (31%), 1p33-p36 (6%), 16p13.1 (6%), and 16q (6%) and gains of 14 (25%), 12 (14%), and 7p15-p21 (6%). No tumor exhibited high-level amplification. The associations between each CI and pathological features, including the growth pattern, tumor size, and mitotic activity, were not evident. The only CI repeatedly detected in tumors with metastasis was monosomy 22, which presented in 2 of the 4 cases with metastasis but also in 2 of the 5 cases without recurrence for more than 5 years.

CONCLUSIONS

Monosomy 22 was the most common CI in GCTs, which often coexisted with trisomy 14 (in 55% cases). Deletion of 22q seems to be, albeit not very specific, associated with the risk of early metastases of stage I disease. The role of loss-of-function mutation(s) of certain putative tumor suppressor gene(s) on 22q is worthy of further investigations.

Detection of chromosomal abnormalities by comparative genomic hybridization

PURPOSE OF REVIEW

Comparative genomic hybridization (CGH) is a modified in-situ hybridization technique. In this type of analysis, two differentially labeled genomic DNAs (study and reference) are cohybridized to normal metaphase spreads or to microarray. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome. Thus, CGH allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment.

RECENT FINDINGS

Since its development, comparative genomic hybridization has been applied mostly as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. It is also a powerful tool for detection and identification of unbalanced chromosomal abnormalities in prenatal, postnatal and preimplantation diagnostics.

SUMMARY

The development of comparative genomic hybridization and increase in resolution analysis by using the microarray-based technique offer new information on chromosomal pathologies and thus better management of patients.

Comparative Genomic Hybridization in Central and Peripheral Nervous System Tumors of Childhood and Adolescence

Brain tumors amount to less than 2% of all malignant neoplasms. However, they account for approximately 20% of all childhood cancers and are the leading cause of cancer mortality among children. Recently, enormous progress has been achieved in the field of pediatric neuro-oncology regarding the classification of children's brain tumors, as well as the understanding of the genetic events involved in their pathogenesis; thus leading to an emerging role of molecular diagnostic approaches using novel tools. Comparative genomic hybridization (CGH) is a technique that has revolutionized cytogenetic knowledge in the past decade. It permits the detection of chromosomal copy number changes without the need for cell culturing and gives a global overview of chromosomal gains and losses throughout the whole genome of a tumor. A survey of CGH-related publications on central and peripheral nervous system tumors in the pediatric and adolescent population revealed 884 cases. The CNS tumor groups most frequently examined by CGH were embryonal tumors (268 cases/30.3%) and ependymomas (241/27.2%), followed by astrocytic (163/18.4%), peripheral nerve (73/8.2%), choroid plexus tumors (56/6.3%), and craniopharyngiomas (38/4.3%). The most common CNS tumor entities were medulloblastomas (238/26.9%), classic ependymomas (160/18.1%), anaplastic ependymomas (70/7.9%), pleomorphic xanthoastrocytomas (53/6.0%), and pilocytic astrocytomas (50/5.6%). This article provides a short review of the CGH technique and its pitfalls, summarizes the current CGH-related data on pediatric brain tumors and muses on the future of CGH.