Assessment of clonal relationships in ipsilateral and bilateral multiple breast carcinomas by comparative genomic hybridisation and hierarchical clustering analysis

Bilateral Mastectomy and Breast Cancer Mortality

Importance

The benefit of bilateral mastectomy for women with unilateral breast cancer in terms of deaths from breast cancer has not been shown.

Objectives

To estimate the 20-year cumulative risk of breast cancer mortality among women with stage 0 to stage III unilateral breast cancer according to the type of initial surgery performed.

Design, Settings, and Participants

This cohort study used the Surveillance, Epidemiology, and End Results (SEER) Program registry database to identify women with unilateral breast cancer (invasive and ductal carcinoma in situ) who were diagnosed from 2000 to 2019. Three closely matched cohorts of equal size were generated using 1:1:1 matching according to surgical approach. The cohorts were followed up for 20 years for contralateral breast cancer and for breast cancer mortality. The analysis compared the 20-year cumulative risk of breast cancer mortality for women treated with lumpectomy vs unilateral mastectomy vs bilateral mastectomy. Data were analyzed from October 2023 to February 2024.

Exposures

Type of breast surgery performed (lumpectomy, unilateral mastectomy, or bilateral mastectomy).

Main Outcomes and Measures

Contralateral breast cancer or breast cancer mortality during the 20-year follow-up period among the groups treated with lumpectomy vs unilateral mastectomy vs bilateral mastectomy.

Results

The study sample included 661 270 women with unilateral breast cancer (mean [SD] age, 58.7 [11.3] years). After matching, there were 36 028 women in each of the 3 treatment groups. During the 20-year follow-up, there were 766 contralateral breast cancers observed in the lumpectomy group, 728 contralateral breast cancers in the unilateral mastectomy group, and 97 contralateral cancers in the bilateral mastectomy group. The 20-year risk of contralateral breast cancer was 6.9% (95% CI, 6.1%-7.9%) in the lumpectomy-unilateral mastectomy group. The cumulative breast cancer mortality was 32.1% at 15 years after developing a contralateral cancer and was 14.5% for those who did not develop a contralateral cancer (hazard ratio, 4.00; 95% CI, 3.52-4.54, using contralateral breast cancer as a time-dependent covariate). Deaths from breast cancer totaled 3077 women (8.54%) in the lumpectomy group, 3269 women (9.07%) in the unilateral mastectomy group, and 3062 women (8.50%) in the bilateral mastectomy group.

Conclusions and Relevance

This cohort study indicates that the risk of dying of breast cancer increases substantially after experiencing a contralateral breast cancer. Women with breast cancer treated with bilateral mastectomy had a greatly diminished risk of contralateral breast cancer; however, they experienced similar mortality rates as patients treated with lumpectomy or unilateral mastectomy.

Evolution of synchronous female bilateral breast cancers and response to treatment

Synchronous bilateral breast cancer (sBBC) occurs after both breasts have been affected by the same germline genetics and environmental exposures. Little evidence exists regarding immune infiltration and response to treatment in sBBCs. Here we show that the impact of the subtype of breast cancer on levels of tumor infiltrating lymphocytes (TILs, n = 277) and on pathologic complete response (pCR) rates (n = 140) differed according to the concordant or discordant subtype of breast cancer of the contralateral tumor: luminal breast tumors with a discordant contralateral tumor had higher TIL levels and higher pCR rates than those with a concordant contralateral tumor. Tumor sequencing revealed that left and right tumors (n = 20) were independent regarding somatic mutations, copy number alterations and clonal phylogeny, whereas primary tumor and residual disease were closely related both from the somatic mutation and from the transcriptomic point of view. Our study indicates that tumor-intrinsic characteristics may have a role in the association of tumor immunity and pCR and demonstrates that the characteristics of the contralateral tumor are also associated with immune infiltration and response to treatment.

Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything

Clonal analysis of tumour sequencing data enables the evaluation of the relationship of histologically distinct synchronous lesions, such as co-existing benign areas, and temporally distinct tumours, such as primary-recurrence comparisons. In this review, we summarise statistical approaches that are commonly employed to define tumour clonal relatedness using data from bulk DNA technologies. We discuss approaches using total copy number, allele-specific copy number and mutation data, and the relative genomic resolution required for analysis and summarise some of the current tools for inferring clonal relationships. We argue that the impact of the biological context is critical in selecting any particular approach, such as the relative genomic complexity of the lesions being compared, and we recommend considering this context before employing any method to a new dataset.

Phylogenetic analysis of combined lobular and ductal carcinoma of the breast

Breast cancer manifests in diverse forms, with particular reference to various cell types harboring different mutations and gene expression profiles. To elucidate the clonal relationship between cancer cells in tumors composed of both ductal and lobular phenotypes, two combined lobular and ductal carcinoma (CLDC) cases were analyzed, including one mixed ductal‑lobular carcinoma (MDL) lesion, by direct sequencing of the mitochondrial DNA D‑loop, digital PCR targeting of chromosomes 1q and 16q, as well as next‑generation sequencing. DNA was extracted from formalin‑fixed paraffin‑embedded tissue sections of different histological types, including invasive ductal carcinoma, invasive lobular carcinoma, ductal carcinoma in situ, lobular carcinoma in situ, flat epithelial atypia, non‑neoplastic mammary gland and extramammary organs, using laser‑assisted microdissection. Mutations detected by the comprehensive cancer panel were validated by SYBR green allele‑specific quantitative PCR (RRM1, AKT1, PIK3CA, RALGDS, EGFR, TP53, IL21R, DPYD, SGK1, CDH1, TIMP3 and KMT2C). CLDC, which shared the basic genetic alterations of 1q gain or 16q loss, progresses to invasive lobular or ductual carcinoma with the accumulation of further mutations. Cancer cells contained in an MDL lesion shared closely related genetic alterations, suggesting that these cells have the same origin, despite different histological features, namely 'lobular' or 'ductal'. By contrast, multiple lesions located away from the main tumor, diagnosed as CLDC (excluding an MDL lesion) were not always identical with different genetic alterations, despite being diagnosed as ductal carcinoma in situ. Thus, MDL should be defined as a distinct category separate from CLDC, whose components of 'lobular' and 'ductal' may have the same cellular origin.

Mitochondrial DNA analysis efficiently contributes to the identification of metastatic contralateral breast cancers

Purpose

In daily practice, a contralateral breast cancer (CBC) is usually considered as a new independent tumor despite the indications of several studies showing that the second neoplasia may be a metastatic spread of the primary tumor. Recognition of clonal masses in the context of multiple synchronous or metachronous tumors is crucial for correct prognosis, therapeutic choice, and patient management. Mitochondrial DNA (mtDNA) sequencing shows high informative potential in the diagnosis of synchronous neoplasms, based on the fact that somatic mtDNA mutations are non-recurrent events, whereas tumors sharing them have a common origin. We here applied this technique to reveal clonality of the CBC with respect to the first tumor.

Methods

We analyzed 30 sample pairs of primary breast cancers and synchronous or metachronous CBCs with detailed clinical information available and compared standard clinico-pathological criteria with mtDNA sequencing to reveal the metastatic nature of CBCs.

Results

MtDNA analysis was informative in 23% of the cases, for which it confirmed a clonal origin of the second tumor. In addition, it allowed to solve two ambiguous cases where histopathological criteria had failed to be conclusive and to suggest a clonal origin for two additional cases that had been classified as independent by pathologists.

Conclusion

Overall, the mtDNA-based classification showed a more accurate predictive power than standard histopathology in identifying cases of metastatic rather than bilateral breast cancers in our cohort, suggesting that mtDNA sequencing may be a more precise and easy-to-use method to be introduced in daily routine to support and improve histopathological diagnoses.

Synchronous bilateral breast cancer: a nationwide study on histopathology and etiology

PURPOSE

The aim of the present study was to describe histopathologic characteristics of synchronous bilateral breast cancer (SBBC), and by comparing SBBC to unilateral breast cancer (UBC), identify possible etiological mechanisms of SBBC.

METHODS

Patients with primary SBBC (diagnosed within 4 months) and UBC diagnosed in Denmark between 1999 and 2015 were included. Detailed data on histopathology were retrieved from the Danish Breast Cancer Group database and the Danish Pathology Register. Associations between bilateral disease and the different histopathologic characteristics were evaluated by odds ratios and estimated by multinomial regression models.

RESULTS

1214 patients with SBBC and 59,221 with UBC were included. Patients with SBBC more often had invasive lobular carcinomas (OR 1.29; 95% CI 1.13-1.47), a clinically distinct subtype of breast cancer, than UBC patients. Further, they were older than UBC patients, more often had multifocal cancer (OR 1.13; 95% CI 1.01-1.26), and a less aggressive subtype than UBC patients. Invasive lobular carcinoma was associated with having multiple tumors in breast tissue-both in the form of bilateral disease and multifocal disease, and this association was independent of laterality. No similar pattern was observed for other tumor characteristics.

CONCLUSION

We identified two etiological mechanisms that could explain some of the occurrence of SBBC. The high proportion of less aggressive carcinomas and higher age of SBBC compared to UBC patients suggests that many are diagnosed at a subclinical stage as slow-growing tumors have a higher probability of simultaneous diagnosis. The high proportion of invasive lobular carcinoma observed in bilateral and multifocal disease, being independent of laterality, suggests that these patients have an increased propensity to malignant tumor formation in breast tissue.

Testing tumors from different anatomic sites for clonal relatedness using somatic mutation data

A common task for the cancer pathologist is to determine, in a patient suffering from cancer, whether a new tumor in a distinct anatomic site from the primary is an independent occurrence of cancer or a metastasis. As mutational profiling of tumors becomes more widespread in routine clinical practice, this diagnostic task can be greatly enhanced by comparing mutational profiles of the tumors to determine if they are sufficiently similar to conclude that the tumors are clonally related, that is, one is a metastasis of the other. We present here a likelihood ratio test for clonal relatedness in this setting and provide evidence of its validity. The test is unusual in that there are two possible alternative hypotheses, representing the two anatomic sites from which the single clonal cell could have initially emerged. Although evidence for clonal relatedness is largely provided by the presence of exact mutational matches in the two tumors, we show that it is possible to observe data where the test is statistically significant even when no matches are observed. This can occur when the mutational profile of one of the tumors is closely aligned with the anatomic site of the other tumor, suggesting indirectly that the tumor originated in that other site. We exhibit examples of this phenomenon and recommend a strategy for interpreting the results of these tests in practice.

Systemic investigations into the molecular features of bilateral breast cancer for diagnostic purposes

Introduction: Many breast cancer (BC) patients develop the disease bilaterally. The emergence of two tumors in the same host is unlikely to be a random co-incidence: bilateral BC (biBC) patients are enriched by women who are susceptible to this disease due to genetic or non-genetic factors.Areas covered: Data on molecular pathogenesis and translational aspects of biBC research are summarized.Expert opinion: Studies on concordant and discordant molecular events occurring in paired tumors resemble twin studies, as they help to reveal core components of BC pathogenesis and to analyze interactions between host factors and tumor phenotype. Mutation profiling of biBC pairs suggested that most biBCs are clonally independent malignancies, although some instances of presumably contralateral metastatic spread were shown as well. Many biBCs, especially synchronous ones, demonstrate the similarity of essential tumor characteristics, which can be explained by sharing of genetic background, hormonal milieu, metabolic environment, and external exposures. biBC is strongly associated with BC-predisposing germline mutations; therefore, clinical management of biBC patients must include comprehensive genetic testing. Some contralateral metachronous BCs demonstrate high-level microsatellite instability (MSI-H). MSI-H is sometimes observed in radiation- and chemotherapy-induced tumors; therefore, it is possible that some second BCs are causally related to the therapy applied for the first cancer. MSI-H tumors are responsive to immune checkpoint blockade; hence, MSI-H analysis is advisable for biBC molecular testing. Systematic cataloging of biBC molecular portraits is likely to provide valuable information on fundamental aspects of cancer pathogenesis.

Revisiting multifocal breast cancer: a clonality study of ductal carcinoma using whole exome sequencing

Multifocal breast cancer (MFBC), ductal type, has been hypothesized to arise by one of two mechanisms: either through intramammary/intralymphatic spread from a single index tumor (MBC-1), or as multiple independent tumors with each focus carrying its corresponding ductal carcinoma in-situ (MBC-2). In order to improve our understanding of MFBC pathogenesis, we employed laser capture microdissection coupled with whole-exome sequencing to study clonal origin in MFBC. We selected three cases of MBC-1 (C1 to C3) and MBC-2 (C4 to C6) and analyzed three foci from each case. MBC-1 cases were histologically similar and showed a strong predilection for satellite foci, vascular invasion and nodal metastasis when compared to MBC-2. Our bioinformatics approach provided strong evidence for clonal relationships in MBC-1, as demonstrated by distinct clusters of genes conserved across all tumor foci. Conversely, no gene clusters were shared across all the foci in MBC-2, suggesting multiple independent tumors. These findings provide further support for the two distinct pathogenetic mechanisms in MFBC.

An EM algorithm to improve the estimation of the probability of clonal relatedness of pairs of tumors in cancer patients

Background

We previously introduced a random-effects model to analyze a set of patients, each of which has two distinct tumors. The goal is to estimate the proportion of patients for which one of the tumors is a metastasis of the other, i.e. where the tumors are clonally related. Matches of mutations within a tumor pair provide the evidence for clonal relatedness. In this article, using simulations, we compare two estimation approaches that we considered for our model: use of a constrained quasi-Newton algorithm to maximize the likelihood conditional on the random effect, and an Expectation-Maximization algorithm where we further condition the random-effect distribution on the data.

Results

In some specific settings, especially with sparse information, the estimation of the parameter of interest is at the boundary a non-negligible number of times using the first approach, while the EM algorithm gives more satisfactory estimates. This is of considerable importance for our application, since an estimate of either 0 or 1 for the proportion of cases that are clonal leads to individual probabilities being 0 or 1 in settings where the evidence is clearly not sufficient for such definitive probability estimates.

Conclusions

The EM algorithm is a preferable approach for our clonality random-effect model. It is now the method implemented in our R package Clonality, making available an easy and fast way to estimate this model on a range of applications.

An array consisting of glycosylated quantum dots conjugated to MoS2 nanosheets for fluorometric identification and quantitation of lectins and bacteria

A fluorescent array based on the use of saccharide-functionalized multicolored quantum dots (s-QDs) and of 4-mercaptophenylboronic acid-functionalized MoS₂ nanosheets (PBA-MoS₂) was constructed for multiple identification and quantitation of lectins and bacteria. In this array, the fluorescence of the s-QDs is quenched by the PBA-MoS₂ nanosheets. In the presence of multiple lectins, s-QDs differentially detach from the surface of PBA-MoS₂ nanosheets, producing distinct fluorescence response patterns due to both quenching and enhancement of fluorescence. By analyzing the fluorescence responses with linear discriminant analysis, multiple lectins and bacteria were accurately identified with 100% accuracy. The limits of detection of Concanavalin A, Pisum sativum agglutinin, Peanut agglutinin, and Ricius communis I agglutinin are as low as 3.7, 8.3, 4.2 and 3.9 nM, respectively. The array has further been evidenced to be potent for distinguishing and quantifying different bacterial species by recognizing their surface lectins. The detection limits of Escherichia coli and Enterococcus faecium are 87 and 66 cfu mL^-1, respectively. Graphical abstract Schematic of a fluorometric array based on the use of saccharides-functionalized quantum dots (s-QDs) and 4-mercaptophenylboronic acid-functionalized MoS₂ (PBA- MoS₂) nanosheets. This array was successfully applied to simultaneously analysis of lectins, bacteria in real samples with high sensitivity and accuracy.

Malignant canine mammary tumours: Preliminary genomic insights using oligonucleotide array comparative genomic hybridisation analysis

Neoplastic mammary disease in female dogs represents a major health concern for dog owners and veterinarians, but the genomic basis of the disease is poorly understood. In this study, we performed high resolution oligonucleotide array comparative genomic hybridisation (oaCGH) to assess genome wide DNA copy number changes in 10 malignant canine mammary tumours from seven female dogs, including multiple tumours collected at one time from each of three female dogs. In all but two tumours, genomic imbalances were detected, with losses being more common than gains. Canine chromosomes 9, 22, 26, 27, 34 and X were most frequently affected. Dissimilar oaCGH ratio profiles were observed in multiple tumours from the same dogs, providing preliminary evidence for probable independent pathogenesis. Analysis of adjacent samples of one tumour revealed regional differences in the number of genomic imbalances, suggesting heterogeneity within tumours.

Comprehensive Genomic Profiling Aids in Distinguishing Metastatic Recurrence from Second Primary Cancers

BACKGROUND

Metastatic recurrence after treatment for locoregional cancer is a major cause of morbidity and cancer-specific mortality. Distinguishing metastatic recurrence from the development of a second primary cancer has important prognostic and therapeutic value and represents a difficult clinical scenario. Advances beyond histopathological comparison are needed. We sought to interrogate the ability of comprehensive genomic profiling (CGP) to aid in distinguishing between these clinical scenarios.

MATERIALS AND METHODS

We identified three prospective cases of recurrent tumors in patients previously treated for localized cancers in which histologic analyses suggested subsequent development of a distinct second primary. Paired samples from the original primary and recurrent tumor were subjected to hybrid capture next-generation sequencing-based CGP to identify base pair substitutions, insertions, deletions, copy number alterations (CNA), and chromosomal rearrangements. Genomic profiles between paired samples were compared using previously established statistical clonality assessment software to gauge relatedness beyond global CGP similarities.

RESULTS

A high degree of similarity was observed among genomic profiles from morphologically distinct primary and recurrent tumors. Genomic information suggested reclassification as recurrent metastatic disease, and patients received therapy for metastatic disease based on the molecular determination.

CONCLUSIONS

Our cases demonstrate an important adjunct role for CGP technologies in separating metastatic recurrence from development of a second primary cancer. Larger series are needed to confirm our observations, but comparative CGP may be considered in patients for whom distinguishing metastatic recurrence from a second primary would alter the therapeutic approach. The Oncologist 2017;22:152-157Implications for Practice: Distinguishing a metastatic recurrence from a second primary cancer can represent a difficult clinicopathologic problem but has important prognostic and therapeutic implications. Approaches to aid histologic analysis may improve clinician and pathologist confidence in this increasingly common clinical scenario. Our series provides early support for incorporating paired comprehensive genomic profiling in clinical situations in which determination of metastatic recurrence versus a distinct second primary cancer would influence patient management.

Disease evolution and heterogeneity in bilateral breast cancer

Bilateral breast cancers (BBC) are currently treated as independent tumors arising in the same patient. Herein, we investigated whether BBC indeed evolve independently at the genomic level. We examined paired targeted next generation sequencing genotypes from 155 paraffin tumors corresponding to 76 BBC patients (75 women and one man; 52 concurrent and 24 metachronous), for coding mutations (amino acid changing, minor allele frequency <0.1%) and single nucleotide polymorphism (SNP) zygosity. Germline genotypes were available for 29 patients. Mutations were present in 80 tumors (54/76 patients; 71%), were mostly tumor-private (90%), more frequent in TP53 (19%), PIK3CA (14%), CDH1, GATA3, MLL3. TP53 mutations were more frequent in metachronous tumors (P<0.001); hormone receptor negative (P<0.001); with higher Ki-67 (P=0.002); and, in younger patients (P=0.01). Hypermutated tumors, all TP53 mutated, were diagnosed as the first incidence in 5 patients; their metachronous counterparts were mutation poor without TP53 involvement. Paired tumors shared common mutations at intratumoral frequency >20% in 10/54 comparable BBC (18.5%), 8/10 concurrent. SNP zygosity status was less preserved in metachronous, compared to concurrent disease. Pathogenic germline mutations were present in 10/29 patients, 9 in BRCA1 and one in TP53 (p.Phe341Val, first report in the germline). BBC demonstrated extensive inter- and intra-patient heterogeneity in the present thus far largest series of corresponding paired genotypes. The majority evolve independently and unpredictably, supporting current clinical practice. A considerable minority though, retains clonal origin and may be regarded as a distinct group for therapeutic interventions among concurrent BBC.

Comparative genomic analysis reveals bilateral breast cancers are genetically independent

Bilateral breast cancer (BBC) poses a major challenge for oncologists because of the cryptic relationship between the two lesions. The purpose of this study was to determine the origin of the contralateral breast cancer (either dependent or independent of the index tumor). Here, we used ultra-deep whole-exome sequencing and array comparative genomic hybridization (aCGH) to study four paired samples of BBCs with different tumor subtypes and time intervals between the developments of each tumor. We used two paired primary breast tumors and corresponding metastatic liver lesions as the control. We tested the origin independent nature of BBC in three ways: mutational concordance, mutational signature clustering, and clonality analysis using copy number profiles. We found that the paired BBC samples had near-zero concordant mutation rates, which were much lower than those of the paired primary/metastasis samples. The results of a mutational signature analysis also suggested that BBCs are independent of one another. A clonality analysis using aCGH data further revealed that paired BBC samples was clonally independent, in contrast to clonal related origin found for paired primary/metastasis samples. Our preliminary findings show that BBCs in Han Chinese women are origin independent and thus should be treated separately.

Prior Adjuvant Tamoxifen Treatment in Breast Cancer Is Linked to Increased AIB1 and HER2 Expression in Metachronous Contralateral Breast Cancer

Aim

The estrogen receptor coactivator Amplified in Breast Cancer 1 (AIB1) has been associated with an improved response to adjuvant tamoxifen in breast cancer, but also with endocrine treatment resistance. We hereby use metachronous contralateral breast cancer (CBC) developed despite prior adjuvant tamoxifen for the first tumor as an “in vivo”-model for tamoxifen resistance. AIB1-expression in the presumable resistant (CBC after prior tamoxifen) and naïve setting (CBC without prior tamoxifen) is compared and correlated to prognosis after CBC.

Methods

From a well-defined population-based cohort of CBC-patients we have constructed a unique tissue-microarray including >700 patients.

Results

CBC developed after adjuvant tamoxifen more often had a HER2-positive/triple negative-subtype and a high AIB1-expression (37% vs. 23%, p = 0.009), than if no prior endocrine treatment had been administered. In patients with an estrogen receptor (ER) positive CBC, a high AIB1-expression correlated to an inferior prognosis. However, these patients seemed to respond to tamoxifen, but only if endocrine therapy had not been administered for BC1.

Conclusions

Metachronous CBC developed after prior endocrine treatment has a decreased ER-expression and an increased HER2-expression. This is consistent with endocrine treatment escape mechanisms previously suggested, and indicates metachronous CBC to be a putative model for studies of treatment resistance “in vivo”. The increased AIB1-expression in CBC developed after prior tamoxifen suggests a role of AIB1 in endocrine treatment resistance. In addition, we found indications that the response to tamoxifen in CBC with a high AIB1-expression seem to differ depending on previous exposure to this drug. A different function for AIB1 in the tamoxifen treatment naïve vs. resistant setting is suggested, and may explain previously conflicting results where a high AIB1-expression has been correlated to both a good response to adjuvant tamoxifen and tamoxifen resistance.

Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors

Background

Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal) pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC) mutations/ # total HC mutations).

Methods

Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas.

Results

We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48) and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value <0.01), across renal cell, testicular, and colorectal cancer. The CLS test correctly classified all validation samples but one, which it appears may have been incorrectly classified in the published data. As proof-of-concept we then applied the CLS test to two new cases of invasive synchronous bilateral breast cancer at our institution, each with one hormone receptor positive (ER+/PR+/HER2-) lobular and one triple negative ductal carcinoma. High confidence mutations were identified by exome sequencing and results were validated using deep targeted sequencing. The first tumor pair had CLS of 81% (p-value < 10–15), supporting clonality. In the second pair, no common mutations of 184 variants were validated (p-value >0.99), supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the clonal pair.

Conclusion

We have developed the statistical properties of a carefully defined Clonal Likelihood Score test from mutational profiling of tumor DNA. Under identified conditions, the test appears to reliably distinguish between synchronous tumors of clonal and of independent origin in several cancer types. This approach may have scientific and clinical utility.

Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour

BACKGROUND

Patients with breast cancer have an increased risk of developing subsequent breast cancers. It is important to distinguish whether these tumours are de novo or recurrences of the primary tumour in order to guide the appropriate therapy. Our aim was to investigate the use of DNA methylation profiling and array comparative genomic hybridization (aCGH) to determine whether the second tumour is clonally related to the first tumour.

METHODS

Methylation-sensitive high-resolution melting was used to screen promoter methylation in a panel of 13 genes reported as methylated in breast cancer (RASSF1A, TWIST1, APC, WIF1, MGMT, MAL, CDH13, RARβ, BRCA1, CDH1, CDKN2A, TP73, and GSTP1) in 29 tumour pairs (16 ipsilateral and 13 contralateral). Using the methylation profile of these genes, we employed a Bayesian and an empirical statistical approach to estimate clonal relationship. Copy number alterations were analysed using aCGH on the same set of tumour pairs.

RESULTS

There is a higher probability of the second tumour being recurrent in ipsilateral tumours compared with contralateral tumours (38 % versus 8 %; p <0.05) based on the methylation profile. Using previously reported recurrence rates as Bayesian prior probabilities, we classified 69 % of ipsilateral and 15 % of contralateral tumours as recurrent. The inferred clonal relationship results of the tumour pairs were generally concordant between methylation profiling and aCGH.

CONCLUSION

Our results show that DNA methylation profiling as well as aCGH have potential as diagnostic tools in improving the clinical decisions to differentiate recurrences from a second de novo tumour.

Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing

INTRODUCTION

By convention, a contralateral breast cancer (CBC) is treated as a new primary tumor, independent of the first cancer (BC1). Although there have been indications that the second tumor (BC2) sometimes may represent a metastatic spread of BC1, this has never been conclusively shown. We sought to apply next-generation sequencing to determine a "genetic barcode" for each tumor and reveal the clonal relationship of CBCs.

METHODS

Ten CBC patients with detailed clinical information and available fresh frozen tumor tissue were studied. Using low-coverage whole genome DNA-sequencing data for each tumor, chromosomal rearrangements were enumerated and copy number profiles were generated. Comparisons between tumors provided an estimate of clonal relatedness for tumor pairs within individual patients.

RESULTS

Between 15-256 rearrangements were detected in each tumor (median 87). For one patient, 76 % (68 out of 90) of the rearrangements were shared between BC1 and BC2, highly consistent with what has been seen for true primary-metastasis pairs (>50 %) and thus confirming a common clonal origin of the two tumors. For most of the remaining cases, BC1 and BC2 had similarly low overlap as unmatched randomized pairs of tumors from different individuals, suggesting the CBC to represent a new independent primary tumor.

CONCLUSION

Using rearrangement fingerprinting, we show for the first time with certainty that a contralateral BC2 can represent a metastatic spread of BC1. Given the poor prognosis of a generalized disease compared to a new primary tumor, these women need to be identified at diagnosis of CBC for appropriate determination of treatment. Our approach generates a promising new method to assess clonal relationship between tumors. Additional studies are required to confirm the frequency of CBCs representing metastatic events.

Uncovering the genomic heterogeneity of multifocal breast cancer

Multifocal breast cancer (MFBC), defined as multiple synchronous unilateral lesions of invasive breast cancer, is relatively frequent and has been associated with more aggressive features than unifocal cancer. Here, we aimed to investigate the genomic heterogeneity between MFBC lesions sharing similar histopathological parameters. Characterization of different lesions from 36 patients with ductal MFBC involved the identification of non‐silent coding mutations in 360 protein‐coding genes (171 tumour and 36 matched normal samples). We selected only patients with lesions presenting the same grade, ER, and HER2 status. Mutations were classified as ‘oncogenic’ in the case of recurrent substitutions reported in COSMIC or truncating mutations affecting tumour suppressor genes. All mutations identified in a given patient were further interrogated in all samples from that patient through deep resequencing using an orthogonal platform. Whole‐genome rearrangement screen was further conducted in 8/36 patients. Twenty‐four patients (67%) had substitutions/indels shared by all their lesions, of which 11 carried the same mutations in all lesions, and 13 had lesions with both common and private mutations. Three‐quarters of those 24 patients shared oncogenic variants. The remaining 12 patients (33%) did not share any substitution/indels, with inter‐lesion heterogeneity observed for oncogenic mutation(s) in genes such as PIK3CA, TP53, GATA3, and PTEN. Genomically heterogeneous lesions tended to be further apart in the mammary gland than homogeneous lesions. Genome‐wide analyses of a limited number of patients identified a common somatic background in all studied MFBCs, including those with no mutation in common between the lesions. To conclude, as the number of molecular targeted therapies increases and trials driven by genomic screening are ongoing, our findings highlight the presence of genomic inter‐lesion heterogeneity in one‐third, despite similar pathological features. This implies that deeper molecular characterization of all MFBC lesions is warranted for the adequate management of those cancers. © 2015 The Authors. Pathological Society of Great Britain and Ireland.

Characteristics of Multifocal and Multicentric Breast Cancers

BACKGROUND

Multifocality and multicentricity are increasingly recognized in breast cancer. However, little is known about the characteristics and biology of these cancers and the clinical implications are controversial.

METHODS

A retrospective, institutional database was used to compare characteristics of multifocal (MF) and multicentric (MC) breast cancers with unifocal (UF) cancers to study concordance of histology and receptor status among primary and secondary foci and to evaluate predictors of lymph node positivity using multivariate logistic regression.

RESULTS

Of 1495 invasive cancers, 1231 (82.3 %) were UF, 169 (11.3 %) were MF, and 95 (6.4 %) were MC cancers. When MF and MC cancers were compared with UF cancers, MC but not MF cancers were associated with young age at diagnosis, larger tumor size, lymphovascular invasion, and node positivity. MF but not MC tumors were more likely to be ER/PR+Her2+ tumors and less likely to be triple-negative cancers compared with UF tumors. MF tumors were more likely to be infiltrating ductal carcinomas with an extensive intraductal component, and MC tumors were more likely to be infiltrating lobular carcinomas. Concordance of histology and receptor status between primary and secondary foci was high and was similar for both MF and MC cancers. Multicentricity remained an independent predictor of lymph node positivity on multivariate analysis.

CONCLUSION

MF and MC tumors seem to be biologically different diseases. MC is clinicopathologically more aggressive than MF disease and is more frequently associated with younger age and larger tumor size and also is an independent predictor of node positivity.

HER2-Positive Metaplastic Spindle Cell Carcinoma Associated with Synchronous Bilateral Apocrine Carcinoma of the Breast

Apocrine carcinoma, which is strictly defined as over 90% of tumor cells showing apocrine differentiation, is a rare variant of breast cancer. Here we report an uncommon case in which apocrine carcinomas developed concurrently in both breasts; in addition, a sarcomatoid spindle cell lesion was coincident in the right breast. Both apocrine carcinomas were immunohistochemically negative for estrogen receptor (ER) and progesterone receptor (PgR), but diffusely positive for androgen receptor (AR), GCDFP-15, and HER2. The presence of intraductal components in bilateral carcinomas and the absence of lymph node metastasis suggested that they were more likely to be individual primary lesions rather than metastatic disease. The spindle cell lesion showed a relatively well-circumscribed nodule contiguous with the apocrine carcinoma. HER2 oncoprotein overexpression was observed not only in the apocrine carcinoma, but also in the spindle cell lesion. Since the spindle cell component was intimately admixed with apocrine carcinoma and had focal cytokeratin expression, we diagnosed it as metaplastic spindle cell carcinoma, which was originated from the apocrine carcinoma. To our knowledge, this is the first case report of a patient with synchronous bilateral apocrine carcinomas coinciding with metaplastic carcinoma.

Frequent copy number gains at 1q21 and 1q32 are associated with overexpression of the ETS transcription factors ETV3 and ELF3 in breast cancer irrespective of molecular subtypes

Several ETS transcription factors are involved in the pathogenesis of human cancers by different mechanisms. As gene copy number gain/amplification is an alternative mechanism of oncogenic activation and 1q gain is the most common copy number change in breast carcinoma, we investigated how that genomic change impacts in the expression of the three 1q ETS family members ETV3, ELK4, and ELF3. We have first evaluated 141 breast carcinomas for genome-wide copy number changes by chromosomal CGH and showed that 1q21 and 1q32 were the two chromosome bands with most frequent genomic copy number gains. Second, we confirmed by FISH with locus-specific BAC clones that cases showing 1q gain/amplification by CGH showed copy number increase of the ETS genes ETV3 (located in 1q21~23), ELF3, and ELK4 (both in 1q32). Third, gene expression levels of the three 1q ETS genes, as well as their potential targets MYC and CRISP3, were evaluated by quantitative real-time PCR. We here show for the first time that the most common genomic copy number gains in breast cancer, 1q21 and 1q32, are associated with overexpression of the ETS transcription factors ETV3 and ELF3 (but not ELK4) at these loci irrespective of molecular subtypes. Among the three 1q ETS genes, ELF3 has a relevant role in breast carcinogenesis and is also the most likely target of the 1q copy number increase. The basal-like molecular subtype presented the worst prognosis regarding disease-specific survival, but no additional prognostic value was found for 1q copy number status or ELF3 expression. In addition, we show that there is a correlation between the expression of the oncogene MYC, irrespectively of copy number gain at its loci in 8q24, and the expression of both the transcriptional repressor ETV3 and the androgen respondent ELK4.

Evaluation of Biomarkers in Multifocal/Multicentric Invasive Breast Carcinomas

Background. The purpose of this study was to evaluate whether breast carcinoma biomarkers vary among separate tumor foci of multifocal/multicentric (MF/MC) breast carcinomas and whether this variation correlates with morphological features and tumor grade. Design. We reviewed the biomarker profiles of MF/MC invasive breast carcinomas diagnosed between January 2001 and June 2010 at our institution. Estrogen receptor (ER), progesterone receptor (PR), and human epidermal receptor protein (HER2) results were classified as positive or negative. Results. Out of the 51 patients included in the study, 6 cases had 2 tumor foci with different morphologies, 7 cases had 2 foci with similar morphology but different grades, and 38 cases had 2 tumor foci with similar morphologies and grades. Out of the 38 patients who had MF/MC tumors with the same morphology and grade, only 1 patient had a difference in ER and PR status between foci. Out of the 7 patients who had morphologically similar tumors with different grades, 4 had similar results in both tumor foci, 3 had different results for ER and PR, and another had differing results for HER2 between the foci. All 6 patients who had MF/MC foci with different morphologies exhibited similar ER, PR, and HER2 results between the foci. Conclusion. Regardless of the similarity in tumor morphology or grade, a small number of cases included foci that exhibited different tumor marker expression, which might affect the treatment strategy. Therefore, our results suggest that the evaluation of tumor markers in different foci should be considered in MF/MC tumors for accurate treatment strategies.

Analysis of gene alterations of mitochondrial DNA D-loop regions to determine breast cancer clonality

Background:

It has been a challenge to determine breast cancer clonality accurately. The aim of the present study was to assess methods using formalin-fixed paraffin-embedded (FFPE) tissue to differentiate new primary tumours from true recurrences that are associated with poorer prognoses and often require more aggressive treatment.

Methods:

We investigated the novel method of analysing gene alterations of mitochondrial DNA D-loop region (GAMDDL) and compared it with the conventional method of analysing the X-chromosome-linked human androgen receptor (HUMARA). The FFPE sections of primary and secondary breast cancers, the non-neoplastic mammary gland, and lymph nodes were examined.

Results:

Informative rates for HUMARA, GAMDDL, and combined analyses were 42.1%, 76.9%, and 89.5%, respectively. All of the 10 contralateral breast cancers were determined to be non-clonal. In contrast, 3 out of 8 (37.5%) of the ipsilateral secondary tumours shared a clonal origin with the primary tumour and were classified as true recurrences, whereas 4 out of 8 (50%) were classified as new primary tumours.

Conclusion:

GAMDDL analysis represents a novel and useful molecular method for examining the precise cell lineages of primary and secondary tumours, and was more accurate than HUMARA in determining clonality.

Tumor Stage Affects Risk and Prognosis of Contralateral Breast Cancer: Results From a Large Swedish-Population–Based Study

Purpose

The number of breast cancer survivors at risk of developing contralateral breast cancer (CBC) is increasing. However, ambiguity remains regarding risk factors and prognosis for women with CBC.

Patients and Methods

In a cohort of 42,670 women with breast cancer in the Uppsala/Örebro and Stockholm regions in Sweden in 1992 to 2008, we assessed risk factors for and prognosis of metachronous CBC by using survival analysis. Breast cancer–specific survival for women with CBC was evaluated and compared with results for women with unilateral breast cancer (UBC) by using time-dependent Cox-regression modeling.

Results

An increased risk for CBC was observed among women who had primary breast cancer with ≥ 10 involved lymph nodes compared with node-negative women (adjusted hazard ratio [HR], 1.8; 95% CI, 1.2 to 2.7). The prognosis was poorer in women with CBC than with UBC. The hazard of dying from breast cancer was especially high for women with a short interval time to CBC (adjusted HR, 2.3; 95% CI, 1.8 to 2.8 for CBC diagnosed ≤ 5 years v UBC) and gradually decreased with longer follow-up time but remained higher than the hazard originating from the primary tumor for ≥ 10 years.

Conclusion

Women with advanced-stage primary breast cancer had an increased risk of developing CBC. CBC is associated with an increased risk of dying from breast cancer throughout a long period of follow-up after the primary tumor. Our findings suggest that the event of CBC marks a new clinical situation in terms of investigations for metastases, treatment considerations, and follow-up strategy.

12q amplification defines a subtype of extraskeletal osteosarcoma with good prognosis that is the soft tissue homologue of parosteal osteosarcoma

Extraskeletal osteosarcomas are rare tumors with neoplastic cells synthesizing bone, usually associated with poor prognosis. We present the case of a 40-year-old man with an extraskeletal osteosarcoma that was treated by surgery and adjuvant radiotherapy. Thirteen years after the diagnosis, he remains disease-free, without any recurrences or metastases. Histopathological analysis favored the diagnosis of chondroblastic extraskeletal osteosarcoma grade II. G-banding, comparative genomic hybridization (CGH), and real-time PCR for the MDM2 and CDK4 genes were performed to describe the genetic profile of this tumor and revealed aberrations that are common findings of parosteal osteosarcomas. Ring chromosomes, giant marker chromosomes, and a telomeric association were found with G-banding. CGH revealed that 12q was amplified in the ring and giant markers identified by G-banding. Real-time PCR for MDM2 and CDK4 confirmed the amplification of these genes located in 12q. Our findings suggest that a variant of extraskeletal osteosarcoma, which is genotypically similar to parosteal osteosarcoma, exists and is associated with good prognosis.

Patterns of metastasis in women with metachronous contralateral breast cancer

Background:

The understanding of metastatic patterns after metachronous contralateral breast cancer (CBC) may help determine the biological nature of CBC.

Methods:

A cohort of 8478 women with breast cancer treated at Guy’s and St Thomas’ NHS Foundation Trust between 1975 and 2006 were studied. Organ-specific 5-year cumulative incidence and incidence rate ratios were assessed for women diagnosed with unilateral breast cancer (UBC), CBC within 5 years and CBC more than 5 years of the initial diagnosis.

Results:

Women diagnosed with CBC within 5 years had a higher incidence of metastases in all organs compared with UBC. Women with a short interval time to CBC developed metastasis more rapidly and were more likely to develop visceral and distant cutaneous metastases compared with bone metastasis.

Conclusion:

These findings explain poor prognosis of women with early occurring CBC and suggest that some of these CBCs are indicators of aggressive and/or systemic disease.

Cytogenetic analysis of tumor clonality

All or almost all neoplasias subjected to systematic cytogenetic scrutiny have been found to harbor acquired chromosomal aberrations. The paradigm stemming from the study of hematopoietic malignancies and sarcomas is that cancers are of monoclonal origin (i.e., they have developed from a single transformed somatic progenitor) because all the neoplastic parenchyma cells share at least one primary chromosomal abnormality, with subsequent clonal evolution along the lines of Darwinian selection occurring among the various subclones carrying secondary aberrations. When carcinomas began to be studied more extensively by cytogenetic methods, however, sometimes many cytogenetically unrelated clones were found, in seeming contradiction to the monoclonal hypothesis. Also studies of multiple samples from the same patient led to a rethinking of what the cytogenetic evidence really revealed about tumor clonality, both in its early stages and during disease development. The observed cytogenetic heterogeneity in, for example, tumors of the breast and pancreas vastly surpasses that of leukemias, lymphomas, connective tissue tumors, or even most epithelial, including uroepithelial, tumors. Theoretical reasoning as well as the available experimental data we here review show that the clonal evolution of neoplastic cell populations follows either of four principal pathways: (1) initial monoclonality is retained throughout the entire course of the disease with no additional, secondary aberrations accrued as judged by karyotypic appearance; (2) tumorigenesis is monoclonal but additional aberrations develop with time leading to secondary clonal heterogeneity (clonal divergence); (3) polyclonal tumorigenesis exists from the beginning but is followed by an overall reduction in genomic complexity with time (clonal convergence) due to selection among cytogenetically unrelated clones during tumor progression, resulting in secondary oligo- or monoclonality; or (4) polyclonal tumorigenesis with early clonal convergence is followed by later clonal divergence due to the acquisition of additional cytogenetic changes by the clone(s) that survived during the middle phases of tumor progression. Further studies of individual tumor cells are necessary to elicit precise information about the cell-to-cell variability that exists in many, especially epithelial, neoplasms and which holds the key to a more profound understanding of the complex issue of tumor clonality during all stages of cancer development.

A case-match study comparing unilateral with synchronous bilateral breast cancer outcomes

PURPOSE

There is controversy about whether patients with synchronous bilateral breast cancer (SBBC) have similar or worse outcomes compared with patients with unilateral breast cancer. The purpose of this study was to determine whether survival outcomes for patients with SBBC can be estimated from the characteristics of their individual cancers.

PATIENTS AND METHODS

Patients had invasive breast cancer, without metastases or inflammatory disease, diagnosed in British Columbia between 1989 and 2000. There were 207 cases with SBBC (diagnosed ≤ 2 months apart) and 15,497 with unilateral breast cancer. By using 10-year breast cancer-specific survival (BCSS) estimates, the higher-risk cancer of each SBBC case was determined and matched with three breast cancers from the unilateral cohort to select 621 high-risk matches. The priority sequence of matching the prognostic and predictive variables was positive lymph node number, primary tumor size, age, grade, lymphovascular invasion, estrogen receptor status, local therapy used, margin status, treating clinic, diagnosis year, and type of systemic therapy used.

RESULTS

With a median follow-up of 10.2 years, the overall 10-year BCSS was significantly higher for the unilateral cohort (81%; 95% CI, 81% to 82%) than for the SBBC cases (71%; 95% CI, 63% to 77%). The SBBC cases had significantly higher mean age and stage at presentation. The 10-year BCSS was 74% (95% CI, 69% to 77%) for the high-risk matches.

CONCLUSION

BCSS was not significantly different between the SBBC cases and their high-risk matches.

Occult malignancy in patients undergoing contralateral prophylactic mastectomy

OBJECTIVE

To identify factors that predict for occult malignancy or high-risk lesions (HRL) in the contralateral breast among women undergoing contralateral prophylactic mastectomy (CPM).

BACKGROUND

A growing number of women are choosing to undergo CPM, yet the benefit of this procedure for the average woman with breast cancer remains uncertain. The identification of reliable predictors of occult malignancy or HRL in the contralateral breast may aid in selecting patients most likely to benefit from CPM.

METHODS

Patients undergoing mastectomy with CPM for their first diagnosis of unilateral stage 0 to III breast cancer were retrospectively identified (1997-2005). Univariate and multivariate logistic regression was used to identify factors predictive of HRL and/or occult contralateral breast cancer (CBC).

RESULTS

Among 2965 patients, 407 (13%) underwent CPM. Occult CBC was identified in 24 (6%) patients, and 114 (28%) had an HRL. On univariate analysis, multifocality/multicentricity of the index cancer was the only factor associated with occult malignancy in the CPM (OR 2.88, P = 0.04). On multivariate analysis, patient age and progesterone receptor positivity of the index cancer were associated with finding either malignancy or a HRL in the CPM.

CONCLUSIONS

The diagnosis of multifocality/multicentricity invasive index cancer was associated with occult malignancy in the CPM; however, lack of standardized definitions and differences in pathologic evaluation limit the application of this finding in the preoperative setting. Until reliable predictors for occult disease are identified, the low rates of occult CBC do not support the use of CPM in average-risk women with newly diagnosed breast cancer.

Risk factors for metachronous contralateral breast cancer suggest two aetiological pathways

Although many studies show an increased risk of metachronous contralateral breast cancer (CBC) in women with a positive family history and young age at diagnosis of the initial breast cancer, the aetiological pathways are still enigmatic. In a cohort of 8478 primary breast cancer patients diagnosed between 1975 and 2006, 558 cases of metachronous CBC were identified. Using multivariate Cox proportional hazards models, we analysed risk factors assessed at the time of the first primary tumour, including patient demographics, tumour characteristics and treatment among 4681 breast cancer patients for whom data on key variables were available. The analysis was performed separately in patients who developed CBC without and with prior recurrence(s). Risk of CBC without prior recurrent disease was increased by a positive family history [adjusted relative risk (RR) 2.8 (95% confidence interval (CI) 1.4-5.5)]; and decreased by endocrine treatment [RR 0.6 (95% CI 0.4-1.0)]. We found an increased risk of CBC with prior recurrent disease with younger age [RR 1.2 (95% CI 1.4-3.0)]; positive family history [RR 2.1 (95%CI 0.8-5.0)]; and extensive lymph node involvement [RR 2.0 (95% CI 1.2-3.6)]. Our results suggest that nodal status of the primary tumour may be as important a risk factor as family history or age, which indicates a high susceptibility to breast cancer or an impaired host defence mechanism. It may also imply that some CBCs are metastases from the first primary tumour, particularly in patients who present with recurrent disease before CBC.

Acute megakaryoblastic leukemia with a four-way variant translocation originating the RBM15-MKL1 fusion gene

Acute megakaryoblastic leukemia (AMKL) with t(1;22)(p13;q13) is a subset of acute myeloid leukemia (AML) representing <1% of all cases and about 70% of pediatric AMKL in the first year of life. We present a case of a 7-month-old female in whom the bone marrow karyotype showed the derivative chromosome der(22)t(1;22)(p13;q13). The RBM15-MKL1 fusion transcript was detected by RT-PCR and confirmed by sequencing analyses. FISH analyses revealed the presence of the four-way translocation t(1;22;17;18)(p13;q13;q22;q12).

Rethinking the prosaicism of mosaicism; is it in us?

Exponential advances in the quantitation of DNA variation and epigenetic states seem poised to convert much of biological research into a statistical exercise. But these developments also invite us to reimagine well-worn biological concepts on a grander scale. Somatic mosaicism refers to postzygotic mutations persisting in the individual, occasionally conspicuous to dermatologists as Blaschkoid, checkerboard, phylloid and patchy morphologies. A thoughtful examination of cutaneous mosaicism suggests, however, that virtually all of us may be somatic mosaics. Such genetic variability within individuals might explain localized presentations of disease and implies that some tissues literally evolve throughout life. We discuss here (i) the likely ubiquity of somatic mosaicism, (ii) the broad range of possible biological consequences and (iii) how experimentalists and clinicians may begin establishing genotype-to-phenotype correlates.

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.

Synchronous multiple ipsilateral breast cancers: implications for patient management

Interest in the presence and management of synchronous multiple ipsilateral breast cancer has been reported since the early 1920s. The demonstration of multiple foci of breast cancer has been reported in 9-75% of breast cancer related specimens. The large difference in reported incidence is multifactorial and related to the definitions applied, mode of detection and pathological assessment. However, randomised clinical trials comparing total mastectomy and segmental mastectomy with or without radiation over many years have shown no difference in distant disease-free survival or overall survival in patients with synchronous multiple ipsilateral breast cancer compared with unifocal breast cancer. This review examines the current definitions, incidence, pathological assessment, staging and surgical options of synchronous multiple ipsilateral breast cancer.

Diagnostic and prognostic utility of molecular markers in synchronous bilateral breast carcinoma

Histologic criteria have a limited role in determining whether the synchronous bilateral breast carcinomas represent two primaries or a metastasis to the contralateral breast. We studied the molecular analysis of synchronous bilateral breast carcinoma and whether they are originating from a single or different clone. We examined 17 patients with breast carcinoma, including 12 patients with synchronous bilateral carcinomas and control group of 5 infiltrating ductal carcinomas with regional lymph node metastases. Mutations were quantitatively determined to detect loss of heterozygosity (LOH) and microsatellite size alterations for a broad panel of 15 markers, involving 10 chromosomes using polymerase chain reaction. The carcinomas were classified as de novo or metastasis based on three levels of concordance: (1) marker-affected tumors were considered concordant if 50% or more of the same markers were mutated, (2) same gene copy affected, and (3) temporal sequence of mutation acquisition. In synchronous bilateral breast carcinoma patients, molecular analysis showed discordant mutations in all cases, supporting the diagnosis of de novo bilateral primary breast carcinomas. In patients with lymph node metastases, the primary breast carcinoma and metastases shared the same mutations, revealing a metastatic lesion. In conclusion, the application of molecular technology may play an important role for the differential diagnosis of dual primary carcinomas vs a metastatic breast cancer to contralateral breast. In this study, synchronous bilateral breast cancers represent two independent primaries rather than metastatic events.

Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs

Background

Today, no objective criteria exist to differentiate between individual primary tumors and intra- or intermammary dissemination respectively, in patients diagnosed with two or more synchronous breast cancers. To elucidate whether these tumors most likely arise through clonal expansion, or whether they represent individual primary tumors is of tumor biological interest and may have clinical implications. In this respect, high resolution genomic profiling may provide a more reliable approach than conventional histopathological and tumor biological factors.

Methods

32 K tiling microarray-based comparative genomic hybridization (aCGH) was used to explore the genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs, and was compared with histopathological and tumor biological parameters.

Results

Based on global copy number profiles and unsupervised hierarchical clustering, five of ten (p = 1.9 × 10^-5) unilateral tumor pairs displayed similar genomic profiles within the pair, while only one of eight bilateral tumor pairs (p = 0.29) displayed pair-wise genomic similarities. DNA index, histological type and presence of vessel invasion correlated with the genomic analyses.

Conclusion

Synchronous unilateral tumor pairs are often genomically similar, while synchronous bilateral tumors most often represent individual primary tumors. However, two independent unilateral primary tumors can develop synchronously and contralateral tumor spread can occur. The presence of an intraductal component is not informative when establishing the independence of two tumors, while vessel invasion, the presence of which was found in clustering tumor pairs but not in tumor pairs that did not cluster together, supports the clustering outcome. Our data suggest that genomically similar unilateral tumor pairs may represent a more aggressive disease that requires the addition of more severe treatment modalities, and underscores the importance of evaluating the clonality of multiple tumors for optimal patient management. In summary, our findings demonstrate the importance of evaluating the properties of both tumors in order to determine the most optimal patient management.

High-resolution mapping of DNA breakpoints to define true recurrences among ipsilateral breast cancers

BACKGROUND

To distinguish new primary breast cancers from true recurrences, pangenomic analyses of DNA copy number alterations (CNAs) using single-nucleotide polymorphism arrays have proven useful.

METHODS

The pangenomic profiles of 22 pairs of primary breast carcinoma (ductal or lobular) and ipsilateral breast cancers from the same patients were analyzed. Hierarchical clustering was performed using CNAs and DNA breakpoint information. A partial identity score developed using DNA breakpoint information was used to quantify partial identities between two tumors. The nature of ipsilateral breast cancers (true recurrence vs new primary tumor) as defined using the clustering methods and the partial identity score was compared with that based on clinical characteristics. Metastasis-free survival was compared among patients with primary tumors and true recurrences as defined using the partial identity score and by clinical characteristics. All statistical tests were two-sided.

RESULTS

All methods agreed on the nature of ipsilateral breast cancers for 14 pairs of samples. For five pairs, the clinical definition disagreed with both clustering methods. For three pairs, the two clustering methods were discordant and the one using DNA breakpoints agreed with the clinical definition. The partial identity score confirmed the nature of ipsilateral breast cancers as defined by clustering of DNA breakpoints in 21 of 22 pairs. The difference in metastasis-free survival of patients with new primary tumors and those with true recurrences was not statistically significant when tumors were defined based on clinical and histologic characteristics (5-year metastasis-free survival: 76%, 95% confidence interval [CI] = 52% to 100% for new primary tumors and 38%, 95% CI = 17% to 83% for true recurrences; P = .18; new primary tumor vs true recurrence, hazard ratio = 2.8, 95% CI = 0.6 to 13.7), but the difference was statistically significant when tumors were defined using the partial identity score (5-year metastasis-free survival: 100% for new primary tumors and 29%, 95% CI = 11% to 78% for true recurrences; P = .01).

CONCLUSIONS

DNA breakpoint information more often agreed with the clinical determination than CNAs in this population. The partial identity score, which was calculated based on DNA breakpoints, allows statistical discrimination between new primary tumors and true recurrences that could outperform the clinical determination in terms of prognosis.

Clonal relationship between Hashimoto thyroiditis and thyroid lymphoma

BACKGROUND

Although Hashimoto thyroiditis (HT) is a predisposing factor for B-lineage thyroid lymphoma, clonal B-cell populations in HT are rare.

AIM

To investigate whether there is a clonal relationship between HT and primary thyroid lymphoma.

METHODS

Clonalilty and sequence similarity was determined by PCR followed by sequencing and comparing immunoglobulin heavy chain (IgH) gene rearrangement sequences to germline sequences and to each other.

RESULTS

12/20 patients with primary thyroid lymphoma had a previous history and histological diagnosis of HT. Clonal IgH bands associated with a polyclonal background were present in four of these 12 cases of HT; of these four, three had reproducible clonal IgH bands from the subsequently developed lymphoma. The range of similarity (homology) of multiple clonal bands in HT with the germline IgH varied from 90% to 96.3%. Multiple clonal bands in HT had sequence similarity (homology) of 62-100% with the clonal band in the lymphoma from the same patient. At least one clonal band in HT had more than 96% similarity (homology) with the clonal band of lymphoma in all three cases.

CONCLUSION

Sequence similarity between the clonal bands in HT and subsequently developed thyroid lymphoma is supportive of the argument that primary thyroid lymphoma may evolve from HT.

Genomic alterations in sporadic synchronous primary breast cancer using array and metaphase comparative genomic hybridization

Synchronous primary breast cancer describes the occurrence of multiple tumors affecting one or both breasts at initial diagnosis. This provides a unique opportunity to identify tissue-specific genomic markers that characterize each tumor while controlling for the individual genetic background of a patient. The aim of this study was to examine the genomic alterations and degree of similarity between synchronous cancers. Using metaphase comparative genomic hybridization and array comparative genomic hybridization (aCGH), the genomic alterations of 23 synchronous breast cancers from 10 patients were examined at both chromosomal and gene levels. Synchronous breast cancers, when compared to their matched counterparts, were found to have a common core set of genetic alterations, with additional unique changes present in each. They also frequently exhibited features distinct from the more usual solitary primary breast cancers. The most frequent genomic alterations included chromosomal gains of 1q, 3p, 4q, and 8q, and losses of 11q, 12q, 16q, and 17p. aCGH identified copy number amplification in regions that are present in all 23 tumor samples, including 1p31.3-1p32.3 harboring JAK1. Our findings suggest that synchronous primary breast cancers represent a unique type of breast cancer and, at least in some instances, one tumor may give rise to the other.

Chromosome analysis and molecular cytogenetic investigations of an epithelioid hemangioendothelioma

Epithelioid hemangioendothelioma is a rare, well-differentiated endothelial tumor with a wide spectrum of clinical behavior and for which genetic data are extremely limited. We present a case of an epithelioid hemangioendothelioma in a 22-year-old male, which was analyzed with multiple cytogenetic approaches. Conventional cytogenetic analysis detected structural abnormalities of 11q13 and 11q14, rings, and marker chromosomes. Multi-color FISH (mFISH) and high-resolution multi-color banding (mBAND) analyses demonstrated that the aberrations of chromosome 11 were deletions and that the ring and marker chromosomes consisted of 12(q14 approximately q21) material. Comparative genomic hybridization (CGH) analysis revealed gains of 11(q13 approximately q14) and 12(q11 approximately q21), loss of 11(q21 approximately qter), and 2 amplicons at 12(q12 approximately q13) and 12(q14 approximately q21). Our data indicate that a subset of epithelioid hemangioendotheliomas may be characterized by complex rearrangements involving deletions and gains of 11q and 12q amplifications. The present case also shows that, in order to describe and understand such complex chromosome aberrations, chromosome analysis must be complemented with several molecular cytogenetic techniques.