Next-Generation Sequencing in Contralateral Breast Cancer Could Affect Treatment Decisions

November 23, 2015
Colin G. Evans, PhD

A new method to elucidate the clonal relationship between tumors used tissues and clinical details from patients with contralateral breast cancer, and for the first time, next-generation sequencing.

A new method to elucidate the clonal relationship between tumors has been published inBreast Cancer Research.1The study used tissues and clinical details from patients with contralateral breast cancer (CBC), and for the first time, next-generation sequencing (NGS)2conclusively showed that a tumor in the contralateral breast can arise as a metastatic clone.

The issue of whether or not contralateral tumors are metastatic clones has important implications for patient treatment and prognosis, which increases the importance of identifying women in whom the contralateral tumor is a metastasis and not a new primary tumor.1

The research team used whole-genome sequencing (WGS) to most accurately characterize the genomes of contralateral breast tumors, a method they term as chromosomal “rearrangement fingerprinting.” They discussed other methods, such as X-chromosome inactivation status, p53 mutations, and partial allelotyping, noting that none of these tests can conclusively confirm clonal relationships between tumors.1


The researchers obtained detailed clinical information (patient and tumor) on 10 patients with contralateral breast cancer. Nine of the patients had two invasive tumors, and in one patient, the contralateral tumor was an in-situ lesion. The authors explained that this was included to represent a situation where a patient was presumed to have two independent primary tumors.

WGS was conducted on the ten CBC pairs, using a strategy that ensured improved physical genome coverage. Their methods provided a median sequence coverage of 6.5 (1.8-11.2), with a median physical coverage of 14.7 (6.9-28.4). The median number of chromosomal rearrangements was 87 per tumor (15-256).1

The researchers wanted to know how many identical rearrangements could be found in tumor samples from different individuals. They investigated all possible pairings between the patients. This would indicate instances where overlap could occur by chance or be due to unfinished sorting of germline events. They found that between 0 to 25 (median 4) rearrangements could be shared by two tumors from different individuals. This gave a combined shared fraction of 0% to 18% (median 2%).1

Turning to matched patient pairs (comparing tumors from the same individual) they found a median of 28 (6-68) shared rearrangements between breast cancer 1 (BC1) and breast cancer 2 (BC2). This time, the combined shared fraction ranged from 6%-76% (median 13%).1

However, the data for one of the patients (patient 8) differed markedly. The analysis uncovered there were 76% (n = 68) of shared rearrangements between BC1 and BC2. There were 19 rearrangements unique to BC1 and 3 to BC2. The authors state, “Patient 8’s extreme degree of similarity of chromosomal rearrangements unequivocally supports BC2 being the result of metastatic spread from BC1.” They also refer to other work they have conducted that employed the same techniques examining the primary tumor and distant metastases. That work showed the primary tumor always shares upward of 50% of rearrangements with its metastasis.1

In contrast, seven of the remaining patients had far fewer rearrangements in common between BC1 and BC2. Their combined shared fractions were between 6% and 15% (median of 10%), and the authors concluded that the CBCs in these cases developed independently from the primary tumor. In two patients the rearrangement overlap was 39% and 46%, and although this certainly aroused suspicion that they could be contralateral metastases, DNA samples (which were not available) would have been needed to establish whether or not this was the case.1

When the WGS was used to construct copy number variation profiles, the same patterns emerged, with the data for patient 8 again indicating BC2 to be a metastasis from BC1.1

When comparing the clinical histological characteristics of the tumors from the patients the authors found that routine pathological markers did not accurately delineate new primary tumors from contralateral metastases.1

Next Steps in Contralateral Breast Cancer Treatment

The authors state this analysis is a new method that not only casts new light on the management of CBC, but also applicable to other cancer types, when issues of “new primary” versus metastasis impact clinical treatment issues. In the case of breast cancer, the present view is to treat CBCs as separate tumors. However, if BC2 is a metastasis, then the patient would have a worse prognosis and need an alternative treatment approach versus a primary tumor. The authors conclude, that once accurately identified, “With intensified treatment for these patients there may be a possibility to prevent further spread, and avoid the development of a generalized incurable breast cancer.”1


  1. Alkner S, Tang MH, Brueffer C, et al. 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.Breast Cancer Res. 2015;17(1):102.doi: 10.1186/s13058-015-0608-x.
  2. Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, et al. The Cancer Genome Atlas Pan-Cancer analysis project.Nat Genet. 2013;45(10):1113-20.doi: 10.1038/ng.2764.