Abstract P4-07-04: Genomic analysis of paired DCIS and subsequent recurrence to assess clonal relatedness in screen detected DCIS
Authors: Shah Vandna , Megalios Anargyros , Shami Rana , Sridharan Mathini , de Souza Carolina Salinas , Kumar Tapsi , Clements Karen , Futreal Andrew , Pinder Sarah , Thompson Alastair , Sawyer Elinor Jane ,   Sloane Steering Committee, CRUK Grand Challenge PRECISION Team
Published: March 2020

Abstract
In order to understand the clonal relatedness of DCIS and subsequent recurrence, 40 patients with primary DCIS that developed a subsequent ipsilateral event (28 invasive and 12 pure DCIS) and 17 with a subsequent contralateral event, were identified within the Sloane project, a prospective national cohort study of DCIS embedded in the UK Breast Screening Programme. Median follow up was 5.4 years.
All cases were reviewed by a breast histopathologist and macro-dissected to separate the DCIS or invasive disease from the normal tissue. DNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen). Somatic copy number aberrations were assessed using the HumanCytoSNP-12 BeadChip Kit (Illumina) and ASCAT. Targeted sequencing of a custom panel of 120 breast cancer-associated genes was performed using the SureSelect XT low input Target Enrichment System (Agilent Technologies). Prior to undertaking clonal related analysis, the relatedness of the samples was confirmed by cryptic relatedness analysis in PLINK v1.07.
Clonal relatedness was assessed using two methods. The first used copy number data, available for all samples, where each breakpoint was compared between the pairs of tumours from the same individual and a concordance score calculated based on the presence of shared and unique breakpoints. The second used targeted sequencing, available on 23 paired ipsilateral cases and 7 contralateral paired recurrences, that was run through the previously described Clonality package (Biometrics. 2018).
The results of the clonal relatedness analysis are summarized in below.
Evidence of clonal relatedness on copy number and / or mutation analysisEquivocal on mutation analysisNot clonal on mutation or copy number analysisNot clonal by copy numberPrimary DCIS & Ipsilateral invasive recurrence (28 pairs)1648Primary DCIS & Ipsilateral DCIS recurrence (12 pairs)1101Primary DCIS & Contralateral recurrence (16 pairs)1213Recurrent synchronous DCIS and invasive disease (12 pairs)1110
There were 2 cases where mutation data showed clear evidence of clonal relatedness but copy number did not, suggesting that the copy number approach may underestimate relatedness. There was also a proportion of cases where the pairs shared only one mutation and it was not possible to ascertain conclusively whether they were related, particularly when the shared mutation was a common driver mutation in PIK3CA that could have arisen by chance in unrelated samples.
Of the 28 primary DCIS that developed ipsilateral invasive recurrence, 8 cases (29%) showed no evidence of clonal relatedness by one or other method. Of these 3 recurred in the original tumour bed, 3 in a different quadrant and in 2 the site of recurrence was unknown. Of the 12 primary DCIS that developed an ipsilateral DCIS recurrence 92% showed evidence of clonal relatedness and also recurred earlier than the invasive recurrences, mean time to recurrence 2.9 years compared to 4.15 years for recurrent invasive disease (P=0.04, Student’s t-test). The mutations that were most commonly shared between the primary and recurrence were PIK3CA and TP53, followed by KMT2C, CAD and DNAH2. As expected, the majority of the contralateral cases were unrelated.
Of the 28 cases of DCIS that recurred ipsilaterally with invasive disease 16 had synchronous DCIS at the time of detection of the invasive disease and in 12 cases we were able to analyse the two synchronous components separately. In all cases the synchronous recurrent DCIS and invasive components showed evidence of clonal relatedness.
This study shows synchronous DCIS and IDC are clonally related as is DCIS that recurs as DCIS in the majority of cases. However, 29% of DCIS that recurred as invasive disease showed no evidence of clonal relatedness. It remains to be seen whether exome sequencing of the unrelated lesions would reveal evidence of relatedness or whether they are truly new primaries.
Citation Format: Vandna Shah, Anargyros Megalios, Rana Shami, Mathini Sridharan, Carolina Salinas de Souza, Tapsi Kumar, Karen Clements, Andrew Futreal, Sarah Pinder, Alastair Thompson, Elinor Jane Sawyer, Sloane Steering Committee, CRUK Grand Challenge PRECISION Team. Genomic analysis of paired DCIS and subsequent recurrence to assess clonal relatedness in screen detected DCIS [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-07-04.