Metadata supporting data files of the related manuscript: Homologous recombination DNA repair defects in PALB2-associated breast cancers

The related study sought to define the repertoire of somatic genetic alterations in Partner and Localizer of BRCA2 (PALB2)-associated breast cancers and to determine whether PALB2-associated breast cancers display bi-allelic inactivation of PALB2 and/or genomic features of Homologous recombination deficiency (HRD). Additionally, the genomic landscape of breast cancers from pathogenic PALB2 germline mutation carriers was compared to that of breast cancers arising in BRCA1 or BRCA2 germline mutation carriers, and to that of non-BRCA1/2/PALB2-associated breast cancers.

Participant consent:

This study was approved by Memorial Sloan Kettering Cancer Center’s Institutional Review Board (IRB) and by the local ethics committees/ IRBs of the authors’ institutions. Written informed consents were obtained as required by the protocols approved by the IRBs/local ethics committees of the respective authors’ institutions. This study is in compliance with the Declaration of Helsinki.

Study description and methodology:

The aim of the study was to characterize the repertoire of somatic genetic alterations in PALB2-associated breast cancers and to determine whether bi-allelic inactivation of PALB2 and/or genomic features of HRD are present in these tumors, with the aim to identifying features that may aid in the selection of patients likely to benefit from HRD-directed therapies. This was achieved by carrying out a number of assays including massively parallel sequencing.

This study included 24 invasive breast cancers (invasive ductal carcinomas) from women with pathogenic PALB2 germline mutations. All tumor samples included in this study were derived from formalin-fixed paraffin-embedded (FFPE) material. Immunohistochemistry was used to assess estrogen receptor (ER) and HER2 status of the tumor samples. HER2 amplification was assessed in selected cases by fluorescence in situ hybridization (FISH). Genomic DNA was extracted from tumor and matched normal blood or saliva samples. Fourteen cases were subjected to whole-exome sequencing (WES) and WES sequencing data from two cases were retrieved from The Cancer Genome Atlas (TCGA). In addition, 8 cases were analysed by targeted capture massively parallel sequencing using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay.

Comparisons of mutation burden, mutation frequencies, copy number alterations (CNAs) and genomic features indicative of HRD were conducted between the PALB2-associated breast cancers, non-BRCA1/2/PALB2 associated breast cancers with matched ER and HER2 status (n=683), and BRCA1- (n=17) and BRCA2-associated (n=16) breast cancers with bi-allelic inactivation from TCGA. For information on how massively parallel sequencing, bioinformatics analysis and statistical analysis were performed, please refer to the related manuscript and associated supplementary methods.

Data files:

Data file format: Data files supporting the figures, tables, supplementary figures and supplementary tables are all in Txt file format. Data files supporting supplementary table 4 are in Excel and Txt file formats.

Data file access: WES sequencing data (supporting figures 1-5, table 1, supplementary figures 2-6 and supplementary tables 1-5) can be accessed from: https://identifiers.org/cbioportal:brca_msk_li_2019.

MSK-IMPACT sequencing data (supporting figures 1, 2, 4 and 5, table 1, supplementary figures 2, 4 and 5 and supplementary tables 1-5) can be accessed from: https://identifiers.org/cbioportal:brca_msk_li_2019.

TCGA Breast Cancer sequencing data (supporting figures 4 and 5, supplementary figures 4-6 and supplementary table 5) can be accessed from: https://identifiers.org/cbioportal:brca_tcga_pan_can_atlas_2018 or from the related publication https://doi.org/10.1016/j.cell.2018.02.060.

Additional data supporting supplementary table 4 can be accessed from table 2 and supplementary table 1 of the related publication: https://doi.org/10.1002/path.5055.

Data file description:

Data supporting figure 1: WES and MSK-IMPACT sequencing data showing non-synonymous somatic mutations in 24 PALB2-associated breast cancers.

Data supporting figure 2: WES and MSK-IMPACT sequencing data showing copy number alterations in the 24 PALB2-associated breast cancers analysed by WES or MSK-IMPACT.

Data files supporting figure 3: WES sequencing data analyzed for the assessment of HRD genomic features including mutational signatures, large-scale state transition scores, average deletion length and number of genes affected by copy number alterations in 16 PALB2-associated breast cancers with and without bi-allelic PALB2 inactivation.

Data files supporting figure 4: WES, MSK-IMPACT and TCGA breast cancer sequencing data showing a comparison between all 24 PALB2-associated breast cancers and the 683 ER+/HER2-, ER+/HER2+ and ER-/HER2- non- BRCA1/2/PALB2-associated breast cancers from TCGA. These data files also show a comparison between the ER+/HER2- PALB2-associated breast cancers and 441 ER+/HER2- non-BRCA1/2/PALB2 breast cancers from TCGA.

Data files supporting figure 5: WES, MSK-IMPACT and TCGA breast cancer sequencing data showing a comparison of the most frequently mutated cancer genes and genomic features of HRD in PALB2-associated breast cancers with bi-allelic PALB2- inactivation and breast cancers with bi-allelic BRCA1 or bi-allelic BRCA2 alterations from TCGA.

Data files supporting supplementary figure 2: WES and MSK-IMPACT sequencing data showing cancer cell fractions of non-synonymous somatic mutations affecting 410 cancer genes as defined by ABSOLUTE in the 24 PALB2-associated breast cancers.

Data files supporting supplementary figure 3: WES sequencing data showing the repertoire of recurrent (non-synonymous) somatic mutations and corresponding cancer cell fractions in PALB2-associated breast cancers.

Data files supporting supplementary figure 4: WES, MSK-IMPACT data and TCGA breast cancer sequencing data showing the frequency of copy number alterations (CNAs) (gains, losses, amplifications and homozygous deletions) in PALB2-associated breast cancers and non-BRCA1/2/PALB2 breast cancers from TCGA.

Data files supporting supplementary figure 5: WES, MSK-IMPACT and TCGA breast cancer sequencing data showing the frequency of CNAs (gains, losses, amplifications and homozygous deletions) in PALB2-associated breast cancers with bi-allelic PALB2 alterations and BRCA1- and BRCA2-associated breast cancers with bi-allelic BRCA1 or BRCA2 alterations, respectively, from TCGA.

Data files supporting supplementary figure 6: WES and TCGA breast cancer sequencing data showing measurements of HRD (and distribution of LST scores, Myriad scores and number of telomeric allelic imbalances (NtAI) scores) in PALB2-associated breast cancers and BRCA1/2-associated breast cancers with mono-allelic or bi-allelic inactivation of PALB2 and BRCA1/2, respectively.

Data files supporting table 1: Clinicopathologic, WES and MSK-IMPACT sequencing data (including PALB2 germline mutation, number of somatic mutations, LST score and mutational signature) of the 24 PALB2-associated breast cancers studied.

Data files supporting supplementary table 1: WES and MSK-IMPACT sequencing statistics of tumor and matched normal samples of PALB2-associated breast cancers sequenced by WES or MSK-IMPACT.

Data files supporting supplementary table 2: WES and MSK-IMPACT data showing clonal and subclonal variants, variant allele fraction range and tumor purity of the PALB2-associated breast cancers studied.

Data files supporting supplementary table 3: WES and MSK-IMPACT data showing the non-synonymous somatic mutations identified in the PALB2- associated breast cancers sequenced by WES or MSK-IMPACT targeted massively parallel sequencing.

Data files supporting supplementary table 4: WES and MSK-IMPACT data and data from Lee et al. 2018 (https://doi.org/10.1002/path.5055) showing the clinicopathologic characteristics of the PALB2- associated breast cancers according to bi-allelic inactivation of the PALB2 wild-type allele.

Data files supporting supplementary table 5: WES, MSK-IMPACT and TCGA breast cancer sequencing data comparing the frequencies of somatic mutations affecting 410 cancer genes between PALB2- associated breast cancers and non-BRCA1/2/PALB2-, BRCA1- and BRCA2- associated breast cancers from TCGA.

Data access and terms of use: Data sets generated during this study can be accessed from cBioPortal (https://www.cbioportal.org/). TCGA breast cancer sequencing data can be accessed from cBioPortal and the NCI Genomic Data Commons repository (https://gdc.cancer.gov/). Other datasets can be accessed from the published article: https://doi.org/10.1002/path.5055. See Data file access for specific links to datasets generated or used in this study.