Supplementary Materials

Supplementary Material for:

Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance

Jennifer M. Giltnane, Katherine E. Hutchinson, Thomas P. Stricker, Luigi Formisano, Christian D. Young, Monica V. Estrada, Mellissa J. Nixon, Liping Du, Violeta Sanchez, Paula Gonzalez Ericsson, Maria G. Kuba, Melinda E. Sanders, Xinmeng J. Mu, Eliezer M. Van Allen, Nikhil Wagle, Ingrid A. Mayer, Vandana Abramson, Henry Gómez, Monica Rizzo, Weiyi Toy, Sarat Chandarlapaty, Erica L. Mayer, Jason Christiansen, Danielle Murphy, Kerry Fitzgerald, Kai Wang, Jeffrey S. Ross, Vincent A. Miller, Phillip J. Stephens, Roman Yelensky, Levi Garraway, Yu Shyr, Ingrid Meszoely, Justin M. Balko, Carlos L. Arteaga*

*Corresponding author. Email: carlos.arteaga{at}

Published 9 August 2017, Sci. Transl. Med. 9, eaai7993 (2017)
DOI: 10.1126/scitranslmed.aai7993

This PDF file includes:

  • Materials and Methods
  • Fig. S1. Flowchart of tumor sample availability for study analyses.
  • Fig. S2. Immunohistochemical response of ER+ breast tumors to short-term letrozole, assessed by Ki67 and PR expression.
  • Fig. S3. Log2 copy number ratios on chromosomes 8 and 11 as per WES analysis.
  • Fig. S4. Individual FISH analysis for FGFR1 or CCND1 amplification and comparison with WES log2 CNV values and with RNAseq transcript expression.
  • Fig. S5. Principal components analysis, Database for Annotation, Visualization and Integrated Discovery (DAVID), Gene Set Enrichment (GSE), and iRegulon analyses based on RNAseq data from ER+, letrozole-treated breast tumors and TCGA breast tumors.
  • Fig. S6. RNAseq fusion validation pipeline and comparison of ESR1 transcript expression.
  • Fig. S7. Pharmacological inhibition of FGFR1 and/or CDK4/6 activity mediated by FGFR1 ± CCND1 amplification/overexpression.
  • Fig. S8. ERα transcriptional reporter assays assessing the activity of ERα LBD mutations.
  • Table S1. Statistical correlation of whole exome identified SNVs and CNVs with lack of response to letrozole.
  • Legends for tables S2 to S5
  • Table S6. ESR1 fusion transcripts identified from TCGA RNAseq data.
  • Table S7. Validation and diagrams of putative ESR1 fusions in patient and cell line cDNA.
  • Table S8. Sanger sequences from RT-PCR–validated, NanoString-identified ESR1 fusion transcripts.
  • Table S9. Clinical characteristics of 10 breast cancer patients profiled by FoundationOne harboring the ESR1 c.1265:1267delTGG/ERα p.V422del alteration.
  • Table S10. Primers for PCR and direct sequencing of ESR1 fusions identified by NanoString in patient and cell line cDNA.
  • Table S11. Primer combination to validate NanoString-identified fusions in patient and cell line cDNA.
  • Table S12. CCND1 and FGFR1 cloning primers.
  • References (4453)

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Other Supplementary Material for this manuscript includes the following:

  • Table S2. List of proliferation-associated genes (Excel file).
  • Table S3. Three hundred forty-six putative gene fusion transcripts identified by RNAseq in 50 tumors (Excel file).
  • Table S4. Primer sets for validation of RNAseq-identified putative fusion transcripts (Excel file).
  • Table S5. Summary and sequences of 26 RNAseq-identified, RT-PCR–validated fusion transcripts (Excel file).

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