Supplementary Online Content

Size: px
Start display at page:

Download "Supplementary Online Content"

Transcription

1 Supplementary Online Content Fumagalli D, Venet D, Ignatiadis M, et al. RNA Sequencing to predict response to neoadjuvant anti-her2 therapy: a secondary analysis of the NeoALTTO randomized clinical trial. Published online September 29, JAMA Oncol. doi: / jamaoncol emethods ereferences etable 1. Patient characteristics in the whole and sequenced cohorts etable 2. Distribution of pcr according to PAM50 subtypes efigure 1. Comparison of ERBB2 gene expression levels determined by RNA Sequencing with classical tests used to define the HER2 status efigure 2. Comparison of ERBB2 gene expression levels in function of the laboratory in which the HER2 standard tests were performed efigure 3. Comparison of ER as determined by IHC and ESR1 gene expression efigure 4. Spearman correlation between single genes and gene expression signatures evaluated in our study efigure 5. Association between clinico-pathologic variables, single genes, and gene expression signatures with pcr by treatment arm efigure 6. Effect of single genes and gene expression signatures on pcr when considering the combination arm versus the joined trastuzumab and lapatinib arms evaluated using an interaction test efigure 7. Effect of single genes and gene expression signatures on pcr when considering the combination versus the trastuzumab arm evaluated using an interaction test efigure 8. Effect of clinico-pathological variables, single genes, gene expression signatures, and treatment on EFS using a univariate model efigure 9. Effect of single genes and gene expression signatures on EFS when considering the combination arm versus the joined trastuzumab and lapatinib arms evaluated using an interaction test This supplementary material has been provided by the authors to give readers additional information about their work.

2 emethods Samples selection A total of 630 baseline frozen samples underwent RNA extraction. For this purpose, snap frozen biopsies obtained at study entrance were first embedded in Optimal Cutting Temperature (OCT) compound and a hematoxylin and eosin (H&E) slide was cut, stained and evaluated for tumor cellularity by a breast cancer pathologist. RNA extraction was performed using the TRIzol method (Life Technologies) following the manufacturer s instructions. The extracted RNA was quantified using the Nanodrop 1000 instrument (Thermo Scientific), and its integrity (RIN: RNA Integrity Number) was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Sample adequacy (as defined by a tumor cellularity 30%), sample integrity (as defined by a RIN 5) and nucleic acid yield (as defined by a RNA quantity 1 µg) were used as quality control criteria. As shown in Figure 1, 219 samples were excluded because of low cellularity, 136 samples because of low RIN, and 12 samples because of low RNA quantity so that 263 samples underwent library preparation. Determination of the HER2 and ER status Only HER2 positive patients could participate in the neoaltto trial. The study required that a HER2 positive result was obtained in a laboratory previously certified for the NeoALTTO study by the NeoALTTO Pathologist Board. A laboratory could be completely, partially or not certified, following the decision of the Pathologist Board. The initial HER2 test was performed locally, by IHC and/or FISH/CISH, regardless of whether the local laboratory was certified. In the case of positive or equivocal results from non-certified local laboratories, slides were sent to the central laboratory (Pathology Department, Vall d Hebron Hospital, Barcelona, Spain) for confirmation prior to randomization. Equivocal results from partially certified laboratories also needed confirmation by the central laboratory prior to randomization in the Neo-ALTTO trial. The American Society of Clinical Oncology and College of American Pathologists (ASCO/CAP) guidelines 1 were used as a basis for defining HER2 positive tumors. HER2 positive tumors were defined as:

3 3+ over expression by IHC (> 30% of invasive tumor cells); 2+ or 3+ (in 30% or less neoplastic cells) over expression by IHC AND in situ hybridization (FISH/CISH) test demonstrating HER2 gene amplification; HER2 gene amplification by FISH/CISH (> 6 HER2 gene copies per nucleus, or a FISH ratio [HER2 gene copies to chromosome 17 signals] over 2.2.) Tumors with equivocal IHC results were defined as 3+ staining of 30% or less of invasive neoplastic cells or 2+ staining. Tumors with equivocal FISH/CISH results were defined as 4 to 6 HER2 gene copies per nucleus or a FISH ratio between 1.8 and 2.2. HER2 negative tumors were defined as tumors with a 0 or 1+ score by IHC and/or lack of HER2 gene amplification (less than 4 copies of HER2 gene per nucleus or a FISH ratio below 1.8). Patients with an overall negative of equivocal result were not eligible for participation in the trial. ER status was assessed only in local laboratories, irrespective of their accreditation, and was considered positive or negative as per local guidelines. RNA sequencing experiments. Starting from 1 µg of total RNA, rrna was depleted using the Ribo-Zero Magnetic Kit (Epicentre) according to the manufacturer s instruction. Following purification, the mrna was fragmented. The cleaved RNA fragments were copied into first strand cdna using reverse transcriptase and random primers. This was followed by second strand cdna synthesis and purification using the AMPure XP beads (Agencourt BioSciences Corporation). The cdna fragments underwent an end repair process, the addition of a single A nucleotide and ligation of the adapters. The products were purified using the AMPure XP beads and enriched after digestion of the second strand with PCR to create the final cdna library. Another purification step using the AMPure XP beads followed. Libraries quality control and quantification were performed using the Fragment Analyzer (Advanced Analytical) and the Qubit (Life Technologies). Nine samples failed the library construction step. The remaining 254 (Figure 1) libraries were pooled with three libraries per pool. Clusters were generated in a cbot Cluster Generation System using the Kits TruSeq PE Cluster Kit v3-cbot-

4 HS and HiSeq PE Cluster Kit v4 cbot and sequenced on the Illumina HiSeq 2500 platform with a 2x100 base pairs paired-end mode.

5 ereferences Wolff AC, Hammond MEH, Schwartz JN, et al. American Society of Clinical Oncology/College of American Pathologists Guideline Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer. J Clin Oncol 2007; 25:

6 etable 1. Patient characteristics in the whole and sequenced cohorts Characteristics Whole cohort (N=455) Sequenced cohort (N=254) p-value Age Median Range Tumor Size >=T3 181 (40%) 103 (41%) 0.77 T2 274 (60%) 151 (59%) Nodal Status >=N2, Nx or missing 72 (16%) 38 (15%) 0.61 N0/1 383 (84%) 216 (85%) Hormone Receptor Status Treatment arm negative 223 (49%) 117 (46%) 0.19 positive 232 (51%) 137 (54%) L 154 (34%) 89 (35%) 0.68 T 149 (33%) 79 (31%) L+T 152 (33%) 86 (34%) pcr No 295 (65%) 166 (65%) 0.84 Yes 160 (35%) 88 (35%) Comparison of the clinico-pathologic and treatment characteristics of the whole cohort of patients randomized in the neoaltto trial and the sub-study cohort analyzed in this project. L: Lapatinib; T: trastuzumab

7 etable 2. Distribution of pcr according to PAM50 subtypes Basal Her2 Luminal A Luminal B Normal N % 9% 43% 23% 16% 8% %pcr 38% 52% 17% 17% 24% Classification of the sub-study population according to the subtypes defined by the PAM50 classifier and distribution of observed pcr according to the subtype.

8 efigure 1. Comparison of ERBB2 gene expression levels determined by RNA Sequencing with classical tests used to define the HER2 status A) Comparison between ERBB2 gene expression levels with IHC, using the % stained cells and B) with FISH ratios.

9 efigure 2. Comparison of ERBB2 gene expression levels in function of the laboratory in which the HER2 standard tests were performed ERBB2 expression (FPKM) ERBB2 expression (FPKM) Local lab Central lab Central testing Local testing ESR1 expression (FPKM) A A) ERBB2 expression levels according to where the HER2 standard tests were performed (central testing vs. local testing). B) ERBB2 versus ESR1 expression levels with samples colored according to laboratories in which the HER2 standard tests were performed (red:central; black:local). Red line denotes the cutoff used to determine low versus high expression levels of ERBB2. B

10 efigure 3. Comparison of ER as determined by IHC and ESR1 gene expression A) ESR1 expression levels in the ER+ and ER- patients determined by local IHC. B) ERBB2 and ESR1 gene expression levels determined by RNA sequencing in the ER+ (black) and ER- (red) patients determined by local IHC.

11 efigure 4. Spearman correlation between single genes and gene expression signatures evaluated in our study The color indicates the direction of the correlation (red: anti-correlation; blue: direct correlation); the shape of the ovals indicates the strength of the correlation. Only significant correlations are shown (p<0.05).

12 efigure 5. Association between clinico-pathologic variables, single genes, and gene expression signatures with pcr by treatment arm A) Lapatinib; B) Trastuzumab; C) Combination. Blue represents significant p values.

13 efigure 6. Effect of single genes and gene expression signatures on pcr when considering the combination arm versus the joined trastuzumab and lapatinib arms evaluated using an interaction test Blue indicates effect across arms, red indicates effect specific to the combination arm; dark colors indicate significant correlation.

14 efigure 7. Effect of single genes and gene expression signatures on pcr when considering the combination versus the trastuzumab arm evaluated using an interaction test Blue indicates effect across arms, red indicates effect specific to the combination arm; dark colors indicate significant correlation.

15 efigure 8. Effect of clinico-pathological variables, single genes, gene expression signatures, and treatment on EFS using a univariate model Blue represents significant p values.

16 efigure 9. Effect of single genes and gene expression signatures on EFS when considering the combination arm versus the joined trastuzumab and lapatinib arms evaluated using an interaction test Blue indicates effect across arms, red indicates effect specific to the combination arm; dark colors indicate significant correlation.

Selective depletion of abundant RNAs to enable transcriptome analysis of lowinput and highly-degraded RNA from FFPE breast cancer samples

Selective depletion of abundant RNAs to enable transcriptome analysis of lowinput and highly-degraded RNA from FFPE breast cancer samples DNA CLONING DNA AMPLIFICATION & PCR EPIGENETICS RNA ANALYSIS Selective depletion of abundant RNAs to enable transcriptome analysis of lowinput and highly-degraded RNA from FFPE breast cancer samples LIBRARY

More information

Kristen E. Muller, DO, Jonathan D. Marotti, MD, Vincent A. Memoli, MD, Wendy A. Wells, MD, and Laura J. Tafe, MD

Kristen E. Muller, DO, Jonathan D. Marotti, MD, Vincent A. Memoli, MD, Wendy A. Wells, MD, and Laura J. Tafe, MD AJCP / Original Article Impact of the 2013 ASCO/CAP HER2 Guideline Updates at an Academic Medical Center That Performs Primary HER2 FISH Testing Increase in Equivocal Results and Utility of Reflex Immunohistochemistry

More information

FAQs for UK Pathology Departments

FAQs for UK Pathology Departments FAQs for UK Pathology Departments This is an educational piece written for Healthcare Professionals FAQs for UK Pathology Departments If you would like to discuss any of the listed FAQs further, or have

More information

What is HER2 positive breast cancer in 2018? Updated ASCO-CAP guidelines. Giuseppe Viale University of Milan European Institute of Oncology

What is HER2 positive breast cancer in 2018? Updated ASCO-CAP guidelines. Giuseppe Viale University of Milan European Institute of Oncology What is HER2 positive breast cancer in 2018? Updated ASCO-CAP guidelines Giuseppe Viale University of Milan European Institute of Oncology Mission accomplished! First alarming results Breast Intergroup

More information

National Disease Research Interchange Annual Progress Report: 2010 Formula Grant

National Disease Research Interchange Annual Progress Report: 2010 Formula Grant National Disease Research Interchange Annual Progress Report: 2010 Formula Grant Reporting Period July 1, 2012 June 30, 2013 Formula Grant Overview The National Disease Research Interchange received $62,393

More information

RECENT ADVANCES IN THE MOLECULAR DIAGNOSIS OF BREAST CANCER

RECENT ADVANCES IN THE MOLECULAR DIAGNOSIS OF BREAST CANCER Technology Transfer in Diagnostic Pathology. 6th Central European Regional Meeting. Cytopathology. Balatonfüred, Hungary, April 7-9, 2011. RECENT ADVANCES IN THE MOLECULAR DIAGNOSIS OF BREAST CANCER Philippe

More information

Biomarkers for HER2-directed Therapies : Past Failures and Future Perspectives

Biomarkers for HER2-directed Therapies : Past Failures and Future Perspectives Biomarkers for HER2-directed Therapies : Past Failures and Future Perspectives Ian Krop Dana-Farber Cancer Institute Harvard Medical School Inchon 2018 Adjuvant Trastuzumab Improves Outcomes in HER2+ Breast

More information

Welcome! HER2 TESTING DIAGNOSTIC ACCURACY 4/11/2016

Welcome! HER2 TESTING DIAGNOSTIC ACCURACY 4/11/2016 HER2 TESTING DIAGNOSTIC ACCURACY Can t We Finally Get It Right? Allen M. Gown, M.D. Medical Director and Chief Pathologist PhenoPath Laboratories Seattle, Washington Clinical Professor of Pathology University

More information

Breast cancer: Molecular STAGING classification and testing. Korourian A : AP,CP ; MD,PHD(Molecular medicine)

Breast cancer: Molecular STAGING classification and testing. Korourian A : AP,CP ; MD,PHD(Molecular medicine) Breast cancer: Molecular STAGING classification and testing Korourian A : AP,CP ; MD,PHD(Molecular medicine) Breast Cancer Theory: Halsted Operative breast cancer is a local-regional disease The positive

More information

Optimal algorithm for HER2 testing

Optimal algorithm for HER2 testing Optimal algorithm for HER2 testing The revised definition of IHC 2+ (equivocal) is invasive breast cancer with Weak to moderate complete membrane staining observed in >10% of tumor cells. (see Figure 1

More information

Breast Cancer Interpretation Guide

Breast Cancer Interpretation Guide Breast Cancer Interpretation Guide UCT D O R P NEW ERBB2/ C E P S ht e ZytoLig lor Prob o C l a u 2D D17S12 ng to the i d r o c c a ting for re-tes idelines 2013 ASCO Gu Breast Cancer Interpretation Guide

More information

CANCER. Clinical Validation of Breast Cancer Predictive Markers

CANCER. Clinical Validation of Breast Cancer Predictive Markers Clinical Validation of Breast Cancer Predictive Markers David Hicks, MD Loralee McMahon, MS, HTL(ASCP) CANCER The human body is composed of billions of highly regulated cells Cancer cells no longer respond

More information

A complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis

A complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis APPLICATION NOTE Cell-Free DNA Isolation Kit A complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis Abstract Circulating cell-free DNA (cfdna) has been shown

More information

Applications of IHC. Determination of the primary site in metastatic tumors of unknown origin

Applications of IHC. Determination of the primary site in metastatic tumors of unknown origin Applications of IHC Determination of the primary site in metastatic tumors of unknown origin Classification of tumors that appear 'undifferentiated' by standard light microscopy Precise classification

More information

HER2 CISH pharmdx TM Kit Interpretation Guide Breast Cancer

HER2 CISH pharmdx TM Kit Interpretation Guide Breast Cancer P A T H O L O G Y HER2 CISH pharmdx TM Kit Interpretation Guide Breast Cancer FROM CERTAINTY COMES TRUST For in vitro diagnostic use HER2 CISH pharmdx Kit HER2 CISH pharmdx Kit is intended for dual-color

More information

Supplemental Methods RNA sequencing experiment

Supplemental Methods RNA sequencing experiment Supplemental Methods RNA sequencing experiment Mice were euthanized as described in the Methods and the right lung was removed, placed in a sterile eppendorf tube, and snap frozen in liquid nitrogen. RNA

More information

NIH Public Access Author Manuscript Cancer Epidemiol Biomarkers Prev. Author manuscript; available in PMC 2011 January 1.

NIH Public Access Author Manuscript Cancer Epidemiol Biomarkers Prev. Author manuscript; available in PMC 2011 January 1. NIH Public Access Author Manuscript Published in final edited form as: Cancer Epidemiol Biomarkers Prev. 2010 January ; 19(1): 144 147. doi:10.1158/1055-9965.epi-09-0807. Feasibility Study for Collection

More information

RNA preparation from extracted paraffin cores:

RNA preparation from extracted paraffin cores: Supplementary methods, Nielsen et al., A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor positive breast cancer.

More information

Molecular in vitro diagnostic test for the quantitative detection of the mrna expression of ERBB2, ESR1, PGR and MKI67 in breast cancer tissue.

Molecular in vitro diagnostic test for the quantitative detection of the mrna expression of ERBB2, ESR1, PGR and MKI67 in breast cancer tissue. Innovation for your breast cancer diagnostics PGR G ATA G C G A C G AT C G A A A G A A G T TA G ATA G C G A C G AT C G A A A G A A G T TA G ATA G C G A C G AT C G A A A G A A G T TA G ATA G C G A C ERBB2

More information

Guideline. Associated Documents ASCO CAP 2018 GUIDELINES and SUPPLEMENTS -

Guideline. Associated Documents ASCO CAP 2018 GUIDELINES and SUPPLEMENTS - Guideline Subject: ASCO CAP 2018 HER2 Testing for Breast Cancer Guidelines - Recommendations for Practice in Australasia Approval Date: December 2018 Review Date: December 2022 Review By: HER2 testing

More information

Prosigna BREAST CANCER PROGNOSTIC GENE SIGNATURE ASSAY

Prosigna BREAST CANCER PROGNOSTIC GENE SIGNATURE ASSAY Prosigna BREAST CANCER PROGNOSTIC GENE SIGNATURE ASSAY Methodology The test is based on the reported 50-gene classifier algorithm originally named PAM50 and is performed on the ncounter Dx Analysis System

More information

Prosigna BREAST CANCER PROGNOSTIC GENE SIGNATURE ASSAY

Prosigna BREAST CANCER PROGNOSTIC GENE SIGNATURE ASSAY Prosigna BREAST CANCER PROGNOSTIC GENE SIGNATURE ASSAY GENE EXPRESSION PROFILING WITH PROSIGNA What is Prosigna? Prosigna Breast Cancer Prognostic Gene Signature Assay is an FDA-approved assay which provides

More information

HER2 FISH pharmdx TM Interpretation Guide - Breast Cancer

HER2 FISH pharmdx TM Interpretation Guide - Breast Cancer P A T H O L O G Y HER2 FISH pharmdx TM Interpretation Guide - Breast Cancer For In Vitro Diagnostic Use FDA approved as an aid in the assessment of patients for whom Herceptin TM (trastuzumab) treatment

More information

Supplementary Online Content

Supplementary Online Content Supplementary Online Content Venook AP, Niedzwiecki D, Lenz H-J, et al. Effect of first-line chemotherapy combined with cetuximab or bevacizumab on overall survival in patients with KRAS wild-type advanced

More information

Quantitative Image Analysis of HER2 Immunohistochemistry for Breast Cancer

Quantitative Image Analysis of HER2 Immunohistochemistry for Breast Cancer Quantitative Image Analysis of HER2 Immunohistochemistry for Breast Cancer Guideline from the College of American Pathologists Early Online Release Publication: Archives of Pathology & Laboratory Medicine

More information

2017 OPTIONS FOR INDIVIDUAL MEASURES: REGISTRY ONLY. MEASURE TYPE: Process

2017 OPTIONS FOR INDIVIDUAL MEASURES: REGISTRY ONLY. MEASURE TYPE: Process Measure #449 (NQF 1857): HER2 Negative or Undocumented Breast Cancer Patients Spared Treatment with HER2-Targeted Therapies National Quality Strategy Domain: Efficiency and Cost Reduction 2017 OPTIONS

More information

Data Supplement 1: 2013 Update Rationale and Background Information

Data Supplement 1: 2013 Update Rationale and Background Information Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology /College of American Pathologists Clinical Practice Guideline Update (edited

More information

System-wide Ownership Group: Allina Health Breast Program Committee. Hospital Division Quality Council: August 2018

System-wide Ownership Group: Allina Health Breast Program Committee. Hospital Division Quality Council: August 2018 Oncology Clinical Service Line System-wide Consensus Guidelines: Evaluation and Management of Breast Lumpectomy and Mastectomy Specimens by Surgeons and Pathologists These guidelines apply to clinical

More information

Dr. dr. Primariadewi R, SpPA(K)

Dr. dr. Primariadewi R, SpPA(K) Curriculum Vitae Dr. dr. Primariadewi R, SpPA(K) Education : Medical Doctor from UKRIDA Doctoral Degree from Faculty of Medicine University of Indonesia Pathologist Specialist and Consultant from Faculty

More information

Comparison of Triple Negative Breast Cancer between Asian and Western Data Sets

Comparison of Triple Negative Breast Cancer between Asian and Western Data Sets 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops Comparison of Triple Negative Breast Cancer between Asian and Western Data Sets Lee H. Chen Bioinformatics and Biostatistics

More information

Lecture 5. Primary systemic therapy: clinical and biological endpoints

Lecture 5. Primary systemic therapy: clinical and biological endpoints Lecture 5 Primary systemic therapy: clinical and biological endpoints Valentina Guarneri, M.D., Ph.D. Primary systemic therapy in breast cancer Firstly introduced d into clinical i l practice in 70s for

More information

Gene Signatures in Breast Cancer: Moving Beyond ER, PR, and HER2? Lisa A. Carey, M.D. University of North Carolina USA

Gene Signatures in Breast Cancer: Moving Beyond ER, PR, and HER2? Lisa A. Carey, M.D. University of North Carolina USA Gene Signatures in Breast Cancer: Moving Beyond ER, PR, and HER2? Lisa A. Carey, M.D. University of North Carolina USA When Are Biomarkers Ready To Use? Same Rules for Gene Expression Panels Key elements

More information

Introduction. The HER2 Testing Expert Panel has identified five Clinical Questions that form the core of this Focused Update.

Introduction. The HER2 Testing Expert Panel has identified five Clinical Questions that form the core of this Focused Update. Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/ College of American Pathologists Clinical Practice Guideline Focused Update Wolff, et al. Introduction

More information

Introduction. Approximately 20% of invasive breast cancers

Introduction. Approximately 20% of invasive breast cancers Introduction Approximately 2% of invasive breast cancers overexpress HER2 The current standard of care for neoadjuvant therapy is dual-targeted therapy with trastuzumab and pertuzumab plus chemotherapy

More information

Supplementary Figure 1

Supplementary Figure 1 Supplementary Figure 1 Supplementary Fig. 1: Quality assessment of formalin-fixed paraffin-embedded (FFPE)-derived DNA and nuclei. (a) Multiplex PCR analysis of unrepaired and repaired bulk FFPE gdna from

More information

Assessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray

Assessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray Assessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray Hui Chen, Aysegul A Sahin, Xinyan Lu, Lei Huo, Rajesh R Singh, Ronald Abraham, Shumaila Virani, Bal Mukund Mishra, Russell Broaddus,

More information

Molecular in vitro diagnostic test for the quantitative detection of the mrna expression of ERBB2, ESR1, PGR and MKI67 in breast cancer tissue.

Molecular in vitro diagnostic test for the quantitative detection of the mrna expression of ERBB2, ESR1, PGR and MKI67 in breast cancer tissue. Innovation for your breast cancer diagnostics Now valid ated on: -Roche cob as z 480 A nalyzer -Roche L ightcycle r 480 II - ABI 750 0 Fast -Versant kpcr Cyc ler PGR ESR1 MKI67 Molecular in vitro diagnostic

More information

Supplementary webappendix

Supplementary webappendix Supplementary webappendix This webappendix formed part of the original submission and has been peer reviewed. We post it as supplied by the authors. Supplement to: Kratz JR, He J, Van Den Eeden SK, et

More information

The Role of Pathologic Complete Response (pcr) as a Surrogate Marker for Outcomes in Breast Cancer: Where Are We Now?

The Role of Pathologic Complete Response (pcr) as a Surrogate Marker for Outcomes in Breast Cancer: Where Are We Now? 1 The Role of Pathologic Complete Response (pcr) as a Surrogate Marker for Outcomes in Breast Cancer: Where Are We Now? Terry Mamounas, M.D., M.P.H., F.A.C.S. Medical Director, Comprehensive Breast Program

More information

KAPA Stranded RNA-Seq Library Preparation Kit

KAPA Stranded RNA-Seq Library Preparation Kit KAPA Stranded RNA-Seq Illumina platforms KR0934 v1.13 This provides product information and a detailed protocol for the KAPA Stranded RNA- Seq (Illumina platforms), product codes KK8400 and KK8401. Contents

More information

Neo-adjuvant and adjuvant treatment for HER-2+ breast cancer

Neo-adjuvant and adjuvant treatment for HER-2+ breast cancer Neo-adjuvant and adjuvant treatment for HER-2+ breast cancer Angelo Di Leo «Sandro Pitigliani» Medical Oncology Unit Hospital of Prato Istituto Toscano Tumori Prato, Italy NOAH: Phase III, Open-Label Trial

More information

Supplementary Information Titles Journal: Nature Medicine

Supplementary Information Titles Journal: Nature Medicine Supplementary Information Titles Journal: Nature Medicine Article Title: Corresponding Author: Supplementary Item & Number Supplementary Fig.1 Fig.2 Fig.3 Fig.4 Fig.5 Fig.6 Fig.7 Fig.8 Fig.9 Fig. Fig.11

More information

Positive HER-2 tumor. How to incorporate the new drugs into neoadjuvance

Positive HER-2 tumor. How to incorporate the new drugs into neoadjuvance Oncology Department Vall d Hebron University Hospital Barcelona. Spain Positive HER-2 tumor. How to incorporate the new drugs into neoadjuvance Javier Cortés June/2013 MD Anderson experience Buzdar et

More information

Prediction of HER2 gene status in Her2 2 þ invasive breast cancer: a study of 108 cases comparing ASCO/CAP and FDA recommendations

Prediction of HER2 gene status in Her2 2 þ invasive breast cancer: a study of 108 cases comparing ASCO/CAP and FDA recommendations & 2009 USCAP, Inc All rights reserved 0893-3952/09 $32.00 www.modernpathology.org Prediction of HER2 gene status in Her2 2 þ invasive breast cancer: a study of 108 cases comparing ASCO/CAP and FDA recommendations

More information

HER2 status assessment in breast cancer. Marc van de Vijver Academic Medical Centre (AMC), Amsterdam

HER2 status assessment in breast cancer. Marc van de Vijver Academic Medical Centre (AMC), Amsterdam HER2 status assessment in breast cancer Marc van de Vijver Academic Medical Centre (AMC), Amsterdam 13e Bossche Mamma Congres 17 th June 2015 Modern cancer therapies are based on sophisticated molecular

More information

MEDICAL POLICY. Proprietary Information of YourCare Health Plan

MEDICAL POLICY. Proprietary Information of YourCare Health Plan MEDICAL POLICY SUBJECT: HER-2 TESTING IN INVASIVE BREAST OR PAGE: 1 OF: 7 If the member's subscriber contract excludes coverage for a specific service it is not covered under that contract. In such cases,

More information

Supplementary Online Content

Supplementary Online Content Supplementary Online Content Bell EH, Pugh SL, McElroy JP, et al. Molecular-based recursive partitioning analysis model for glioblastoma in the temozolomide era: a correlative analysis based on NRG Oncology

More information

High Throughput TruSeq Stranded mrna Library Construction on the Biomek FX P

High Throughput TruSeq Stranded mrna Library Construction on the Biomek FX P High Throughput TruSeq Stranded mrna Library Construction on the Biomek FX P Zach Smith and Scott D. Michaels The Center for Genomics and Bioinformatics Indiana University Bloomington, IN USA Mary Blair

More information

Predicting outcome in metastatic breast cancer

Predicting outcome in metastatic breast cancer Predicting outcome in metastatic breast cancer Aleix Prat, MD, PhD Medical Oncology Department Translational Genomics and Targeted Therapeutics in Solid Tumors Monday, 15 th January, Manchester, UK Disclosures

More information

Novel Preoperative Therapies for HER2-Positive Breast Cancer. Debu Tripathy, MD University of Southern California Norris Comprehensive Cancer Center

Novel Preoperative Therapies for HER2-Positive Breast Cancer. Debu Tripathy, MD University of Southern California Norris Comprehensive Cancer Center Novel Preoperative Therapies for HER2-Positive Breast Cancer Debu Tripathy, MD University of Southern California Norris Comprehensive Cancer Center Key Findings to Date in the Neoadjuvant Therapy of HER2+

More information

Low ER+ Breast Cancer. Is This a Distinct Group? Nika C. Gloyeske, MD, David J. Dabbs, MD, and Rohit Bhargava, MD ABSTRACT

Low ER+ Breast Cancer. Is This a Distinct Group? Nika C. Gloyeske, MD, David J. Dabbs, MD, and Rohit Bhargava, MD ABSTRACT Low ER+ Breast Cancer Is This a Distinct Group? Nika C. Gloyeske, MD, David J. Dabbs, MD, and Rohit Bhargava, MD From the Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA.

More information

MEDICAL POLICY. Proprietary Information of Excellus Health Plan, Inc. A nonprofit independent licensee of the BlueCross BlueShield Association

MEDICAL POLICY. Proprietary Information of Excellus Health Plan, Inc. A nonprofit independent licensee of the BlueCross BlueShield Association MEDICAL POLICY SUBJECT: HER-2 TESTING IN INVASIVE BREAST OR PAGE: 1 OF: 7 If a product excludes coverage for a service, it is not covered, and medical policy criteria do not apply. If a commercial product,

More information

Immunohistochemical classification of breast tumours

Immunohistochemical classification of breast tumours Immunohistochemical classification of breast tumours Workshop in Diagnostic Immunohistochemistry September 19 th - 21 th 2018 Anne-Vibeke Lænkholm Department of Surgical Pathology, Zealand University Hospital,

More information

Quantitative Assay for Measurement of HER2 Total Protein Expression and HER2 Dimers

Quantitative Assay for Measurement of HER2 Total Protein Expression and HER2 Dimers Quantitative Assay for Measurement of HER2 Total Protein Expression and HER2 Dimers Policy Number: 2.04.76 Last Review: 12/2017 Origination: 12/2015 Next Review: 12/2018 Policy Blue Cross and Blue Shield

More information

Online Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h)

Online Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h) Online Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h) after feeding. A small slice (~5-1 mm 3 ) was taken

More information

Review of adjuvant and neo-adjuvant abstracts from SABCS 2011 January 7 th 2012

Review of adjuvant and neo-adjuvant abstracts from SABCS 2011 January 7 th 2012 Review of adjuvant and neo-adjuvant abstracts from SABCS 2011 January 7 th 2012 Ruth M. O Regan, MD Professor and Vice-Chair for Educational Affairs, Department of Hematology and Medical Oncology, Emory

More information

HER2 status in breast cancer: experience of a Spanish National Reference Centre

HER2 status in breast cancer: experience of a Spanish National Reference Centre Clin Transl Oncol (2011) 13:000-000 DOI RESEARCH ARTICLES HER2 status in breast cancer: experience of a Spanish National Reference Centre Marta Cuadros Carlos Cano Francisco Javier López Paloma Talavera

More information

(A) PCR primers (arrows) designed to distinguish wild type (P1+P2), targeted (P1+P2) and excised (P1+P3)14-

(A) PCR primers (arrows) designed to distinguish wild type (P1+P2), targeted (P1+P2) and excised (P1+P3)14- 1 Supplemental Figure Legends Figure S1. Mammary tumors of ErbB2 KI mice with 14-3-3σ ablation have elevated ErbB2 transcript levels and cell proliferation (A) PCR primers (arrows) designed to distinguish

More information

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA www.impactjournals.com/oncotarget/ Oncotarget, Supplementary Materials 2016 Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) DNA Supplementary Materials

More information

HER2/neu Evaluation of Breast Cancer in 2019

HER2/neu Evaluation of Breast Cancer in 2019 HER2/neu Evaluation of Breast Cancer in 2019 A.A. Sahin, M.D. Professor of Pathology and Translation Molecular Pathology Section Chief of Breast Pathology ERBB2 (HER2) Background 185-kDa membrane protein

More information

Products for cfdna and mirna isolation. Subhead Circulating Cover nucleic acids from plasma

Products for cfdna and mirna isolation. Subhead Circulating Cover nucleic acids from plasma MACHEREY-NAGEL Products for cfdna and mirna isolation Bioanalysis Subhead Circulating Cover nucleic acids from plasma n Flexible solutions for small and large blood plasma volumes n Highly efficient recovery

More information

Journal of Breast Cancer

Journal of Breast Cancer ORIGINAL ARTICLE Journal of Breast Cancer J Breast Cancer 2009 December; 12(4): 235-40 DOI: 10.4048/jbc.2009.12.4.235 Comparison of Silver-Enhanced in situ Hybridization and Fluorescence in situ Hybridization

More information

For the 5 GATC-overhang two-oligo adaptors set up the following reactions in 96-well plate format:

For the 5 GATC-overhang two-oligo adaptors set up the following reactions in 96-well plate format: Supplementary Protocol 1. Adaptor preparation: For the 5 GATC-overhang two-oligo adaptors set up the following reactions in 96-well plate format: Per reaction X96 10X NEBuffer 2 10 µl 10 µl x 96 5 -GATC

More information

Reviewer's report. Version: 1 Date: 24 May Reviewer: Cathy Moelans. Reviewer's report:

Reviewer's report. Version: 1 Date: 24 May Reviewer: Cathy Moelans. Reviewer's report: Reviewer's report Title: Validation of HER2 testing with core needle biopsy specimens from primary breast cancers in terms of interobserver reproducibility and concordance with surgically resected specimens

More information

Supplementary Data for:

Supplementary Data for: Supplementary Data for: Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies Dominic A. Pearce 1, Laura M. Arthur 1, Arran K. Turnbull 1,

More information

Determination of HER2 Amplification by In Situ Hybridization. When Should Chromosome 17 Also Be Determined?

Determination of HER2 Amplification by In Situ Hybridization. When Should Chromosome 17 Also Be Determined? Anatomic Pathology / FISH f o r HER2: Wh e n to Use Ch r o m o s o m e 17 Determination of HER2 Amplification by In Situ Hybridization When Should Chromosome 17 Also Be Determined? John M.S. Bartlett,

More information

Digitizing the Proteomes From Big Tissue Biobanks

Digitizing the Proteomes From Big Tissue Biobanks Digitizing the Proteomes From Big Tissue Biobanks Analyzing 24 Proteomes Per Day by Microflow SWATH Acquisition and Spectronaut Pulsar Analysis Jan Muntel 1, Nick Morrice 2, Roland M. Bruderer 1, Lukas

More information

Characterisation of structural variation in breast. cancer genomes using paired-end sequencing on. the Illumina Genome Analyser

Characterisation of structural variation in breast. cancer genomes using paired-end sequencing on. the Illumina Genome Analyser Characterisation of structural variation in breast cancer genomes using paired-end sequencing on the Illumina Genome Analyser Phil Stephens Cancer Genome Project Why is it important to study cancer? Why

More information

2018 OPTIONS FOR INDIVIDUAL MEASURES: REGISTRY ONLY. MEASURE TYPE: Process

2018 OPTIONS FOR INDIVIDUAL MEASURES: REGISTRY ONLY. MEASURE TYPE: Process Quality ID #450 (NQF 1858): Trastuzumab Received By Patients With AJCC Stage I (T1c) III And HER2 Positive Breast Cancer Receiving Adjuvant Chemotherapy National Quality Strategy Domain: Effective Clinical

More information

Point of View on Early Triple Negative

Point of View on Early Triple Negative Point of View on Early Triple Negative Valentina Rossi, MD UOSD Oncologia dei Tumori della Mammella Azienda Ospedaliera S.Camillo-Forlanini VRossi@scamilloforlanini.rm.it Outline Neoadjuvant Setting IPSY-2

More information

# Best Practices for IHC Detection and Interpretation of ER, PR, and HER2 Protein Overexpression in Breast Cancer

# Best Practices for IHC Detection and Interpretation of ER, PR, and HER2 Protein Overexpression in Breast Cancer #1034 - Best Practices for IHC Detection and Interpretation of ER, PR, and HER2 Protein Overexpression in Breast Cancer Richard W. Cartun, MS, PhD Andrew Ricci, Jr, MD Department of Pathology Hartford

More information

CATS RNA-seq kit v2. CATS RNA sequencing kit for Illumina. Cat. No. C (12 rxns) C (24 rxns) C (96 rxns) Version 2 I 09.

CATS RNA-seq kit v2. CATS RNA sequencing kit for Illumina. Cat. No. C (12 rxns) C (24 rxns) C (96 rxns) Version 2 I 09. CATS RNA-seq kit v2 CATS RNA sequencing kit for Illumina Cat. No. C05010045 (12 rxns) C05010041 (24 rxns) C05010049 (96 rxns) Version 2 I 09.17 Content Introduction 4 Kit method overview & time table

More information

Supplementary Online Content

Supplementary Online Content Supplementary Online Content Giannakeas V, Sopik V, Narod SA. Association of Radiotherapy With Survival in Women Treated for Ductal Carcinoma In Situ With Lumpectomy or Mastectomy. JAMA Netw Open. 2018;1(4):e181100.

More information

Breast Cancer: ASCO Poster Review

Breast Cancer: ASCO Poster Review Breast Cancer: ASCO Poster Review Carmen Criscitiello, MD, PhD Istituto Europeo di Oncologia Milano HER2+ SUBTYPE Research questions in early HER2+ BC De-escalation of toxicity without compromising efficacy

More information

PD-L1 Analyte Control DR

PD-L1 Analyte Control DR Quality in Control PD-L1 Analyte Control DR PD-L1_PI_v2 Product Codes: HCL019, HCL020 and HCL021 Contents PD-L1 Analyte Control DR 2 What is PD-L1? 3 The Role of PD-L1 in Cancer 3 PD-L1 Assessment 4 PD-L1

More information

Material and Methods. Flow Cytometry Analyses:

Material and Methods. Flow Cytometry Analyses: Material and Methods Flow Cytometry Analyses: Immunostaining of breast cancer cells for HER2 was performed by incubating cells with anti- HER2/neu APC (Biosciences, Cat# 340554), anti-her2/neu PE (Biosciences,

More information

microrna Presented for: Presented by: Date:

microrna Presented for: Presented by: Date: microrna Presented for: Presented by: Date: 2 micrornas Non protein coding, endogenous RNAs of 21-22nt length Evolutionarily conserved Regulate gene expression by binding complementary regions at 3 regions

More information

CATS Total RNA-seq Kit v2 (with rrna depletion)

CATS Total RNA-seq Kit v2 (with rrna depletion) CATS Total RNA-seq Kit v2 (with rrna depletion) CATS Total RNA sequencing kit for Illumina Cat. No. C05010046 (12 rxns) C05010042 (24 rxns) C05010050 (96 rxns) Version 2 I 09.17 Content A. rrna DEPLETION

More information

ACMG/CAP Cytogenetics CY

ACMG/CAP Cytogenetics CY www.cap.org Cytogenetics Analytes/procedures in bold type are regulated for proficiency testing by the Centers for Medicare & Medicaid Services ACMG/CAP Cytogenetics CY Analyte CY Challenges per Shipment

More information

Supplementary Online Content

Supplementary Online Content Supplementary Online Content Peters PJ, Westheimer E, Cohen S, et al. Screening yield of HIV antigen/antibody combination and pooled HIV RNA testing for acute HIV infection in a high-prevalence population.

More information

Gene Expression Profiling for Managing Breast Cancer Treatment. Policy Specific Section: Medical Necessity and Investigational / Experimental

Gene Expression Profiling for Managing Breast Cancer Treatment. Policy Specific Section: Medical Necessity and Investigational / Experimental Medical Policy Gene Expression Profiling for Managing Breast Cancer Treatment Type: Medical Necessity and Investigational / Experimental Policy Specific Section: Laboratory/Pathology Original Policy Date:

More information

Ambient Temperature Stabilization of RNA derived from Jurkat, HeLa and HUVEC Cell Lines for Use in RT-qPCR Assays

Ambient Temperature Stabilization of RNA derived from Jurkat, HeLa and HUVEC Cell Lines for Use in RT-qPCR Assays Ambient Temperature Stabilization of RNA derived from Jurkat, HeLa and HUVEC Cell Lines for Use in RT-qPCR Assays C. Litterst 1, H. Martinez, B. Iverson and R. Nuňez 1 Bio-Rad Laboratories, Life Science

More information

TNBC: What s new Déjà vu All Over Again? Lucy R. Langer, MD MSHS Compass Oncology - SABCS 2016 Review February 21, 2017

TNBC: What s new Déjà vu All Over Again? Lucy R. Langer, MD MSHS Compass Oncology - SABCS 2016 Review February 21, 2017 TNBC: What s new Déjà vu All Over Again? Lucy R. Langer, MD MSHS Compass Oncology - SABCS 2016 Review February 21, 2017 The problem with TNBC 1. Generally more aggressive 2. ONLY chemotherapy 3. No other

More information

Contemporary Classification of Breast Cancer

Contemporary Classification of Breast Cancer Contemporary Classification of Breast Cancer Laura C. Collins, M.D. Vice Chair of Anatomic Pathology Professor of Pathology Beth Israel Deaconess Medical Center and Harvard Medical School Boston, MA Outline

More information

Computer Science, Biology, and Biomedical Informatics (CoSBBI) Outline. Molecular Biology of Cancer AND. Goals/Expectations. David Boone 7/1/2015

Computer Science, Biology, and Biomedical Informatics (CoSBBI) Outline. Molecular Biology of Cancer AND. Goals/Expectations. David Boone 7/1/2015 Goals/Expectations Computer Science, Biology, and Biomedical (CoSBBI) We want to excite you about the world of computer science, biology, and biomedical informatics. Experience what it is like to be a

More information

Bradley M Turner MD, MPH, MHA. Assistant Professor University of Rochester Department of Pathology and Laboratory Medicine

Bradley M Turner MD, MPH, MHA. Assistant Professor University of Rochester Department of Pathology and Laboratory Medicine Bradley M Turner MD, MPH, MHA Assistant Professor University of Rochester Department of Pathology and Laboratory Medicine My real job!!! I have nothing to disclose although Oncotype Dx year end revenues

More information

Product Introduction

Product Introduction Product Introduction Product Codes: HCL026, HCL027 and HCL028 Contents Introduction to HER2 2 HER2 immunohistochemistry 3 Cell lines as controls 5 HER2 Analyte Control DR IHC 7 HER2 Analyte Control DR

More information

2019 COLLECTION TYPE: MIPS CLINICAL QUALITY MEASURES (CQMS) MEASURE TYPE: Process High Priority

2019 COLLECTION TYPE: MIPS CLINICAL QUALITY MEASURES (CQMS) MEASURE TYPE: Process High Priority Quality ID #449 (NQF 1857): HER2 Negative or Undocumented Breast Cancer Patients Spared Treatment with HER2-Targeted Therapies National Quality Strategy Domain: Efficiency and Cost Reduction Meaningful

More information

Genomics Core Facility of the University of Leicester Technical note March 2012

Genomics Core Facility of the University of Leicester Technical note March 2012 Genomics Core Facility of the University of Leicester Technical note March 2012 Consequences of various contaminants on RNA quantification and quality controls Nicolas Sylvius and Mariaelena Repici Department

More information

Intrinsic molecular subtypes of breast cancers categorized as HER2-positive using an alternative chromosome 17 probe assay

Intrinsic molecular subtypes of breast cancers categorized as HER2-positive using an alternative chromosome 17 probe assay Desai et al. reast Cancer Research (2018) 20:75 https://doi.org/10.1186/s13058-018-1005-z SHORT REPORT Intrinsic molecular subtypes of breast cancers categorized as HER2-positive using an alternative chromosome

More information

Setting The setting was secondary care. The economic study was conducted in the USA.

Setting The setting was secondary care. The economic study was conducted in the USA. HER-2 testing and trastuzumab therapy for metastatic breast cancer: a cost-effectiveness analysis Elkin E B, Weinstein K C, Winer E P, Kuntz K M, Schnitt S J, Weeks J C Record Status This is a critical

More information

Analysis of small RNAs from Drosophila Schneider cells using the Small RNA assay on the Agilent 2100 bioanalyzer. Application Note

Analysis of small RNAs from Drosophila Schneider cells using the Small RNA assay on the Agilent 2100 bioanalyzer. Application Note Analysis of small RNAs from Drosophila Schneider cells using the Small RNA assay on the Agilent 2100 bioanalyzer Application Note Odile Sismeiro, Jean-Yves Coppée, Christophe Antoniewski, and Hélène Thomassin

More information

Extracellular Vesicle RNA isolation Kits

Extracellular Vesicle RNA isolation Kits Extracellular Vesicle RNA isolation Kits Summary Section 4 Introduction 42 Exo-TotalRNA and TumorExo-TotalRNA isolation kits 43 Extracellular Vesicle RNA extraction kits Ordering information Products can

More information

Department of Pathology, Loyola University Medical Center, Maywood, IL 60153, USA 2

Department of Pathology, Loyola University Medical Center, Maywood, IL 60153, USA 2 Hindawi Publishing Corporation Pathology Research International Volume 2012, Article ID 947041, 7 pages doi:10.1155/2012/947041 Clinical Study The Effect of Cold Ischemia Time and/or Formalin Fixation

More information

Supplementary Online Content

Supplementary Online Content Supplementary Online Content The Premenopausal Breast Cancer Collaborative Group. Association body mass index and age with premenopausal breast cancer risk in premenopausal women. JAMA Oncol. Published

More information

Optimizing anti-her-2 therapies for ABC Potential role of immunotherapy. Javier Cortes, Ramon y

Optimizing anti-her-2 therapies for ABC Potential role of immunotherapy. Javier Cortes, Ramon y Optimizing anti-her-2 therapies for ABC Potential role of immunotherapy Javier Cortes, Ramon y Cajal University Hospital, Madrid, Spain Vall d Hebron Institute of Oncology (VHIO), Medica Scientia Innovation

More information

Supporting Online Material for

Supporting Online Material for www.sciencemag.org/cgi/content/full/1171320/dc1 Supporting Online Material for A Frazzled/DCC-Dependent Transcriptional Switch Regulates Midline Axon Guidance Long Yang, David S. Garbe, Greg J. Bashaw*

More information

Updates in Molecular Classification of Breast Cancer. Emmanuel Agosto-Arroyo, MD Assistant Member Department of Anatomic Pathology

Updates in Molecular Classification of Breast Cancer. Emmanuel Agosto-Arroyo, MD Assistant Member Department of Anatomic Pathology Updates in Molecular Classification of Breast Cancer Emmanuel Agosto-Arroyo, MD Assistant Member Department of Anatomic Pathology 3/3/2018 Disclosure There are no conflicts of interest. Objectives Describe

More information

Genomic tests to personalize therapy of metastatic breast cancers. Fabrice ANDRE Gustave Roussy Villejuif, France

Genomic tests to personalize therapy of metastatic breast cancers. Fabrice ANDRE Gustave Roussy Villejuif, France Genomic tests to personalize therapy of metastatic breast cancers Fabrice ANDRE Gustave Roussy Villejuif, France Future application of genomics: Understand the biology at the individual scale Patients

More information