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Lobular breast cancer genomic testing

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https://www.readbyqxmd.com/read/27859137/association-between-breast-cancer-genetic-susceptibility-variants-and-terminal-duct-lobular-unit-involution-of-the-breast
#1
Clara Bodelon, Hannah Oh, Nilanjan Chatterjee, Montserrat Garcia-Closas, Maya Palakal, Mark E Sherman, Ruth M Pfeiffer, Berta M Geller, Pamela M Vacek, Donald L Weaver, Rachael E Chicoine, Daphne Papathomas, Jackie Xiang, Deesha A Patel, Zeina G Khodr, Laura Linville, Susan E Clare, Daniel W Visscher, Carolyn Mies, Stephen M Hewitt, Louise A Brinton, Anna Maria Storniolo, Chunyan He, Stephen J Chanock, Gretchen L Gierach, Jonine D Figueroa
Terminal duct lobular units (TDLUs) are the predominant source of future breast cancers, and lack of TDLU involution (higher TDLU counts, higher acini count per TDLU and the product of the two) is a breast cancer risk factor. Numerous breast cancer susceptibility single nucleotide polymorphisms (SNPs) have been identified, but whether they are associated with TDLU involution is unknown. In a pooled analysis of 872 women from two studies, we investigated 62 established breast cancer SNPs and relationships with TDLU involution...
November 9, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27716369/patient-survival-and-tumor-characteristics-associated-with-chek2-p-i157t-findings-from-the-breast-cancer-association-consortium
#2
Taru A Muranen, Carl Blomqvist, Thilo Dörk, Anna Jakubowska, Päivi Heikkilä, Rainer Fagerholm, Dario Greco, Kristiina Aittomäki, Stig E Bojesen, Mitul Shah, Alison M Dunning, Valerie Rhenius, Per Hall, Kamila Czene, Judith S Brand, Hatef Darabi, Jenny Chang-Claude, Anja Rudolph, Børge G Nordestgaard, Fergus J Couch, Steven N Hart, Jonine Figueroa, Montserrat García-Closas, Peter A Fasching, Matthias W Beckmann, Jingmei Li, Jianjun Liu, Irene L Andrulis, Robert Winqvist, Katri Pylkäs, Arto Mannermaa, Vesa Kataja, Annika Lindblom, Sara Margolin, Jan Lubinski, Natalia Dubrowinskaja, Manjeet K Bolla, Joe Dennis, Kyriaki Michailidou, Qin Wang, Douglas F Easton, Paul D P Pharoah, Marjanka K Schmidt, Heli Nevanlinna
BACKGROUND: P.I157T is a CHEK2 missense mutation associated with a modest increase in breast cancer risk. Previously, another CHEK2 mutation, the protein truncating c.1100delC has been associated with poor prognosis of breast cancer patients. Here, we have investigated patient survival and characteristics of breast tumors of germ line p.I157T carriers. METHODS: We included in the analyses 26,801 European female breast cancer patients from 15 studies participating in the Breast Cancer Association Consortium...
October 3, 2016: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/27556229/fine-mapping-of-the-1p11-2-breast-cancer-susceptibility-locus
#3
Hisani N Horne, Charles C Chung, Han Zhang, Kai Yu, Ludmila Prokunina-Olsson, Kyriaki Michailidou, Manjeet K Bolla, Qin Wang, Joe Dennis, John L Hopper, Melissa C Southey, Marjanka K Schmidt, Annegien Broeks, Kenneth Muir, Artitaya Lophatananon, Peter A Fasching, Matthias W Beckmann, Olivia Fletcher, Nichola Johnson, Elinor J Sawyer, Ian Tomlinson, Barbara Burwinkel, Frederik Marme, Pascal Guénel, Thérèse Truong, Stig E Bojesen, Henrik Flyger, Javier Benitez, Anna González-Neira, Hoda Anton-Culver, Susan L Neuhausen, Hermann Brenner, Volker Arndt, Alfons Meindl, Rita K Schmutzler, Hiltrud Brauch, Ute Hamann, Heli Nevanlinna, Sofia Khan, Keitaro Matsuo, Hiroji Iwata, Thilo Dörk, Natalia V Bogdanova, Annika Lindblom, Sara Margolin, Arto Mannermaa, Veli-Matti Kosma, Georgia Chenevix-Trench, Anna H Wu, David Ven den Berg, Ann Smeets, Hui Zhao, Jenny Chang-Claude, Anja Rudolph, Paolo Radice, Monica Barile, Fergus J Couch, Celine Vachon, Graham G Giles, Roger L Milne, Christopher A Haiman, Loic Le Marchand, Mark S Goldberg, Soo H Teo, Nur A M Taib, Vessela Kristensen, Anne-Lise Borresen-Dale, Wei Zheng, Martha Shrubsole, Robert Winqvist, Arja Jukkola-Vuorinen, Irene L Andrulis, Julia A Knight, Peter Devilee, Caroline Seynaeve, Montserrat García-Closas, Kamila Czene, Hatef Darabi, Antoinette Hollestelle, John W M Martens, Jingmei Li, Wei Lu, Xiao-Ou Shu, Angela Cox, Simon S Cross, William Blot, Qiuyin Cai, Mitul Shah, Craig Luccarini, Caroline Baynes, Patricia Harrington, Daehee Kang, Ji-Yeob Choi, Mikael Hartman, Kee Seng Chia, Maria Kabisch, Diana Torres, Anna Jakubowska, Jan Lubinski, Suleeporn Sangrajrang, Paul Brennan, Susan Slager, Drakoulis Yannoukakos, Chen-Yang Shen, Ming-Feng Hou, Anthony Swerdlow, Nick Orr, Jacques Simard, Per Hall, Paul D P Pharoah, Douglas F Easton, Stephen J Chanock, Alison M Dunning, Jonine D Figueroa
The Cancer Genetic Markers of Susceptibility genome-wide association study (GWAS) originally identified a single nucleotide polymorphism (SNP) rs11249433 at 1p11.2 associated with breast cancer risk. To fine-map this locus, we genotyped 92 SNPs in a 900kb region (120,505,799-121,481,132) flanking rs11249433 in 45,276 breast cancer cases and 48,998 controls of European, Asian and African ancestry from 50 studies in the Breast Cancer Association Consortium. Genotyping was done using iCOGS, a custom-built array...
2016: PloS One
https://www.readbyqxmd.com/read/27340177/modeling-invasive-lobular-breast-carcinoma-by-crispr-cas9-mediated-somatic-genome-editing-of-the-mammary-gland
#4
Stefano Annunziato, Sjors M Kas, Micha Nethe, Hatice Yücel, Jessica Del Bravo, Colin Pritchard, Rahmen Bin Ali, Bas van Gerwen, Bjørn Siteur, Anne Paulien Drenth, Eva Schut, Marieke van de Ven, Mirjam C Boelens, Sjoerd Klarenbeek, Ivo J Huijbers, Martine H van Miltenburg, Jos Jonkers
Large-scale sequencing studies are rapidly identifying putative oncogenic mutations in human tumors. However, discrimination between passenger and driver events in tumorigenesis remains challenging and requires in vivo validation studies in reliable animal models of human cancer. In this study, we describe a novel strategy for in vivo validation of candidate tumor suppressors implicated in invasive lobular breast carcinoma (ILC), which is hallmarked by loss of the cell-cell adhesion molecule E-cadherin. We describe an approach to model ILC by intraductal injection of lentiviral vectors encoding Cre recombinase, the CRISPR/Cas9 system, or both in female mice carrying conditional alleles of the Cdh1 gene, encoding for E-cadherin...
June 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27284958/nonamplification-erbb2-genomic-alterations-in-5605-cases-of-recurrent-and-metastatic-breast-cancer-an-emerging-opportunity-for-anti-her2-targeted-therapies
#5
Jeffrey S Ross, Laurie M Gay, Kai Wang, Siraj M Ali, Saranya Chumsri, Julia A Elvin, Ron Bose, Jo-Anne Vergilio, James Suh, Roman Yelensky, Doron Lipson, Juliann Chmielecki, Stanley Waintraub, Brian Leyland-Jones, Vincent A Miller, Philip J Stephens
BACKGROUND: Activating, nonamplification ERBB2 mutations (ERBB2mut) are not detected by immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH), but are detected by DNA sequencing and may predict clinical responses to human epidermal growth factor receptor (HER2)-targeted therapy. The authors queried 5605 advanced/metastatic breast cancers (mBC) to uncover the frequency of ERBB2mut genomic alterations. Clinical responses to anti-HER2 therapeutics were identified. METHODS: DNA was extracted from 40 µm of formalin-fixed paraffin-embedded (FFPE) sections...
September 1, 2016: Cancer
https://www.readbyqxmd.com/read/26554380/mutational-profiling-can-establish-clonal-or-independent-origin-in-synchronous-bilateral-breast-and-other-tumors
#6
Lei Bao, Karen Messer, Richard Schwab, Olivier Harismendy, Minya Pu, Brian Crain, Shawn Yost, Kelly A Frazer, Brinda Rana, Farnaz Hasteh, Anne Wallace, Barbara A Parker
BACKGROUND: Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal) pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC) mutations/ # total HC mutations). METHODS: Statistical properties of a formal test using the CLS were investigated...
2015: PloS One
https://www.readbyqxmd.com/read/26385397/utility-of-oncotype-dx-risk-assessment-in-patients-with-invasive-lobular-carcinoma
#7
Michaela L Tsai, Tamera J Lillemoe, Marsha J Finkelstein, Joel E Money, Barbara Susnik, Erin Grimm, Sung-Hae L Kang, Karen K Swenson
INTRODUCTION/BACKGROUND: Oncotype DX (Genomic Health, Redwood City, CA) uses reverse transcriptase polymerase chain reaction analysis to measure tumor gene expression for determining recurrence risk (RR) and guiding chemotherapy decisions for breast cancer patients. Invasive lobular carcinoma (ILC) is a histologic subtype that has not been the focus of prior studies validating Oncotype DX. The study purpose was to develop a model using histologic tumor characteristics to predict uniformly low Oncotype DX Recurrence Scores (RS) in ILC...
February 2016: Clinical Breast Cancer
https://www.readbyqxmd.com/read/26049741/recognition-of-and-recent-issues-in-hereditary-diffuse-gastric-cancer
#8
REVIEW
Shinya Sugimoto, Hirokazu Komatsu, Yuichi Morohoshi, Takanori Kanai
In East Asian countries, gastric cancer incidence is high, but detection rates for germline CDH1 mutations that cause hereditary diffuse gastric cancers (HDGCs) are low. Consequently, screens and genetic testing for HDGC are often considered unimportant. Since the first germline truncating CDH1 mutations in Japanese patients were reported, some HDGC cases have been reported, and some of these involve large germline rearrangements and de novo mutation of CDH1. New methods for mutation detection--such as multiplex ligation-dependent probe amplification, array comparative genomic hybridization, and exome sequencing--have become available, as have new experimental models, including novel gene-knockout mice and gastric organoids...
August 2015: Journal of Gastroenterology
https://www.readbyqxmd.com/read/25067988/sequence-based-detection-of-mutations-in-cadherin-1-to-determine-the-prevalence-of-germline-mutations-in-patients-with-invasive-lobular-carcinoma-of-the-breast
#9
Allyson L Valente, Seth Rummel, Craig D Shriver, Rachel E Ellsworth
BACKGROUND: Loss of cadherin 1 (CDH1) expression, which is normally involved in cell adhesion and maintenance of tissue architecture, is a hallmark of invasive lobular carcinoma (ILCA). Because hereditary cancers may require different risk reduction, counseling and treatment options than sporadic cancer, it is critical to determine the prevalence of germline CDH1 mutations in patients with ILCA. METHODS: All patients with ILCA (n = 100) previously enrolled in the Clinical Breast Care Project were identified...
2014: Hereditary Cancer in Clinical Practice
https://www.readbyqxmd.com/read/23855743/snvhmm-predicting-single-nucleotide-variants-from-next-generation-sequencing
#10
Jiawen Bian, Chenglin Liu, Hongyan Wang, Jing Xing, Priyanka Kachroo, Xiaobo Zhou
BACKGROUND: The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Single nucleotide variants (SNVs) inferred from next generation sequencing are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNVs detection capability in the regulatory regions of the genome. Post probabilistic based methods are efficient for detection of SNVs in high coverage regions or sequencing data with high depth...
2013: BMC Bioinformatics
https://www.readbyqxmd.com/read/22434525/prevalence-of-brca1-mutations-among-403-women-with-triple-negative-breast-cancer-implications-for-genetic-screening-selection-criteria-a-hellenic-cooperative-oncology-group-study
#11
Florentia Fostira, Marianthi Tsitlaidou, Christos Papadimitriou, Maroulio Pertesi, Eleni Timotheadou, Alexandra V Stavropoulou, Stavros Glentis, Evangelos Bournakis, Mattheos Bobos, Dimitrios Pectasides, Pavlos Papakostas, George Pentheroudakis, Helen Gogas, Pantelis Skarlos, Epaminontas Samantas, Dimitrios Bafaloukos, Paris A Kosmidis, Angelos Koutras, Drakoulis Yannoukakos, Irene Konstantopoulou, George Fountzilas
In spite the close association of the triple-negative breast cancer immunophenotype with hereditary breast cancers and the BRCA1 pathway, there is a lack of population studies that determine the frequency of BRCA1 mutations among triple-negative breast cancer patients. To address this, we have screened a large sample of 403 women diagnosed with triple-negative invasive breast cancer, independently of their age or family history, for germline BRCA1 mutations. Median age at diagnosis was 50 years (range 20-83)...
July 2012: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/21953071/hsa-mir-375-is-differentially-expressed-during-breast-lobular-neoplasia-and-promotes-loss-of-mammary-acinar-polarity
#12
Orsi Giricz, Paul A Reynolds, Andrew Ramnauth, Christina Liu, Tao Wang, Lesley Stead, Geoffrey Childs, Thomas Rohan, Nella Shapiro, Susan Fineberg, Paraic A Kenny, Olivier Loudig
Invasive lobular carcinoma (ILC) of the breast, characterized by loss of E-cadherin expression, accounts for 5-15% of invasive breast cancers and it is believed to arise via a linear histological progression. Genomic studies have identified a clonal relationship between ILC and concurrent lobular carcinoma in situ (LCIS) lesions, suggesting that LCIS may be a precursor lesion. It has been shown that an LCIS diagnosis confers a 15-20% risk of progression to ILC over a lifetime. Currently no molecular test or markers can identify LCIS lesions likely to progress to ILC...
January 2012: Journal of Pathology
https://www.readbyqxmd.com/read/21373875/tp53-genomics-predict-higher-clinical-and-pathologic-tumor-response-in-operable-early-stage-breast-cancer-treated-with-docetaxel-capecitabine-%C3%A2-trastuzumab
#13
MULTICENTER STUDY
Stefan Glück, Jeffrey S Ross, Melanie Royce, Edward F McKenna, Charles M Perou, Eli Avisar, Lin Wu
To determine rates of pathologic complete response (pCR) and near-complete response (npCR) in operable early-stage breast cancer using neoadjuvant capecitabine plus docetaxel, with or without trastuzumab, and investigate biomarkers of pathologic response. Women with operable early-stage breast cancer were enrolled in a multicenter study of neoadjuvant therapy for four 21-day cycles with capecitabine 825 mg/m(2) plus docetaxel 75 mg/m(2) if human epidermal growth factor receptor 2 (HER2)-negative, and additionally, a standard trastuzumab dose if HER2-positive...
April 2012: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/20665886/utility-of-oncotype-dx-risk-estimates-in-clinically-intermediate-risk-hormone-receptor-positive-her2-normal-grade-ii-lymph-node-negative-breast-cancers
#14
Catherine M Kelly, Savitri Krishnamurthy, Giampaolo Bianchini, Jennifer K Litton, Ana M Gonzalez-Angulo, Gabriel N Hortobagyi, Lajos Pusztai
BACKGROUND: Oncotype DX breast cancer assay (Genomic Health, Redwood City, Calif) stratifies patients with early breast cancer according to risk of distant recurrence. The authors hypothesized that the test is ordered when clinicopathological variables yield equivocal risk estimates. The current study also showed how often the test clarifies clinically ambiguous risk status. METHODS: The authors examined clinical/pathological characteristics and calculated risk of recurrence with Adjuvant! for 309 consecutive patients who underwent Oncotype DX testing at M...
November 15, 2010: Cancer
https://www.readbyqxmd.com/read/20591882/hereditary-diffuse-gastric-cancer-updated-consensus-guidelines-for-clinical-management-and-directions-for-future-research
#15
Rebecca C Fitzgerald, Richard Hardwick, David Huntsman, Fatima Carneiro, Parry Guilford, Vanessa Blair, Daniel C Chung, Jeff Norton, Krishnadath Ragunath, J Han Van Krieken, Sarah Dwerryhouse, Carlos Caldas
25-30% of families fulfilling the criteria for hereditary diffuse gastric cancer have germline mutations of the CDH1 (E-cadherin) gene. In light of new data and advancement of technologies, a multidisciplinary workshop was convened to discuss genetic testing, surgery, endoscopy and pathology reporting. The updated recommendations include broadening of CDH1 testing criteria such that: histological confirmation of diffuse gastric criteria is only required for one family member; inclusion of individuals with diffuse gastric cancer before the age of 40 years without a family history; and inclusion of individuals and families with diagnoses of both diffuse gastric cancer (including one before the age of 50 years) and lobular breast cancer...
July 2010: Journal of Medical Genetics
https://www.readbyqxmd.com/read/20099298/molecular-analysis-reveals-a-genetic-basis-for-the-phenotypic-diversity-of-metaplastic-breast-carcinomas
#16
Felipe C Geyer, Britta Weigelt, Rachael Natrajan, Maryou B K Lambros, Dario de Biase, Radost Vatcheva, Kay Savage, Alan Mackay, Alan Ashworth, Jorge S Reis-Filho
Cancers may be composed of multiple populations of submodal clones sharing the same initiating genetic lesions, followed by the acquisition of divergent genetic hits. Intra-tumour genetic heterogeneity has profound implications for cancer clinical management. To determine the extent of intra-tumour genetic heterogeneity in breast cancers, and whether the morphological diversity of breast cancers is underpinned by divergent genetic aberrations, we analysed the genomic profiles of microdissected, morphologically distinct components of six metaplastic breast carcinomas, tumours characterized by the presence of morphological areas with divergent differentiation...
April 2010: Journal of Pathology
https://www.readbyqxmd.com/read/19448591/clinical-validation-of-an-array-cgh-test-for-her2-status-in-breast-cancer-reveals-that-polysomy-17-is-a-rare-event
#17
I-Tien Yeh, Mathew A Martin, Ryan S Robetorye, Aswani R Bolla, Chris McCaskill, Rashmi K Shah, Mercedes E Gorre, Mansoor S Mohammed, Shelly R Gunn
The HER2 gene is an important prognostic and therapeutic marker in newly diagnosed breast cancer. Currently, HER2 status is most frequently determined by immunohistochemical detection of HER2 protein expression on the cellular membrane surface or by fluorescence in situ hybridization analysis of HER2 gene copy number in fixed tissue using locus-specific probes for the HER2 gene and chromosome 17 centromere. However, these methods are problematic because of issues with intra- and inter-laboratory reproducibility and preanalytic variables, such as fixation time...
September 2009: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/19372580/genetic-alterations-and-oncogenic-pathways-associated-with-breast-cancer-subtypes
#18
Xiaolan Hu, Howard M Stern, Lin Ge, Carol O'Brien, Lauren Haydu, Cynthia D Honchell, Peter M Haverty, Brock A Peters, Thomas D Wu, Lukas C Amler, John Chant, David Stokoe, Mark R Lackner, Guy Cavet
Breast cancers can be divided into subtypes with important implications for prognosis and treatment. We set out to characterize the genetic alterations observed in different breast cancer subtypes and to identify specific candidate genes and pathways associated with subtype biology. mRNA expression levels of estrogen receptor, progesterone receptor, and HER2 were shown to predict marker status determined by immunohistochemistry and to be effective at assigning samples to subtypes. HER2(+) cancers were shown to have the greatest frequency of high-level amplification (independent of the ERBB2 amplicon itself), but triple-negative cancers had the highest overall frequencies of copy gain...
April 2009: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/16570270/kif14-mrna-expression-is-a-predictor-of-grade-and-outcome-in-breast-cancer
#19
Timothy W Corson, Brenda L Gallie
Gain of chromosome 1q is a hallmark of breast cancer, and likely reflects oncogene amplification. We previously identified mitotic kinesin KIF14 (kinesin family member 14) as an overexpressed candidate oncogene in the 1q31.3-1q32.1 minimal region of genomic gain in breast cancer cell lines. KIF14 also showed high expression in other cancers, notably an association with survival in lung tumors. We now report KIF14 expression in 99 primary breast tumors and 10 normal breast controls. Measured by real-time RT-PCR, KIF14 was overexpressed 10-fold on average in tumors relative to normals (t test p = 0...
September 1, 2006: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/16314623/allele-imbalance-or-loss-of-heterozygosity-in-normal-breast-epithelium-of-sporadic-breast-cancer-cases-and-brca1-gene-mutation-carriers-is-increased-compared-with-reduction-mammoplasty-tissues
#20
COMPARATIVE STUDY
Pamela S Larson, Benjamin L Schlechter, Antonio de las Morenas, Judy E Garber, L Adrienne Cupples, Carol L Rosenberg
PURPOSE: Normal-appearing breast epithelium can contain genetic abnormalities, including allele imbalance (AI), also referred to as loss of heterozygosity. Whether abnormalities are associated with cancer or cancer risk is unknown. PATIENTS AND METHODS: We performed a miniallelotype, using 20 microsatellites, on each of 460 histologically normal, microdissected breast terminal ducto-lobular units (TDLUs) from three groups of women: sporadic breast cancer patients (SP; n = 18), BRCA1 gene mutation carriers (BRCA1; n = 16), and controls undergoing reduction mammoplasty (RM; n = 18)...
December 1, 2005: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
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