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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28212807/prevalence-of-brca1-and-brca2-large-genomic-rearrangements-in-tunisian-high-risk-breast-ovarian-cancer-families-implications-for-genetic-testing
#1
Aouatef Riahi, Habiba Chabouni-Bouhamed, Maher Kharrat
Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Thus, large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are responsible for 4-28% of all inherited BRCA mutations. In this study, Multiplex ligation-dependent probe amplification (MLPA) assay was used for detection of large rearrangements of BRCA1 and BRCA2 genes in 36 unrelated high-risk breast/ovarian cancer patients negative for BRCA1/2 point mutations...
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28210550/evaluating-the-performance-of-national-comprehensive-cancer-network-nccn-breast-and-ovarian-genetic-familial-high-risk-assessment-referral-criteria-for-breast-cancer-women-in-an-asian-surgical-breast-clinic
#2
Geok-Hoon Lim, Eillen Borje, John C Allen
BACKGROUND: Globally, resources for genomic services vary. Current National Comprehensive Cancer Network (NCCN) breast and ovarian genetic/familial high risk assessment criteria for further genetic risk evaluation are useful, but lack specificity for reliably excluding patients with low a priori risk. This may result in patient overload in lesser-equipped genetics clinics. Since we use Manchester and the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk assessment models in our genetics clinic to determine whether genetic testing is warranted, we chose Manchester and BOADICEA as the reference standard to compare how the NCCN breast and ovarian genetic/familial high risk assessment criteria for further genetic risk evaluation performs against these two risk assessment models in referring breast cancer patients for genetic evaluation...
February 2017: Gland Surgery
https://www.readbyqxmd.com/read/28205193/new-therapeutic-strategies-for-triple-negative-breast-cancer
#3
REVIEW
Borbála Székely, Andrea L M Silber, Lajos Pusztai
Relatively few clinically important therapeutic advances have occurred in the treatment of triple-negative breast cancer (TNBC) since the introduction of taxanes as adjuvant therapy over 20 years ago. However, this is rapidly changing due to a variety of conceptually important clinical trials and emerging new options such as immune checkpoint inhibitors and antibody-drug conjugates. Evidence also increasingly supports that platinum drugs and inhibitors of poly (ADP-ribose) polymerase, or PARP, are particularly effective in the treatment of germline BRCA-mutant cancers, including TNBC...
February 15, 2017: Oncology (Williston Park, NY)
https://www.readbyqxmd.com/read/28205045/characteristics-of-brca1-2-mutations-carriers-including-large-genomic-rearrangements-in-high-risk-breast-cancer-patients
#4
Boyoung Park, Ji Yeon Sohn, Kyong-Ah Yoon, Keun Seok Lee, Eun Hae Cho, Myong Cheol Lim, Moon Jung Yang, Soo Jin Park, Moo Hyun Lee, See Youn Lee, Yoon Jung Chang, Dong Ock Lee, Sun-Young Kong, Eun Sook Lee
PURPOSE: We investigated the prevalence of BRCA1/2 small mutations and large genomic rearrangements in high risk breast cancer patients who attended a genetic counseling clinic. METHODS: In total 478 patients were assessed for BRCA1/2 mutations by direct sequencing, of whom, 306 were identified as non-carriers of BRCA1/2 mutation and assessed for large rearrangement mutations by multiplex ligation-dependent probe amplification. Family history and clinicopathological characteristics of patients were evaluated...
February 15, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28205043/a-polygenic-risk-score-for-breast-cancer-risk-in-a-taiwanese-population
#5
Yi-Chen Hsieh, Shih-Hsin Tu, Chien-Tien Su, Er-Chieh Cho, Chih-Hsiung Wu, Mao-Chih Hsieh, Shiyng-Yu Lin, Yun-Ru Liu, Chin-Sheng Hung, Hung-Yi Chiou
BACKGROUND: Multiple common variants identified by genome-wide association studies showed limited evidence of the risk of breast cancer in Taiwan. In this study, we analyzed the breast cancer risk in relation to 13 individual single-nucleotide polymorphisms (SNPs) identified by a GWAS in an Asian population. METHODS: In total, 446 breast cancer patients and 514 healthy controls were recruited for this case-control study. In addition, we developed a polygenic risk score (PRS) including those variants significantly associated with breast cancer risk, and also evaluated the contribution of PRS and clinical risk factors to breast cancer using receiver operating characteristic curve (AUC)...
February 15, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28197806/recruiting-families-at-risk-for-hereditary-breast-and-ovarian-cancer-from-a-statewide-cancer-registry-a-methodological-study
#6
Maria C Katapodi, Deb Duquette, James J Yang, Kari Mendelsohn-Victor, Beth Anderson, Christos Nikolaidis, Emily Mancewicz, Laurel L Northouse, Sonia Duffy, David Ronis, Kara J Milliron, Nicole Probst-Herbst, Sofia D Merajver, Nancy K Janz, Glenn Copeland, Scott Roberts
PURPOSE: Cancer genetic services (counseling/testing) are recommended for women diagnosed with breast cancer younger than 45 years old (young breast cancer survivors-YBCS) and at-risk relatives. We present recruitment of YBCS, identification and recruitment of at-risk relatives, and YBCS willingness to contact their cancer-free, female relatives. METHODS: A random sample of 3,000 YBCS, stratified by race (Black vs. White/Other), was identified through a population-based cancer registry and recruited in a randomized trial designed to increase use of cancer genetic services...
February 14, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28182268/racial-disparities-in-brca-testing-and-cancer-risk-management-across-a-population-based-sample-of-young-breast-cancer-survivors
#7
Deborah Cragun, Anne Weidner, Courtney Lewis, Devon Bonner, Jongphil Kim, Susan T Vadaparampil, Tuya Pal
BACKGROUND: Breast cancer (BC) disparities may widen with genomic advances. The authors compared non-Hispanic white (NHW), black, and Hispanic BC survivors for 1) cancer risk-management practices among BRCA carriers and 2) provider discussion and receipt of genetic testing. METHODS: A population-based sample of NHW, black, and Hispanic women who had been diagnosed with invasive BC at age 50 years or younger from 2009 to 2012 were recruited through the state cancer registry...
February 9, 2017: Cancer
https://www.readbyqxmd.com/read/28179634/rapid-and-cost-effective-high-throughput-sequencing-for-identification-of-germline-mutations-of-brca1-and-brca2
#8
Somayeh Ahmadloo, Hirofumi Nakaoka, Takahide Hayano, Kazuyoshi Hosomichi, Hua You, Emi Utsuno, Takafumi Sangai, Motoi Nishimura, Kazuyuki Matsushita, Akira Hata, Fumio Nomura, Ituro Inoue
Genetic testing for breast cancer predisposing genes, BRCA1 and BRCA2, can take advantage for early identification of carriers with pathogenic germline mutations. However, conventional approaches based on Sanger sequencing are laborious and expensive. Next-generation sequencing technology has a great impact on investigation of medical genomics and now applied clinical genetics. We provide a protocol based on a pool and capture method followed by high-throughput sequencing, which realizes a rapid, high-quality, high-accuracy and low-cost testing for mutations in BRCA1 and BRCA2 by using small amounts of input DNA...
February 9, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28179588/tp53-based-interaction-analysis-identifies-cis-eqtl-variants-for-tp53bp2-fbxo28-and-fam53a-that-associate-with-survival-and-treatment-outcome-in-breast-cancer
#9
Rainer Fagerholm, Sofia Khan, Marjanka K Schmidt, Montserrat García-Closas, Päivi Heikkilä, Jani Saarela, Jonathan Beesley, Maral Jamshidi, Kristiina Aittomäki, Jianjun Liu, H Raza Ali, Irene L Andrulis, Matthias W Beckmann, Sabine Behrens, Fiona M Blows, Hermann Brenner, Jenny Chang-Claude, Fergus J Couch, Kamila Czene, Peter A Fasching, Jonine Figueroa, Giuseppe Floris, Gord Glendon, Qi Guo, Per Hall, Emily Hallberg, Ute Hamann, Bernd Holleczek, Maartje J Hooning, John L Hopper, Agnes Jager, Maria Kabisch, Renske Keeman, Veli-Matti Kosma, Diether Lambrechts, Annika Lindblom, Arto Mannermaa, Sara Margolin, Elena Provenzano, Mitul Shah, Melissa C Southey, Joe Dennis, Michael Lush, Kyriaki Michailidou, Qin Wang, Manjeet K Bolla, Alison M Dunning, Douglas F Easton, Paul D P Pharoah, Georgia Chenevix-Trench, Carl Blomqvist, Heli Nevanlinna
TP53 overexpression is indicative of somatic TP53 mutations and associates with aggressive tumors and poor prognosis in breast cancer. We utilized a two-stage SNP association study to detect variants associated with breast cancer survival in a TP53-dependent manner. Initially, a genome-wide study (n = 575 cases) was conducted to discover candidate SNPs for genotyping and validation in the Breast Cancer Association Consortium (BCAC). The SNPs were then tested for interaction with tumor TP53 status (n = 4,610) and anthracycline treatment (n = 17,828)...
February 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28179314/dna-methylation-in-breast-tumor-from-high-risk-women-in-the-breast-cancer-family-registry
#10
Hui-Chen Wu, Melissa C Southey, Hanina Hibshoosh, Regina M Santella, Mary Beth Terry
To examine DNA methylation profiles in breast tumors of women with a strong breast cancer family history, we measured methylation by bisulfite sequencing in 40 genes in 40 breast tumor tissues from women in the Breast Cancer Family Registry. We selected candidate genes from analysis of the Cancer Genome Atlas project (TCGA) breast data. Compared to TCGA breast cancer, BCFR cases are younger and more likely to be ER-negative. Overall, we found that many of the methylation differences between BCFR tumor and normal adjacent tissues were smaller than that in TCGA samples...
2017: Anticancer Research
https://www.readbyqxmd.com/read/28177554/identifying-relations-between-imaging-phenotypes-and-molecular-subtypes-of-breast-cancer-model-discovery-and-external-validation
#11
Jia Wu, Xiaoli Sun, Jeff Wang, Yi Cui, Fumi Kato, Hiroki Shirato, Debra M Ikeda, Ruijiang Li
PURPOSE: To determine whether dynamic contrast enhancement magnetic resonance imaging (DCE-MRI) characteristics of the breast tumor and background parenchyma can distinguish molecular subtypes (ie, luminal A/B or basal) of breast cancer. MATERIALS AND METHODS: In all, 84 patients from one institution and 126 patients from The Cancer Genome Atlas (TCGA) were used for discovery and external validation, respectively. Thirty-five quantitative image features were extracted from DCE-MRI (1...
February 8, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28166748/body-mass-index-modifies-the-relationship-between-%C3%AE-h2ax-a-dna-damage-biomarker-and-pathological-complete-response-in-triple-negative-breast-cancer
#12
Maddalena Barba, Patrizia Vici, Laura Pizzuti, Luigi Di Lauro, Domenico Sergi, Anna Di Benedetto, Cristiana Ercolani, Francesca Sperati, Irene Terrenato, Claudio Botti, Lucia Mentuccia, Laura Iezzi, Teresa Gamucci, Clara Natoli, Ilio Vitale, Marcella Mottolese, Ruggero De Maria, Marcello Maugeri-Saccà
BACKGROUND: Body mass index (BMI) is largely investigated as a prognostic and predictive factor in triple-negative breast cancer (TNBC). Overweight and obesity are linked to a variety of pathways regulating tumor-promoting functions, including the DNA damage response (DDR). The DDR physiologically safeguards genome integrity but, in a neoplastic background, it is aberrantly engaged and protects cancer cells from chemotherapy. We herein verified the role of BMI on a previously assessed association between DDR biomarkers and pathological complete response (pCR) in TNBC patients treated with neoadjuvant chemotherapy (NACT)...
February 6, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28155638/a-network-based-pathway-expanding-approach-for-pathway-analysis
#13
Qiaosheng Zhang, Jie Li, Haozhe Xie, Hanqing Xue, Yadong Wang
BACKGROUND: Pathway analysis combining multiple types of high-throughput data, such as genomics and proteomics, has become the first choice to gain insights into the pathogenesis of complex diseases. Currently, several pathway analysis methods have been developed to study complex diseases. However, these methods did not take into account the interaction between internal and external genes of the pathway and between pathways. Hence, these approaches still face some challenges. Here, we propose a network-based pathway-expanding approach that takes the topological structures of biological networks into account...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28155606/clinical-utility-of-neoadjuvant-endocrine-therapy-for-hormone-receptor-positive-breast-cancer
#14
Hans-Christian Kolberg, Bahriye Aktas, Cornelia Liedtke
Primary endocrine therapy is an option in cases of hormone receptor positive and HER2 negative non-metastatic breast cancer. Aromatase inhibitors are considered therapy of choice in postmenopausal patients. In premenopausal patients aromatase inhibitors in combination with LHRH-analogues are regarded superior to tamoxifen. Three different settings have to be discriminated: • Patients too frail for surgery are candidates for primary endocrine therapy in order to control the disease. Treatment duration is determined by the course of the disease...
February 1, 2017: Reviews on Recent Clinical Trials
https://www.readbyqxmd.com/read/28152871/breast-cancer-specific-mortality-in-patients-with-early-stage-hormone-receptor-positive-invasive-breast-cancer-and-oncotype-dx-recurrence-score-results-in-the-seer-database
#15
Valentina Petkov, Dave P Miller, Nadia Howlader, Nathan Gliner, Will Howe, Nicola C Schussler, Kathleen Cronin, Frederick L Baehner, Lynne Penberthy
: 176 Background: NCI's SEER Program provides cancer incidence and survival statistics for ~28% of the US. New research models are needed to characterize the use and impact of genomic tests on patient outcomes. Genomic Health and SEER collaborated to electronically supplement SEER registries with Recurrence Score (RS) results, and have evaluated breast cancer specific mortality (BCSM) in early stage hormone receptor (HR)+ HER2- invasive breast cancer. METHODS: Pts were eligible for pre-specified node negative (N-) disease analysis if HR+, HER2- (by RT-PCR), no prior malignancy, 40-85 years of age, and diagnosed between Jan 2004 (Oncotype DX available Jan 2004) and Dec 2011 (SEER survival analysis complete through 2012)...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28152863/breast-oncology-precision-medicine-genomic-testing-and-treatment-at-the-population-level
#16
Yun Li, Allison W Kurian, Steven J Katz
: 288 Background: The 21-gene assay used to estimate breast cancer recurrence and tailor chemotherapy (chemo) receipt has demonstrated predictive validity and clinical utility. Yet it is unclear how involved patients are in the decision to perform the test, or how oncologists use results to recommend systemic chemo. We examined the patient experience with assay testing, physician recommendations, and chemo receipt based on test results. METHODS: The iCanCare study surveyed a weighted random sample of newly diagnosed patients with early-stage breast cancer who were treated in 2013-14, identified through the population-based SEER registries of Los Angeles and Georgia about 3 months after surgical treatment, and merged with SEER data (N=2632, RR=70%)...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28152829/prevalence-and-predictors-of-second-opinions-from-medical-oncologists-for-early-stage-breast-cancer-results-from-the-icancare-study
#17
Christopher Ryan Friese, Irina Bondarenko, Reshma Jagsi, Steven J Katz
: 185 Background: A second medical oncology opinion (SMO) may facilitate chemotherapy decision-making. However, little is known about the interplay between SMOs, treatment decision-making and chemotherapy use. METHODS: We surveyed women newly diagnosed with early-stage invasive breast cancer and treated in 2013-2014 (response rate 70%), accrued approximately 3 months after surgery through 2 population-based SEER registries (Georgia and Los Angeles), about their experiences with medical oncologists, decision-making, and chemotherapy use...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28152798/patient-uptake-and-satisfaction-with-advanced-genomic-technologies-offered-through-an-employee-benefit-program
#18
Kelly Z Knickelbein, Julie Goldstein, Sara Riordan, Paul Billings
: 72 Background: Access to advanced genomic technologies for the diagnosis and treatment of cancer is important. As part of an employee benefit program, we offered genomic technologies, such as somatic tumor and inherited germline genetic testing, as well as clinical trial information, medical second opinions, and genetic counseling, as appropriate, to enrollees with cancer. Genetic counselors served as cancer navigators through the process. The study aimed to assess uptake of the services offered and satisfaction with the program...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28152060/expression-quantitative-trait-loci-qtl-in-tumor-adjacent-normal-breast-tissue-and-breast-tumor-tissue
#19
Alejandro Quiroz-Zárate, Benjamin J Harshfield, Rong Hu, Nick Knoblauch, Andrew H Beck, Susan E Hankinson, Vincent Carey, Rulla M Tamimi, David J Hunter, John Quackenbush, Aditi Hazra
We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses' Health Study (NHS) diagnosed from 1990-2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array...
2017: PloS One
https://www.readbyqxmd.com/read/28139749/germline-large-genomic-alterations-on-7q-in-patients-with-multiple-primary-cancers
#20
R A R Villacis, T R Basso, L M Canto, A F Nóbrega, M I Achatz, S R Rogatto
Patients with multiple primary cancers (MPCs) are suspected to have a hereditary cancer syndrome. However, only a small proportion may be explained by mutations in high-penetrance genes. We investigate two unrelated MPC patients that met Hereditary Breast and Ovaria Cancer criteria, both presenting triple negative breast tumors and no mutations in BRCA1, BRCA2 and TP53 genes. Germline rearrangements on chromosome 7q, involving over 40 Mb of the same region, were found in both patients: one with mosaic loss (80% of cells) and the other with cnLOH (copy-neutral loss of heterozygosity) secondary to maternal allele duplication...
January 31, 2017: Scientific Reports
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