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Breast cancer genome analysis in time and space: biomarker development strategy

Published on Jun 1, 2018in Biomarkers in Medicine2.268
· DOI :10.2217/bmm-2018-0109
Ioannis D Kyrochristos3
Estimated H-index: 3
,
Demosthenes E Ziogas5
Estimated H-index: 5
+ 1 AuthorsDimitrios H Roukos4
Estimated H-index: 4
(Academy of Athens)
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Abstract
  • References (22)
  • Citations (1)
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References22
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#1Balázs Győrffy (Semmelweis University)H-Index: 25
#2Lőrinc Sándor Pongor (Semmelweis University)H-Index: 6
Last. Libero SantarpiaH-Index: 28
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Sequence variations in coding and non-coding regions of the genome can affect gene expression and signalling pathways, which in turn may influence disease outcome. In this study, we integrated somatic mutations, gene expression and clinical data from 930 breast cancer patients included in the TCGA database. Genes associated with single mutations in molecular breast cancer subtypes were identified by the Mann-Whitney U-test and their prognostic value was evaluated by Kaplan-Meier and Cox regressi...
8 CitationsSource
#1Siew-Kee Low (JFCR: Japanese Foundation for Cancer Research)H-Index: 1
#2Hitoshi Zembutsu (JFCR: Japanese Foundation for Cancer Research)H-Index: 32
Last. Yoshio Nakamura (U of C: University of Chicago)H-Index: 164
view all 3 authors...
21 CitationsSource
#1Joshua D. Cohen (Johns Hopkins University)H-Index: 7
#2Ammar A. Javed (Johns Hopkins University)H-Index: 12
Last. Anne Marie Lennon (Johns Hopkins University)H-Index: 29
view all 40 authors...
The earlier diagnosis of cancer is one of the keys to reducing cancer deaths in the future. Here we describe our efforts to develop a noninvasive blood test for the detection of pancreatic ductal adenocarcinoma. We combined blood tests for KRAS gene mutations with carefully thresholded protein biomarkers to determine whether the combination of these markers was superior to any single marker. The cohort tested included 221 patients with resectable pancreatic ductal adenocarcinomas and 182 control...
102 CitationsSource
#1A. Nicolini (UniPi: University of Pisa)H-Index: 32
#2Paola Ferrari (UniPi: University of Pisa)H-Index: 16
Last. Michael J. Duffy (UCD: University College Dublin)H-Index: 5
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Abstract Following a diagnosis of breast cancer, the most immediate challenges in patient management are the determination of prognosis and identification of the most appropriate adjuvant systemic therapy. Determining prognosis can best be addressed with a combination of traditional clinicopathological prognostic factors, biomarkers such as HER2/ neu and specific multigene genes tests. Amongst the best validated prognostic multigene tests are uPA/PAI1, Oncotype DX and MammaPrint. Oncotype DX and...
46 CitationsSource
The unmet clinical needs of high relapse and cancer-related death rates are reflected by the poor understanding of the genome-wide mutational landscape and molecular mechanisms orchestrating therapeutic resistance. Emerging potential solutions to this challenge include the exploration of cancer genome dynamic evolution in time and space. Breakthrough next-generation sequencing (NGS) applications including multiregional NGS for intratumor heterogeneity identification, repeated cell-free DNA/circu...
18 CitationsSource
#1Esther Rheinbay (Broad Institute)H-Index: 15
#2Prasanna Parasuraman (Harvard University)H-Index: 3
Last. Gad Getz (Broad Institute)H-Index: 137
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High-depth sequencing of targeted regions in primary breast cancer identifies mutated promoter elements with recurrent mutations at specific and/or nearby bases, suggesting selection of certain non-coding events.
100 CitationsSource
#1Celine Lefebvre (French Institute of Health and Medical Research)H-Index: 22
#2Thomas Bachelot (French Institute of Health and Medical Research)H-Index: 30
Last. Fabrice Andre (University of Paris-Sud)H-Index: 78
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Background Major advances have been achieved in the characterization of early breast cancer (eBC) genomic profiles. Metastatic breast cancer (mBC) is associated with poor outcomes, yet limited information is available on the genomic profile of this disease. This study aims to decipher mutational profiles of mBC using next-generation sequencing. Methods and Findings Whole-exome sequencing was performed on 216 tumor–blood pairs from mBC patients who underwent a biopsy in the context of the SAFIR01...
87 CitationsSource
#1Trung Nghia VuH-Index: 8
#2Setia PramanaH-Index: 7
Last. Yudi PawitanH-Index: 46
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// Trung Nghia Vu 1, * , Setia Pramana 1, * , Stefano Calza 1, 2, * , Chen Suo 1 , Donghwan Lee 1, 3 , Yudi Pawitan 1 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE 17177 Stockholm, Sweden 2 Department of Molecular and Translational Medicine, University of Brescia, 25125 Brescia, Italy 3 Department of Statistics, Ewha Womans University, Seodaemun-gu, Seoul 120-750, South Korea * These authors have contributed equally to this work Correspondence to: Yudi Pawitan...
10 CitationsSource
#1Ruli GaoH-Index: 11
#2Alexander Davis (University of Texas Health Science Center at Houston)H-Index: 4
Last. Nicholas NavinH-Index: 27
view all 13 authors...
Nicholas Navin and colleagues use highly multiplexed single-nucleus sequencing to investigate DNA copy number evolution in patients with triple-negative breast cancer. Their data suggest that most copy number alterations are acquired at the earliest stages of tumor evolution in short punctuated bursts, followed by stable clonal expansions that form the tumor mass.
153 CitationsSource
#1Charles Swanton (Francis Crick Institute)H-Index: 66
#2Jean-Charles Soria (French Institute of Health and Medical Research)H-Index: 79
Last. Fabrice Andre (French Institute of Health and Medical Research)H-Index: 78
view all 19 authors...
Recent advances in biotechnologies have led to the development of multiplex genomic and proteomic analyses for clinical use. Nevertheless, guidelines are currently lacking to determine which molecular assays should be implemented in metastatic cancers. The first MAP conference was dedicated to exploring the use of genomics to better select therapies in the treatment of metastatic cancers. Sixteen consensus items were covered. There was a consensus that new technologies like next-generation seque...
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#1Bikesh Kumar Singh (NITRR: National Institute of Technology, Raipur)H-Index: 9
Abstract Early detection of breast cancer plays crucial role in planning and result of associated treatment. The purpose of this article is threefold: (i) to investigate whether or not clinical features obtained using routine blood analysis combined with anthropometric measurements can be utilized for envisaging breast cancer using predictive machine learning techniques; (ii) to explore the role of various machine learning components such as feature selection, data division protocols and classif...
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