دورية أكاديمية
أعرض في EDS

Using microarray-based subtyping methods for breast cancer in the era of high-throughput RNA sequencing.

التفاصيل البيبلوغرافية
العنوان: Using microarray-based subtyping methods for breast cancer in the era of high-throughput RNA sequencing.
المؤلفون: Pedersen CB; Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Kongens Lyngby, Denmark.; Center for Genomic Medicine, Rigshospitalet - Copenhagen University Hospital, Denmark., Nielsen FC; Center for Genomic Medicine, Rigshospitalet - Copenhagen University Hospital, Denmark., Rossing M; Center for Genomic Medicine, Rigshospitalet - Copenhagen University Hospital, Denmark., Olsen LR; Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Kongens Lyngby, Denmark.; Center for Genomic Medicine, Rigshospitalet - Copenhagen University Hospital, Denmark.
المصدر: Molecular oncology [Mol Oncol] 2018 Dec; Vol. 12 (12), pp. 2136-2146. Date of Electronic Publication: 2018 Oct 29.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: John Wiley & Sons, Inc Country of Publication: United States NLM ID: 101308230 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-0261 (Electronic) Linking ISSN: 15747891 NLM ISO Abbreviation: Mol Oncol
أسماء مطبوعة: Publication: 2017- : Hoboken, New Jersey : John Wiley & Sons, Inc.
Original Publication: Amsterdam : Elsevier
مواضيع طبية MeSH: Transcriptome*, Breast Neoplasms/*genetics , Gene Expression Profiling/*methods , Oligonucleotide Array Sequence Analysis/*methods, Female ; Gene Expression Regulation, Neoplastic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, RNA/methods
مستخلص: Breast cancer is a highly heterogeneous disease that can be classified into multiple subtypes based on the tumor transcriptome. Most of the subtyping schemes used in clinics today are derived from analyses of microarray data from thousands of different tumors together with clinical data for the patients from which the tumors were isolated. However, RNA sequencing (RNA-Seq) is gradually replacing microarrays as the preferred transcriptomics platform, and although transcript abundances measured by the two different technologies are largely compatible, subtyping methods developed for probe-based microarray data are incompatible with RNA-Seq as input data. Here, we present an RNA-Seq data processing pipeline, which relies on the mapping of sequencing reads to the probe set target sequences instead of the human reference genome, thereby enabling probe-based subtyping of breast cancer tumor tissue using sequencing-based transcriptomics. By analyzing 66 breast cancer tumors for which gene expression was measured using both microarrays and RNA-Seq, we show that RNA-Seq data can be directly compared to microarray data using our pipeline. Additionally, we demonstrate that the established subtyping method CITBCMST (Guedj et al., ), which relies on a 375 probe set-signature to classify samples into the six subtypes basL, lumA, lumB, lumC, mApo, and normL, can be applied without further modifications. This pipeline enables a seamless transition to sequencing-based transcriptomics for future clinical purposes.
(© 2018 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.)
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فهرسة مساهمة: Keywords: RNA sequencing; breast cancer; gene expression; molecular subtyping
سلسلة جزيئية: GENBANK GSE43358
تواريخ الأحداث: Date Created: 20181006 Date Completed: 20190823 Latest Revision: 20190823
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC6275246
DOI: 10.1002/1878-0261.12389
PMID: 30289602
قاعدة البيانات: MEDLINE
الوصف
تدمد:1878-0261
DOI:10.1002/1878-0261.12389