№ files_lp_4_process_3_073638
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Comprehensive methods for molecular profiling of breast tumors and survival modeling integrating gene expression, proteomics, and metabolomics datasets.
Year:
2014-2018
Research focus:
Breast cancer molecular profiling and survival analysis
Document type:
Supplementary methods
Institution:
National Cancer Institute, Center for Cancer Research; Affymetrix; Illumina; Qiagen
Techniques:
Gene expression profiling, RNA sequencing, mass spectrometry-based proteomics, LASSO Cox regression
Sample type:
Human breast tumor tissues and treated cell lines
Number of samples:
61 tumors in discovery set; additional cell line experiments
Data analysis software:
R packages (Oligo, limma, DESeq2, survival, glmnet, glmpath, survcomp), Picard, Trimmomatic, TopHat, HTSeq, Proteome Discoverer, SEQUEST HT
Genes analyzed:
28,869 genes
Proteins identified:
~4,000 with ≥2 peptides and ≥15% tissue representation
Metabolites analyzed:
398 metabolites
Treatment conditions:
Deoxycholate 20 µM and 50 µM in cell lines
Statistical methods:
Wald statistics, Benjamini-Hochberg adjustment, LASSO feature selection, Kaplan-Meier survival analysis, concordance index (C-index)
Clinical variables:
Age, race/ethnicity, disease stage and grade, node status, menopausal status, neoadjuvant/hormone/chemotherapy
Price: 8 / 10 USD
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Year:
2023
Region / City:
United States
Subject:
Proteomics, Sample Preparation
Document Type:
Standard Operating Procedure (SOP)
Institution:
Proteomics and Metabolomics Core
Author:
David Kakhniashvili, Ph.D.
Target Audience:
Researchers in proteomics, molecular biology, bioinformatics
Effective Period:
Not specified
Approval Date:
Not specified
Date of Changes:
Not specified
Year:
2022
Region / City:
Duluth, MN
Subject:
Genomics, Proteomics, Actinobacteriophages
Document Type:
Abstract
Institution:
College of St. Scholastica
Author:
Ella K Achterkirch, Julia L Carlson, Jonah C Giermann, Ellie J Peddle, Harrison S Reinke, Rachel A Rhein, Houa Thao, Daniel E Westholm
Target Audience:
Researchers in genomics and proteomics
Period of Validity:
N/A
Approval Date:
N/A
Date of Modifications:
N/A
Context:
This is an academic abstract detailing the comparative genomics and proteomics of two actinobacteriophages, LittleMunchkin and Venti, focusing on their genome sequences, potential genes, and lysogeny analysis.
Facility Director:
Anna Schmoker, Ph.D.
Facility Location:
Rubin 7, Dartmouth Hitchcock Medical Center
Contact email:
[email protected]
Contact phone:
(603) 646-5573
Year:
2024
Region / City:
Dartmouth, NH
Field:
Proteomics, Mass Spectrometry
Document Type:
Facility Description
Institution:
Dartmouth College
Target Audience:
Researchers at Dartmouth College
Action Period:
From November 2024
Approval Date:
November 2024
Changes Date:
Not specified
Year:
2026
Region / City:
New York
Topic:
Mass spectrometry, proteomics
Document type:
Research Resource
Institution:
Albert Einstein College of Medicine
Author:
Not specified
Target audience:
Researchers, scientists in proteomics
Period of validity:
Ongoing
Approval date:
Not specified
Date of changes:
Not specified
Year:
2023
Region / City:
United States
Subject:
Proteomics, Sample Preparation
Document Type:
Standard Operating Procedure (SOP)
Institution:
Proteomics and Metabolomics Core
Author:
David Kakhniashvili, Ph.D.
Target Audience:
Researchers in proteomics, molecular biology, bioinformatics
Effective Period:
Not specified
Approval Date:
Not specified
Date of Changes:
Not specified
Year:
2025
Region / City:
North West NHS GMS region
Topic:
ctDNA testing for NSCLC and breast cancer
Document Type:
Notification
Organization:
NHS England
Author:
Genomics Unit
Target Audience:
NHS Trusts
Period of Action:
2025/26 financial year
Approval Date:
7 November 2025
Date of Changes:
N/A
Context:
Notification regarding the continuation and expansion of ctDNA testing for lung and breast cancer in the North West NHS region for the 2025/26 financial year.
Year:
2024
Region / City:
International
Subject:
Nuclear medicine, breast cancer, estrogen receptor imaging
Document type:
Procedure standard / Practice guideline
Organization:
SNMMI, EANM
Authors:
David Mankoff, Sona Balogova, Lisa Dunnwald, Farrokh Dehdashti, Erik DeVries, Laura Evangelista, Michel Van Krutchen, Sofia Carriho Vaz, Amy Fowler, Hannah Linden, Gary Ulaner
Target audience:
Nuclear medicine practitioners, oncologists
Scope period:
Current clinical practice
Approval date:
2024
Revision cycle:
Every 5 years or sooner if indicated
Description:
Clinical guideline detailing standardized procedures for [18F]FES PET imaging of estrogen receptor expression in breast cancer patients, including methodology, interpretation, and quality assurance for diagnostic nuclear medicine.
Version:
4.4.0.0
Protocol Posting Date:
June 2021
CAP Laboratory Accreditation Program Protocol Required Use Date:
March 2022
Authors:
Patrick L. Fitzgibbons, MD, FCAP; James L. Connolly, MD
Note:
Accreditation Requirements
Year:
2021
Region / City:
Global
Theme:
Oncology, Breast Cancer
Document Type:
Protocol
Organization / Institution:
CAP (College of American Pathologists)
Author:
Patrick L. Fitzgibbons, MD, FCAP; James L. Connolly, MD
Target Audience:
Medical professionals, pathologists
Period of Validity:
From March 2022
Date of Approval:
June 2021
Date of Changes:
June 2021
Year:
2024
Region / City:
Not specified
Subject:
Pathology, Oncology
Document Type:
Protocol
Organization / Institution:
CAP (College of American Pathologists)
Author:
Uma G. Krishnamurti, MD, PhD; Kimberly H. Allison, MD; Patrick L. Fitzgibbons, MD, FCAP; James L. Connolly, MD
Target Audience:
Pathologists, Medical Institutions
Period of Validity:
March 2025
Approval Date:
Not specified
Date of Last Change:
June 2024
Version:
1.2.0.0
Protocol posting date:
March 2023
Document type:
Clinical pathology protocol
Medical field:
Breast pathology, oncology
Procedures covered:
Needle biopsy, fine needle aspiration, other biopsy procedures
Tumor types included:
Invasive breast carcinoma of any type, with or without ductal carcinoma in situ
Tumor types excluded:
Ductal carcinoma in situ without invasion, Paget disease without invasion, phyllodes tumor, lymphoma, sarcoma
Authors:
Patrick L. Fitzgibbons, MD, FCAP; James L. Connolly, MD
Organization:
College of American Pathologists
Accreditation status:
Recommended for clinical care, not required for accreditation
Intended use:
Reporting of biopsy specimens
Updates:
Optional reporting of largest invasive focus; revised lymphatic and/or vascular invasion terminology
Year:
2017
Region / City:
Georgia
Subject:
Cancer prevention, screening, and healthcare services
Document Type:
Evaluation Plan
Organization:
Georgia Department of Public Health
Author:
Janet Y Shin, Kia Powell-Threets
Target Audience:
Health professionals, stakeholders involved in cancer prevention and treatment
Period of validity:
6/30/2017 – 6/29/2022
Approval Date:
1/31/2018
Amendment Date:
5/15/2018
Version:
GMMMG version 1.1
Replaces version:
GMMMG version 1.0
Clinical content last reviewed:
July 2024
Next review date:
July 2026
Date published:
27th February 2025
CRG approval:
12th November 2024
GMMMG approval:
12th December 2024
GM CEGC approval:
17th December 2024
Note:
Background
Year:
2019
Region / city:
West Middlesex, Chelsea & Westminster Hospital
Topic:
Breast Cancer Follow-Up Care
Document Type:
Standard Operating Policy
Organization:
Chelsea & Westminster Hospital NHS Trust
Author:
Dr. Pippa Riddle, Dr. Mark Bower, Mr. Musa Barkeji
Target Audience:
Medical and clinical staff involved in breast cancer follow-up care
Validity Period:
2019 - Ongoing
Review Date:
August 2020
Approval Date:
Not specified
Changes Date:
Not specified
Year:
2015
Region / city:
United Kingdom
Topic:
Menopause, breast cancer, hot flushes, night sweats, management, patient care
Document Type:
Research study
Organization / institution:
University of Southampton, University of Warwick, Mount Vernon Cancer Centre, Breast Cancer Care, Kings College London, Independent Cancer Patient Voice, National Cancer Research Institute (NCRI)
Author:
Fenlon D, Morgan A, Khambaita P, Mistry P, Dunn J, Ah-See M.L., Pennery E, Hunter MS
Target audience:
Health professionals, breast cancer patients
Period of validity:
2015 onwards
Date of approval:
2015
Date of changes:
N/A
Context:
This research study presents findings on the management of hot flushes and night sweats among women with breast cancer in the UK, highlighting current practices and the need for improved treatment guidelines.
Year:
2013
Region / City:
N/A
Topic:
Breast MRI Protocol
Document Type:
Protocol
Institution / Organization:
ACRIN
Author:
Nola Hylton, PhD
Target Audience:
Medical professionals involved in breast MRI
Period of Effectiveness:
N/A
Approval Date:
N/A
Modification Date:
N/A
Year:
2024
Region / City:
International
Subject:
Breast Cancer, Genetic Testing
Document Type:
Expert Consensus Report
Organization / Institution:
ESMO Precision Oncology Working Group
Author:
ESMO Precision Oncology Working Group
Target Audience:
Clinicians, Medical Oncologists, Geneticists
Period of validity:
2024
Approval Date:
Not specified
Date of Changes:
Not specified
Year:
2013
Region / city:
Not specified
Topic:
Breast cancer, radiotherapy, surgical procedures
Document type:
Audit report
Organization / institution:
Not specified
Author:
Dr John McGrane
Target audience:
Radiotherapy professionals, surgical teams, oncology departments
Period of validity:
Not specified
Approval date:
28 April 2013
Date of last review:
16 April 2018
Book Name:
Disease and Health: Research Developments
Manuscript Number:
Ms_BPR_4732
Title of the Manuscript:
Racial Disparity in Quadruple Negative Breast Cancer: Aggressive Biology and Potential Therapeutic Targeting and Prevention
Type of Article:
Book Chapter
Source Article:
Cancers, Volume 14 (Issue 18): 1–15, 2022
DOI:
10.3390/cancers14184484
Journal:
Cancers
Year:
2022
Reviewer:
Sadaf Shafi Gadoo
Reviewer Affiliation:
Government Medical College Srinagar
Country:
India
Subject Area:
Oncology; Breast Cancer Research; Racial Health Disparities
Disease Focus:
Quadruple-Negative Breast Cancer (QNBC)
Population Focus:
Black/African-American Women
Peer Review Outcome:
Scientifically correct; language suitable; references not sufficient or recent
Ethical Issues Reported:
None indicated
Year:
2017
Region / city:
Oxford, UK
Topic:
Cancer staging
Document type:
Classification guide
Organization / institution:
UICC
Author:
Brierley JD, Gospodarowicz MK, Wittekind C
Target audience:
Medical professionals, oncologists
Period of validity:
From 1 January 2018
Date of approval:
2017
Date of changes:
N/A
Year:
2020
Region / City:
Guntur
Theme:
Medical Research
Document Type:
Research Article
Institution:
International Journal of Clinical and Diagnostic Pathology
Author:
Dr. Hima Bindu Gurram, Dr. Yarlagadda Krishna Bharathi, Dr. V. Satyanarayana
Target Audience:
Medical professionals, Researchers
Period of validity:
2020
Approval Date:
3/13/2020
Modification Date:
N/A