Dataset Information

Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements.

ABSTRACT: NIST standard reference material (SRM) 2373 was developed to improve the measurements of the HER2 gene amplification in DNA samples. SRM 2373 consists of genomic DNA extracted from five breast cancer cell lines with different amounts of amplification of the HER2 gene. The five components are derived from the human cell lines SK-BR-3, MDA-MB-231, MDA-MB-361, MDA-MB-453, and BT-474. The certified values are the ratios of the HER2 gene copy numbers to the copy numbers of selected reference genes DCK, EIF5B, RPS27A, and PMM1. The ratios were measured using quantitative polymerase chain reaction and digital PCR, methods that gave similar ratios. The five components of SRM 2373 have certified HER2 amplification ratios that range from 1.3 to 17.7. The stability and homogeneity of the reference materials were shown by repeated measurements over a period of several years. SRM 2373 is a well characterized genomic DNA reference material that can be used to improve the confidence of the measurements of HER2 gene copy number.

SUBMITTER: He HJ

PROVIDER: S-EPMC4906140 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements.

He Hua-Jun HJ Almeida Jamie L JL Lund Steve P SP Steffen Carolyn R CR Choquette Steve S Cole Kenneth D KD

Biomolecular detection and quantification 20160309

NIST standard reference material (SRM) 2373 was developed to improve the measurements of the HER2 gene amplification in DNA samples. SRM 2373 consists of genomic DNA extracted from five breast cancer cell lines with different amounts of amplification of the HER2 gene. The five components are derived from the human cell lines SK-BR-3, MDA-MB-231, MDA-MB-361, MDA-MB-453, and BT-474. The certified values are the ratios of the HER2 gene copy numbers to the copy numbers of selected reference genes DC ...[more]

PMID: 27335805

Similar Datasets

Project description:To gain confidence in results of omic-data acquisitions, methods must be benchmarked using validated quality control materials. We report data combining both untargeted and targeted metabolomics assays for the analysis of four new human fecal reference materials developed by the U.S. National Institute of Standards and Technologies (NIST) for metagenomics and metabolomics measurements. These reference grade test materials (RGTM) were established by NIST based on two different diets and two different samples treatments, as follows: firstly, homogenized fecal matter from subjects eating vegan diets, stored and submitted in either lyophilized (RGTM 10162) or aqueous form (RGTM 10171); secondly, homogenized fecal matter from subjects eating omnivore diets, stored and submitted in either lyophilized (RGTM 10172) or aqueous form (RGTM 10173). We used four untargeted metabolomics assays (lipidomics, primary metabolites, biogenic amines and polyphenols) and one targeted assay on bile acids. A total of 3563 compounds were annotated by mass spectrometry, including 353 compounds that were annotated in more than one assay. Almost half of all compounds were annotated using hydrophilic interaction chromatography/accurate mass spectrometry, followed by the lipidomics and the polyphenol assays. In total, 910 metabolites were found in at least 4-fold different levels in fecal matter from vegans versus omnivores, specifically for peptides, amino acids and lipids. In comparison, only 251 compounds showed 4-fold differences between lyophilized and aqueous fecal samples, including DG O-34:0 and methionine sulfoxide. A range of diet-specific metabolites were identified to be significantly different between vegans and omnivores, exemplified by citrinin and C17:0-acylcarnitine for omnivores, and curcumin and lenticin for vegans. Bioactive molecules like acyl alpha-hydroxy-fatty acids (AAHFA) were differentially regulated in vegan versus omnivore fecal materials, highlighting the importance of diet-specific reference materials for dietary biomarker studies.

Dataset Information

Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements.

Publications

Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets