Identification of novel endogenous controls for accurate qPCR normalization in 2D v/s 3D triple negative breast cancer cell line model

Project Details


The primary objective of the present project was to identify novel endogenous controls that could be used universally in all culturing conditions for accurate normalization of qPCR results in triple negative MDA-MB-436 breast cancer cell line. After identification, the selected controls were tested and validated under a myriad of culturing conditions like confluence, 3d organoid models, etc. The project started with the transcriptomic analysis of TCGA (The Cancer Genome Atlas) data which is the most referred and largest public database for gene expression in various types of cancers. 10 candidate reference genes that are expressed uniformly and showcased least variation were selected from the database. These selected genes (novel genes) were studied with commonly used controls (15 traditional genes) thereby creating a pool of about 25 candidate genes. The MDA-MB-436 cells were cultured in multiple lineages and over multiple passages thereby creating a big pool of biological replicates for analysis and investigation. We identified and validated novel controls which are more stable than the traditionally used genes, thereby allowing for accurate normalization of qPCR results. Such studies are of prime importance to rationalize the effects of experimental errors, technical variations etc. amongst laboratories. The project was implemented at the Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradins University (RSU). The results of the project were presented as “Oral Presentation” in the RSU International Student Conference 2022 that took place in March 2022.

Layman's description

Student Research and Innovation Grant (SRIG)
Effective start/end date9/04/218/04/22

UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This project contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being


  • breast cancer
  • Breast cancer cell lines
  • MDA-MB-236
  • triple negative
  • reference genes
  • normalization
  • RT-qPCR
  • gene expression

Field of Science

  • 1.6 Biological sciences

Smart Specialization Area

  • Biomedicine, medical technologies and biotechnology


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