Gene Globe

Frequently asked questions

Discover key insights into genes and variants critical for breast cancer research and how they can be detected using digital PCR

dPCR LNA Mutation Assays offer significant advantages to cancer researchers working on precise and sensitive mutation detection. These assays are specifically designed for use with the QIAcuity Digital PCR System and are enhanced with Locked Nucleic Acid (LNA) technology. This enhancement greatly improves the specificity and sensitivity of mutation detection, making it possible to identify DNA sequence mutations at very low abundance, with a sensitivity as fine as 0.1% in a single nanoplate well.

The key benefits of dPCR LNA Mutation Assays for cancer researchers include:

High precision and sensitivity: The use of duplex, hydrolysis probe-based assays allows for highly precise detection of mutations. The presence of both mutant and wild-type probes in the same reaction ensures that researchers can detect and quantify minor genetic variations with great accuracy, crucial for studies in heterogeneous cancer samples where only a few cells may carry the mutation.
Enhanced specificity: The integration of LNA into the probes increases the binding affinity and specificity towards the target sequences, minimizing the risk of non-specific bindings and improving the overall reliability of the assays.
Multiplexing capability: Each assay is capable of detecting mutations using two different fluorescent dye combinations, allowing for the simultaneous analysis of mutant and wild-type alleles within the same reaction. This multiplexing ability is particularly useful in applications requiring the analysis of multiple targets, such as assessing co-occurring mutations in cancer.
Flexibility in sample analysis: By dividing the reaction across multiple wells, even greater sensitivity can be achieved, facilitating the detection of extremely rare mutations. This is especially valuable in cancer research, where detecting low-frequency mutations can inform prognosis and treatment strategies.
Streamlined workflow: Supplied in a single-tube format with ready-to-use primer pairs and probes, these assays simplify the experimental setup, enabling efficient and straightforward integration into existing research workflows.

BRCA1 (Breast Cancer Gene 1) is a tumor suppressor whose mutations are associated with a significant increase in the risk of breast and ovarian cancers. These mutations hinder the gene's role in DNA repair, leading to genomic instability and cancer. BRCA1 mutations are particularly impactful in hereditary breast cancer syndromes, significantly raising the risk of early-onset breast cancer. Targeting these genetic vulnerabilities is crucial in the development of therapeutic strategies and management of cancer risk.

BRCA1 c.185_186delAG: The 185delAG mutation results from the deletion of two nucleotides, adenine (A) and guanine (G), at position 185 in the BRCA1 gene. This deletion occurs early in the gene's coding sequence and leads to a frameshift, producing a significantly truncated BRCA1 protein. The truncated protein lacks critical regions essential for its role in DNA repair and tumor suppression. The absence of these functional domains prevents BRCA1 from participating in the repair of double strand breaks via homologous recombination, leading to genomic instability and significantly increasing the risk of breast cancer.
BRCA1 c.5382_5383insC: The 5382insC mutation results from the insertion of a cytosine (C) at position 5382 in the BRCA1 gene. This insertion causes a frameshift mutation that alters the reading frame, resulting in a premature stop codon. The truncated BRCA1 protein produced is unable to effectively engage in DNA repair processes, diminishing the cell's ability to maintain genomic stability and promoting tumorigenesis.

BRCA2 (Breast Cancer Gene 2) functions similarly to BRCA1, aiding in DNA repair and maintaining genomic stability. Mutations in BRCA2 disrupt these critical processes, significantly increasing the risk of developing breast, ovarian and other cancers. BRCA2 mutations are inherited and play a crucial role in hereditary breast cancer syndromes, profoundly impacting cancer risk. Genetic testing for individuals at risk is very important, as these mutations offer insights into personalized prevention and treatment options.

BRCA2 c.6174delT: This mutation involves the deletion of thymine (T) at position 6174, producing a truncated BRCA2 protein that lacks a portion of its DNA binding domain, essential for repairing DNA double-strand breaks. The mutant protein's impaired DNA repair capability leads to genetic mutation accumulation and elevated breast cancer risk.
BRCA2 c.5946delT: Similar to 6174delT, this mutation's deletion of thymine (T) at position 5946 results in a truncated protein. This loss compromises the critical BRCA2 functionality in DNA repair, undermining genomic integrity and contributing to cancer development.

PALB2 (Partner and Localizer of BRCA2) interacts with BRCA2 in DNA repair and, when mutated, can elevate breast cancer risk. While PALB2 mutations confer a lower risk compared to BRCA1/2 mutations, their discovery is crucial for understanding individual risk profiles and guiding cancer prevention strategies. PALB2 is an emerging marker for targeted therapy research, emphasizing the need for comprehensive genetic screening in affected families.

PALB2 c.509_510delGA: This frameshift mutation involves the deletion of two nucleotides, guanine (G) and adenine (A), which alters the reading frame of the PALB2 gene. This change results in the production of a truncated protein that is unable to fulfill its role in DNA repair alongside BRCA2. The loss of function in this crucial repair pathway increases the susceptibility to breast cancer by allowing DNA damage to accumulate, potentially leading to cancerous changes within cells.
PALB2 c.1592delT: This mutation represents a deletion of a single thymine (T) nucleotide at position 1592. It is another frameshift mutation that disrupts the normal sequence of the PALB2 gene, resulting in an abnormal protein product. The consequent deficiency in the gene's repair function compromises genomic integrity and significantly raises the risk of developing breast cancer, highlighting the critical role of PALB2 in maintaining cellular health and preventing tumorigenesis.
PALB2 c.3113+5G>A: This splice site mutation occurs in the intronic region near exon 13 of the PALB2 gene, specifically changing a guanine (G) to adenine (A) at the +5 position of the intron following exon 12. By altering the gene's natural splicing process, this mutation can lead to an incorrectly spliced PALB2 mRNA, potentially resulting in a dysfunctional protein that is incapable of effectively participating in the homologous recombination repair of DNA double-strand breaks. The compromised DNA repair mechanism significantly contributes to the elevated risk of breast cancer associated with this mutation, underscoring the importance of precise genomic maintenance for cancer prevention.

PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) is a critical component of the PI3K/AKT signaling pathway, and mutations in this gene are prevalent in breast cancer. These mutations activate the PI3K/AKT signaling pathway, promoting tumor growth and survival. The occurrence of PIK3CA mutations underscores the potential for targeted therapy, with inhibitors of PIK3CA showing considerable promise in treating cancers that harbor such genetic alterations. The identification of PIK3CA mutations is essential for customizing treatment to the individual profiles of patients, thereby improving outcomes in hormone receptor-positive, HER2-negative breast cancers.

PIK3CA c.1633G>A / E545K: The E545K mutation results from a single nucleotide change, leading to the substitution of glutamic acid with lysine at codon 545 in the PIK3CA gene. This point mutation lies within exon 9 and enhances the lipid kinase activity of the PI3K enzyme abnormally. The increased activity promotes cell growth and survival pathways, such as mTOR signaling, that are typically tightly regulated, contributing to breast cancer progression.
PIK3CA c.1624G>A / E542K: The E542K mutation results from a single nucleotide change, leading to the substitution of glutamic acid with lysine at codon 542 in the PIK3CA gene. This point mutation lies within exon 9 and alters the enzyme's structure, increasing its activity. The enhanced activity contributes to deregulated growth signaling pathways, such as mTOR signaling, that are characteristic of cancer cells.
PIK3CA c.3140A>G / H1047R: The H1047R mutation results from a single nucleotide change, leading to the substitution of histidine with arginine at codon 1047 in the PIK3CA gene. This point mutation lies within exon 20 in the kinase domain and leads to a gain of function, with increased PI3K enzymatic activity. This mutation drives the constitutive activation of downstream signaling pathways, such as AKT, promoting cell proliferation and survival in the absence of growth signals and facilitating tumorigenesis.

BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) works closely with BRCA1 in DNA repair processes, particularly in the repair of double-strand breaks. Mutations in BRIP1 can compromise the effectiveness of DNA repair, leading to increased genomic instability and a higher risk of developing breast and ovarian cancer. Like mutations in BRCA1, BRIP1 mutations can elevate the risk of early-onset breast cancer, although the overall risk increase is less pronounced than that associated with BRCA1 or BRCA2 mutations. Identifying mutations in BRIP1 is important for understanding individual risk profiles and can influence decisions regarding cancer surveillance and preventive strategies.

ATM (Ataxia-Telangiectasia Mutated) is a key player in the cellular response to DNA damage. It phosphorylates several downstream proteins, including p53, CHK2 and BRCA1, activating the DNA repair machinery. Mutations in the ATM gene diminish the cell's ability to repair DNA damage, leading to an accumulation of mutations and an increased risk of breast cancer. The role of ATM mutations in breast cancer is complex, with some mutations having a more profound impact on cancer risk than others. Individuals with ATM mutations may benefit from increased surveillance and, in some cases, preventive measures to mitigate their heightened risk of breast cancer.

CHEK2 (Checkpoint Kinase 2) acts as a tumor suppressor that interacts with several other proteins, including BRCA1 and p53, to halt cell division in response to DNA damage. Mutations in CHEK2 can impair this checkpoint function, allowing cells with DNA damage to continue dividing, thereby increasing the risk of cancer development. CHEK2 mutations are associated with a moderately increased risk of breast cancer. The detection of CHEK2 mutations can offer valuable insights into an individual’s cancer risk, guiding recommendations for cancer screening and preventive strategies.

PTEN (Phosphatase and Tensin Homolog) is a tumor suppressor gene that negatively regulates the PI3K/AKT signaling pathway, crucial for controlling cell growth and survival. Mutations or deletions in PTEN lead to unregulated cell proliferation and survival, contributing to the development of breast cancer and other types of cancer. PTEN mutations are often seen in patients with Cowden syndrome, a disorder that significantly increases the risk of breast, thyroid and endometrial cancers. Understanding PTEN status in patients can be critical for assessing cancer risk and determining appropriate surveillance and treatment options.

TP53 (tumor protein p53) is a pivotal tumor suppressor gene involved in DNA repair, apoptosis and cell cycle control. Mutations in TP53 are one of the most common genetic alterations in human cancers, including breast cancer. These mutations can lead to the production of a dysfunctional p53 protein, incapable of performing its normal protective roles against cancer development. The loss of functional p53 protein allows cells with damaged DNA to proliferate, significantly increasing the risk of breast cancer and other types of cancer. TP53 mutations are particularly associated with more aggressive and treatment-resistant forms of breast cancer, making the identification of these mutations important for prognosis and treatment planning.

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