Digital PCR assays for breast cancer gene variants

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Revolutionizing breast cancer research with precision dPCR assays

Breast cancer represents a major public health challenge, with extensive heterogeneity and numerous genetic variants influencing its development, progression and response to therapy. The complexity of breast cancer at the molecular level necessitates precise and sensitive tools for the identification of genetic mutations that can inform personalized treatment strategies.

Digital PCR (dPCR) technology emerges as a pivotal solution, offering unparalleled precision and sensitivity in detecting key genetic markers and driving forward breast cancer research and treatment approaches.

Find and order breast cancer related dPCR assays

Breast cancer's complexity is accentuated by its various subtypes and the genetic variations that drive them, including hormone receptor-positive, HER2-positive and triple-negative breast cancer, each presenting unique challenges and requiring specific treatment approaches. Critical gene variants like BRCA1, BRCA2, PALB2, PIK3CA and others play significant roles in the disease’s pathogenesis and influence treatment outcomes. Mutations in these genes help stratify breast cancer types and identify potential therapeutic targets.

Our collection of dPCR LNA Mutation Assays equips researchers to delve into these genetic intricacies. The precise detection and quantification of mutations in breast cancer relevant genes, enables the exploration of gene-specific dynamics and their implications for therapy and prognosis.

The table below includes COSMIC Variant IDs (COSV), as they provide a unique identifier for each distinct gene mutation and ensure precise reference to your variant of interest.

Gene

Mutation Type

Gene	Mutation Type	Mutation (CDS)	Mutation (AA)	COSMIC ID (COSV)	COSMIC ID (COSM)	Codon	dPCR Mutation Assay
EGFR	Substitution - Missense	c.2155G>A	p.G719S	COSV51767289	COSM6252	719	DMH0000055
EGFR	Substitution - Missense	c.2155G>T	p.G719C	COSV51766606	COSM6253	719	DMH0000280
EGFR	Substitution - Missense	c.2156G>C	p.G719A	COSV51769339	COSM6239	719	DMH0000057
EGFR	Substitution - Missense	c.2303G>T	p.S768I	COSV51768106	COSM6241	768	DMH0000308
EGFR	Substitution - Missense	c.2573T>G	p.L858R	COSV51765161	COSM6224	858	DMH0000386
EGFR	Substitution - Missense	c.2582T>A	p.L861Q	COSV51766344	COSM6213	861	DMH0000006
KRAS	Substitution - Missense	c.34G>A	p.G12S	COSV55497461	COSM517	12	DMH0000519
KRAS	Substitution - Missense	c.34G>C	p.G12R	COSV55497582	COSM518	12	DMH0000284
KRAS	Substitution - Missense	c.34G>T	p.G12C	COSV55497469	COSM516	12	DMH0000309
KRAS	Substitution - Missense	c.35G>A	p.G12D	COSV55497369	COSM521	12	DMH0000286
KRAS	Substitution - Missense	c.35G>C	p.G12A	COSV55497479	COSM522	12	DMH0001055
KRAS	Substitution - Missense	c.35G>T	p.G12V	COSV55497419	COSM520	12	DMH0000285
KRAS	Substitution - Missense	c.37G>A	p.G13S	COSV55509530	COSM528	13	DMH0000331
KRAS	Substitution - Missense	c.37G>C	p.G13R	COSV55502117	COSM529	13	DMH0000332
KRAS	Substitution - Missense	c.37G>T	p.G13C	COSV55497378	COSM527	13	DMH0000195
KRAS	Substitution - Missense	c.38G>A	p.G13D	COSV55497388	COSM532	13	DMH0000289
KRAS	Substitution - Missense	c.38G>C	p.G13A	COSV55497357	COSM533	13	DMH0000334
KRAS	Substitution - Missense	c.38G>T	p.G13V	COSV55522580	COSM534	13	DMH0000527
KRAS	Substitution - Missense	c.38_39delinsAT	p.G13D	COSV55508630	COSM531	13	DMH0000525
PIK3CA	Substitution - Missense	c.263G>A	p.R88Q	COSV55874568	COSM746	88	DMH0000204
PIK3CA	Substitution - Missense	c.333G>T	p.K111N	COSV55876538	COSM27505	111	DMH0000210
PIK3CA	Substitution - Missense	c.1035T>A	p.N345K	COSV55873276	COSM754	345	DMH0000031
PIK3CA	Substitution - Missense	c.1093G>A	p.E365K	COSV55881636	COSM86044	365	DMH0000216
PIK3CA	Substitution - Missense	c.1633G>A	p.E545K	COSV55873239	COSM763	545	DMH0000292
PIK3CA	Substitution - Missense	c.1634A>G	p.E545G	COSV55873220	COSM764	545	DMH0000033
PIK3CA	Substitution - Missense	c.1636C>A	p.Q546K	COSV55873527	COSM766	546	DMH0000037
PIK3CA	Substitution - Missense	c.1637A>G	p.Q546R	COSV55876869	COSM12459	546	DMH0000212
PIK3CA	Substitution - Missense	c.2176G>A	p.E726K	COSV55875460	COSM87306	726	DMH0000206
PIK3CA	Substitution - Missense	c.3129G>T	p.M1043I	COSV55878974	COSM773	1043	DMH0000034
PIK3CA	Substitution - Missense	c.3139C>T	p.H1047Y	COSV55876499	COSM774	1047	DMH0000209
PIK3CA	Substitution - Missense	c.3140A>G	p.H1047R	COSV55873195	COSM775	1047	DMH0000036
PIK3CA	Substitution - Missense	c.3140A>T	p.H1047L	COSV55873401	COSM776	1047	DMH0000062
PIK3CA	Substitution - Missense	c.3145G>C	p.G1049R	COSV55874453	COSM12597	1049	DMH0000050

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Discover the QIAcuity family of dPCR instruments

Explore the QIAcuity family of dPCR instruments, designed to meet the rigorous demands of biomarker research, translational research and clinical applications. With unmatched precision and operational efficiency, these versatile platforms can transform your scientific and diagnostic efforts.

Transform your research capabilities with QIAcuity digital PCR

QIAcuity is a fully automated digital PCR system that combines precision, efficiency and ease of use. Experience unparalleled accuracy and save resources with high-throughput multiplexing, allowing for the simultaneous detection of up to five genetic targets. A seamless transition from existing qPCR workflows ensures minimal disruption while significantly enhancing data quality and throughput.

Streamline your clinical PCR workflows with QIAcuityDx

QIAcuityDx is tailored for IVD applications. This fully automated system enhances diagnostic precision and operational efficiency by reducing hands-on time and ensuring accurate detection and quantification of important genetic variations. Easily develop your own assay menu* by using QIAcuityDx utility mode and IVD medical device consumables, reagents and software.

*FDA ‘Medical Devices; Laboratory Developed Tests’ final rule, May 6, 2024 and European Union regulation requirements on ‘In-House Assays’ (Regulation (EU) 2017/746 -IVDR- Art. 5(5))

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.

Disclaimers

dPCR LNA Mutation Assays are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

The QIAcuity is intended for molecular biology applications. This product is not intended for the diagnosis, prevention or treatment of a disease. Therefore, the performance characteristics of the product for clinical use (i.e., diagnostic, prognostic, therapeutic or blood banking) is unknown.

The QIAcuityDx dPCR System is intended for in vitro diagnostic use, using automated multiplex quantification dPCR technology, for the purpose of providing diagnostic information concerning pathological states.

QIAcuity and QIAcuityDx dPCR instruments are sold under license from Bio-Rad Laboratories, Inc. and exclude rights for use with pediatric applications. The QIAcuityDx medical device is currently under development and will be available in 20 countries in H2 2024.