Single-variant-specific, single-gene-specific and panel diagnostics for somatic mutations in tumors

CENTOGENE's somatic mutation tests are highly sensitive, easy to use, and accurate for identifying even low frequency variants successfully.

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  1. Single-Gene-Specific Somatic Mutation Testing

Somatic mutation testing

Molecular profiling is critical for identifying and characterizing unique somatic variants that accumulate in cancer cells. We offer analytical tests for somatic variants in tumor tissue that can help to identify diagnostic, prognostic or predictive biomarkers.

Next-generation sequencing is becoming more widely adopted as a valuable method for somatic mutation analysis in cancer. CENTOGENE offers hotspot targeted mutation analysis, selective sequencing of gene regions, full gene sequencing and panel testing for the analysis of dozens of cancer-related genes in parallel.

Single genes for somatic mutation testing


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BRAF somatic mutation testing

BRAF encodes B-Raf proto-oncogene, the most potent activator of the mitogen-activated kinase (MAPK) extracellular-regulated kinase (ERK). Mutations in this gene are associated with multiple types of cancers, including non-Hodgkin lymphoma, colorectal cancer, malignant melanoma, thyroid carcinoma, non-small-cell lung carcinoma, and lung adenocarcinoma. Mutations in the RAS/BRAF/MEK/ERK pathway occur in approximately 30% of all cancers, with BRAF mutations in approximately 7% of cancers. 80-90% of all BRAF mutations are characterized by a thymine-to-adenine single-base change at position 1799 that leads to a glutamine-for-valine substitution in exon 15 at residue 600 (V600E). BRAFV600E is a 500-fold gain-of-function mutation leading to constitutive activation of MEK/ERK signaling. The V600K variant accounts for approx. 6–16% of BRAF mutations and seems to be similar in its effects on the tumor. Identification of these variants negatively impacts treatment outcomes for anti-EGFR monoclonal antibodies. BRAFV600E is also specific for papillary thyroid cancer distinguishing these lesions from benign and follicular neoplasms. Analysis for V600E allows better characterizing of indeterminate cases and deciding on necessary treatment options. Tumor cells with a V600E mutation show increased sensitivity to BRAF inhibitors.

CENTOGENE offers multiple screening tests for targeted and general screening of mutations in BRAF gene.

A. Hot spot targeted mutation testing

CENTOGENE offers a quantitative PCR-based approach to selectively screen or monitor c.1799T>A/p.V600E mutation in BRAF gene down to 0.05% allele frequency.

B. Selective sequencing of exon 15

V600E mutation occurring in exon 15 of BRAF gene comprises around 90% of all mutations identified in BRAF-related tumors. For comprehensive screening of all somatic mutations in exon 15 of BRAF gene, CENTOGENE offers selective sequencing of complete exon 15 of BRAF through next generation sequencing that can detect variants at allele frequencies down to at least 5%.

C. Full gene sequencing

Testing of the complete coding region of BRAF gene is offered through next generation sequencing that can detect variants at allele frequencies down to 5%.

D. Panel testing

BRAF analysis is also part of broader multi-gene panels like cancer hotspots panel (detects 77 described mutations in BRAF gene along with commonly described mutations in 49 other oncogenes), myeloid tumor panel (covers exon 15 of BRAF along with selective targeted regions in 21 other oncogenes and tumor suppressor genes involved in hematological malignancies) or solid tumor panel (~96.5% of the coding region of BRAF gene is covered along with over 95% coverage of coding regions of 61 other tumor-related genes) that are all readily available on the CENTOGENE website.

CALR somatic mutation testing

Frequent frameshift deletions or insertions in exon 9 of CALR gene are found in patients with myeloproliferative neoplasms, including myelofibrosis and essential thrombocythemia. CALR mutations are most frequently observed in patients with primary myelofibrosis where no mutations in JAK2 or MPL were found, pointing out to mutually exclusive occurrence of mutations in these genes.

CENTOGENE offers multiple screening tests for targeted and general screening of mutations in CALR gene.

A. Selective sequencing of exon 9

Sequencing exon 9 alone is sufficient to cover all important mutations (including described insertions and deletions) within CALR gene. For rapid screening of important somatic mutations in CALR gene, CENTOGENE offers selective sequencing of CALR exon 9 through next generation sequencing that allows detection of mutations at allele frequency down to at least 5%.

B. Panel testing

CALR analysis is also part of broader multi-gene panels such as cancer hotspot panel that is readily available on the CENTOGENE website.

EGFR somatic mutation testing

~10–25% patients with non-small-cell lung cancer have tumors associated with EGFR mutations that occur primarily within exons 18–21. Mutations within this kinase domain increase the kinase activity of EGFR that leads to hyperactivation of anti-apoptotic Ras signaling cascade, eventually resulting in uncontrolled cell proliferation. Deletions in exon 19 and point mutation p.L858R in Exon 21 together comprise ~90% of all mutations identified within this domain. Studies show that tumors positive with EGFR activating mutations in the kinase domain are more sensitive to tyrosine kinase inhibitors (TKIs). On the contrary, insertions in Exon 20 (with an exception to A763_Y764insFQEA) are associated with decreased sensitivity to TKIs.

CENTOGENE offers multiple screening tests for targeted and general screening of mutations in EGFR gene.

A. Hotspot targeted mutation testing

Approximately 43% of EGFR mutations are a result of a single point mutation c.2573T>G/p.L858R in exon 21 within the tyrosine kinase domain of EGFR protein. For rapid and sensitive screening of this mutation, CENTOGENE offers a quantitative PCR-based approach to selectively screen or monitor individual mutations down to 0.05% allele frequency.

B. Exons 18–21 testing

Testing of exons 18, 19, 20 and 21 of EGFR gene is offered through next generation sequencing that can detect mutations at allele frequency down to 5% or lower.

C. Panel testing

EGFR analysis is also part of broader multi-gene panels like cancer hotspots panel (detects 123 described mutations in EGFR gene along with commonly described mutations in 49 other oncogenes) or solid tumor panel (~99.8% of the coding region of EGFR gene is covered along with over 95% coverage of coding regions of 61 other tumor-related genes) that are readily available on the CENTOGENE website.

IDH1 somatic mutation testing

Isocitrate dehydrogenase (IDH) acts as an NADP-dependent protein that catalyzes decarboxylation of isocitrate into alpha-ketoglutarate. The pathway produces NADPH, which likely provides cellular protection from oxidative damage. IDH1 localizes to the cytoplasm and peroxisomes, whereas the homologue IDH2 localizes to the mitochondria. Mutations in IDH1 gene are frequently observed in lower grade diffuse gliomas (grade II–III), in secondary glioblastomas; and sometimes as well in newly diagnosed glioblastomas. Overall one-third of gliomas and ~6.4% of acute myeloid leukemia (AML) cases carry mutations in IDH1 gene. Of all known IDH1 mutations, R132H in exon 4 of IDH1 gene is the most frequently observed point mutation (~85%) and used as a prognostic marker for central nervous cancer.

CENTOGENE offers multiple screening tests for targeted and general screening of mutations in IDH1 gene.

A. Selective sequencing of exon 4

Over 95% of all IDH1-mutated gliomas and 80% of all IDH1-mutated AML cases show mutations in arginine at position 132 in exon 4 of IDH1 gene. Based on COSMIC database, prominent mutations at this position include c.395G>A/p.R132H that comprises 87.6% of IDH1 mutations in gliomas. In IDH1-related AML cases, c.394C>T/p.R132C and c.395G>A/p.R132H occur at ~35% and ~25% respectively in IDH1 gene. Other mutations at this position include c.394C>G/p.R132G, c.394C>A/p.R132S, c.395G>T/p.R132L and c.395G>C/p.R132P.

CENTOGENE offers selective sequencing of complete exon 4 of IDH1 through next generation sequencing that can confidently detect mutations at allele frequencies down to 5%.

B. Full gene testing

Testing of the complete coding region of IDH1 gene at an overall coverage of 99.3% is offered through next generation sequencing that can detect mutations at allele frequency as low as 5% in tumor samples.

C. Panel testing

IDH1 analysis is also part of broader multi-gene panels like cancer hotspots panel (detects 15 described mutations in IDH1 gene along with commonly described mutations in 49 other oncogenes), myeloid tumor panel (covers exon 4 of IDH1 gene along with selective targeted regions in other oncogenes and tumor suppressor genes involved in hematological malignancies) or solid tumor panel (~99.3% of the coding region of IDH1 gene is covered along with over 95% coverage of coding regions of 61 other tumor-related genes that are readily available on the CENTOGENE website.

IDH2 somatic mutation testing

Isocitrate dehydrogenase (IDH) acts as an NADP-dependent protein that catalyzes decarboxylation of isocitrate into alpha-ketoglutarate. The pathway produces NADPH, which likely provides cellular protection from oxidative damage. IDH1 localizes to the cytoplasm and peroxisomes, whereas the homologue IDH2 localizes to the mitochondria. Mutations in IDH2 are frequently observed in acute myeloid leukemia (AML) cases and to a lower extent also in gliomas. Overall, ~9.1% of AML cases and 1.7% of glioma cases carry mutations in IDH2 gene. Almost all IDH2 mutations occur in exon 4.

CENTOGENE offers multiple screening tests for targeted and general screening of mutations in IDH2 gene.

A. Selective sequencing of exon 4

IDH2-mutated AML cases show mutations in arginine at position 140 in exon 4 of IDH2 gene. On the other hand, arginine at position 172 is the most frequently mutated amino acid in IDH2-mutated gliomas. In AML, frequent IDH2 mutations include c.419G>A/p.R140Q and c.515G>A/p.R172K that occur at ~74.8% and ~20.9% respectively, while c.515G>A/p.R172K and c.515G>T/p.R172M occur at 58.2% and 19.1% respectively in all IDH2-mutated gliomas.

For rapid and comprehensive screening of all R140 and R172 mutations in IDH2 gene, CENTOGENE offers selective sequencing of complete exon 4 of IDH2 through next generation sequencing that can confidently detect mutations at allele frequency down to 5%.

B. Full gene sequencing

Testing of complete coding region of IDH2 gene at an overall coverage of 97.7% is offered through next generation sequencing that can detect mutations at allele frequencies as low as 5%.

C. Panel testing

For general screening of somatic mutations, IDH2 gene mutations/exon(s) are also a part of broader multi-gene panels like cancer hotspots panel (detects 12 described mutations in IDH2 gene along with commonly described mutations in 49 other oncogenes), myeloid tumor panel or solid tumor panel that are readily available on the CENTOGENE website.

JAK2 somatic mutation testing

JAK2 is mutated in 4–9% of B-cell precursor ALL. In BCR-ABL1-negative, high-risk B-cell precursor pediatric acute lymphoblastic leukemia (ALL) patients it can be found together with an IKFZ1 deletion in 87.5% of cases. In addition, a large majority of cases with polycythemia vera, thrombocythemia and idiopathic myelofibrosis show a single V617F mutation in Exon 14 of JAK2 gene. Identification of a JAK2 variant indicates a myeloproliferative component in myelodysplastic syndrome and can be used as a prognostic marker.

CENTOGENE offers multiple screening tests for JAK2 gene to suit the recommendations of different guidelines.

A. Selective sequencing of exons 12, 14 and 16

Over 48.5% of mutations in JAK2 in ALL cases include mutations of arginine residue in the codon 683 in exon 16. A small number of AML patients also show c.1821G>C transversion in exon 14. In the absence of V617 mutation in patients with polycythemia vera or idiopathic erythrocytosis, K539L mutation in exon 12 has been previously reported. For rapid screening of these mutations CENTOGENE offers selective sequencing of exons 12, 14 and 16 using next generation sequencing with a detection limit down to 5% allele frequency.

B. Full gene testing

CENTOGENE offers testing of complete coding region of JAK2 gene at overall 90.8% coverage through next generation sequencing that can detect mutations down to 5% allele frequencies.

C. Panel testing

JAK2 analysis is also part of broader multi-gene panels like cancer hotspots panel (detects five described mutations in JAK2 gene along with commonly described mutations in 49 other oncogenes), myeloid tumor panel or solid tumor panel that are readily available on the CENTOGENE website.

KIT somatic mutation testing

KIT is a tyrosine kinase receptor that regulates cellular proliferation and differentiation. Approximately 85% of gastrointestinal stromal tumors (GISTs) and ~8% of acute myeloid leukemia (AML) cases show mutations in KIT gene. In GIST, ~70% of all detected KIT mutations arise in juxtamembrane domain that is encoded by exon 11. On the other hand, ~38.6% of KIT mutations in AML originate in the activation loop of the kinase domain in exon 17. Secondary KIT mutations in resistant clones are commonly identified in exons 13, 14, 17 and 18.

CENTOGENE offers multiple screening tests for targeted and general screening of mutations in KIT gene.

A. Selective sequencing of exons 8, 9, 11, 13 and 17

Selective sequencing of exons 8, 9, 11, 13 and 17 is sufficient to cover ~85% of all KIT mutations described in GIST and ~40% of all KIT mutations involved in AML. For rapid screening of important somatic mutations in KIT gene, CENTOGENE offers sequencing of the above-mentioned exons through next generation sequencing that allows detection of mutations at allele frequency down to at least 5%.

B. Full gene sequencing

CENTOGENE offers sequencing of complete coding region of KIT gene at an overall coverage of 96% through next generation sequencing where mutations with allele frequency as low as 5% can be confidently detected in tumor samples.

C. Panel testing

For general screening of somatic mutations, KIT gene mutations/exon(s) are also a part of broader multi-gene panels like cancer hotspots panel (detects 139 described mutations in KIT gene along with commonly described mutations in 48 other oncogenes), myeloid tumor panel or solid tumor panel that are readily available on the CENTOGENE website.

KRAS somatic mutation testing

KRAS is a member of the RAS family. Among others it is activated by growth factor receptor tyrosine kinases such as the EGF receptor and non-receptor tyrosine kinases such as ABL1. Activation of KRAS regulates cell proliferation, differentiation and apoptosis. Over 50% of all colorectal cancers show mutations in one of the RAS genes, KRAS or NRAS of which around 36–40% of the mutations occur in KRAS gene alone. These activating mutations in codon 12 and 13 are the majority and lead to an increased resistance towards EGFR-based antibody therapies. The FDA therefore recommends to refrain from this therapeutic option in the case of KRAS codon12 13 mutation.

CENTOGENE offers multiple screening tests for KRAS gene to suit the recommendations of different guidelines.

A. Hotspot targeted mutation testing

c.35G>A/p.G12D (34%), c.35G>T/p.G12V (22%) and c.38G>A/p.G13D (19%) are the most frequent mutations present in codon 12 and 13 of KRAS gene in colorectal cancers where KRAS gene is found to be mutated. For rapid and sensitive screening of these mutations, CENTOGENE offers a quantitative PCR-based approach to selectively screen or monitor individual mutations down to 0.05% allele frequency.

B. Full gene testing

Testing of complete coding region of KRAS gene is offered through next generation sequencing that can detect mutations at allele frequency down to 5% in tumor samples.

C. Panel testing

For general screening of somatic mutations, KRAS exons are also a part of broader multi-gene panels like cancer hotspots panel (detects 63 described mutations in KRAS gene along with commonly described mutations in 49 other oncogenes) or solid tumor panel that are readily available on the CENTOGENE website.

NRAS somatic mutation testing

NRAS is a member of the RAS family. Among others it is activated by growth factor receptor tyrosine kinases such as the EGF receptor and non-receptor tyrosine kinases such as ABL1. Activation of NRAS regulates cell proliferation, differentiation, and apoptosis. Over 50% of all colorectal cancers show mutations in one of the RAS genes, KRAS or NRAS of which around 1–6% of the mutations occur in NRAS gene alone. Activating mutations in codon 12, 13 and 61 are the majority and lead to an increased resistance towards EGFR-based antibody therapies.

CENTOGENE offers multiple screening tests for targeted and general screening of mutations in NRAS gene to suit the recommendations of international guidelines.

A. Hotspot targeted mutation testing

c.181C>A/p.Q61K (27%), c.182A>G/p.Q61R (17%), c.35G>A/p.G12D (16%) and c.34G>T /p.G12C (11%) are the most frequent mutations present in NRAS-mutated tumors. For rapid and sensitive screening of these mutations, CENTOGENE offers a quantitative PCR-based approach to selectively screen or monitor individual mutations down to 0.05% allele frequency.

B. Full gene testing

Testing of complete coding region of NRAS gene is offered through next generation sequencing that can detect mutations at allele frequency down to 5% in tumor samples.

C. Panel testing

For general screening of somatic mutations, NRAS exons are also a part of broader multi-gene panels like cancer hotspots panel (detects 35 described mutations in NRAS gene along with commonly described mutations in 49 other oncogenes), myeloid tumor panel or solid tumor panel that are readily available on the CENTOGENE website.

Our portfolio for somatic mutation testing

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