Cancer Genetics

Cancer Genetics

Cancer Genetics is constantly evolving, as new technologies allow for more personalised medicine. Sonic Genetics provides a growing number of oncology, pharmacogenetic, and diagnostic tests to help:

  • clarify a diagnosis
  • develop a plan
  • and select treatment
Oncology test (leukaemia/lymphoma)
13q FISH
Deletions affecting the long arm of chromosome 13 can be found in a number of mature B-cell lymphoid neoplasms, particularly chronic lymphocytic leukaemia (CLL), and also splenic marginal zone lymphoma and mantle cell lymphoma. Testing provides information regarding prognosis.
20q FISH
Chromosomal abnormalities resulting in deletion of part of the long arm of chromosome 20 (20q) can occur in myeloid neoplasms, including both acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). These abnormalities can have diagnostic and prognostic implications.
5q FISH
Chromosomal abnormalities resulting in deletion at 5q or monosomy 5 can occur in both acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Genes in the deleted region include NPM1, APC and CTNNA1. Deletions at 5q are also relatively common in therapy-related AML/MDS. These abnormalities can have diagnostic, prognostic and therapeutic implications.
6q21 FISH
Deletions affecting the long arm of chromosome 6, including the 6q21 region, are common in mature B-cell lymphoid neoplasms, for example, plasma cell neoplasms, mantle cell lymphoma and B-cell non-Hodgkin lymphoma, particularly lymphoplasmacytic lymphoma. These deletions can assist in subsequent monitoring of disease.
7q FISH
Chromosomal abnormalities resulting in deletion at 7q or monosomy 7 can occur in both acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Genes in the deleted region include EPO, PLANh6 and MET. Deletions at 7q are also common in therapy-related AML/MDS. These abnormalities have prognostic implications.
ALK FISH (lymphoma)
Gene fusions involving the ALK gene and other gene partners can occur in large B-cell lymphomas and T-cell anaplastic large cell lymphomas. These fusions allow diagnosis of a specific subtype of lymphoma.
ATM FISH
Deletions of the ATM gene at 11q22 can be found in patients with chronic lymphocytic leukaemia (CLL). These deletions have prognostic implications.
BCL6 FISH
Gene fusions involving the BCL6 gene at 3q27 can occur in B-cell non-Hodgkin lymphomas (B-NHL), particularly diffuse large B-cell lymphoma (DLBCL). BCL6 gene fusions are also seen in patients with follicular lymphoma or marginal zone lymphoma. These gene fusions have diagnostic and prognostic implications.
BCR/ABL1 FISH (lymphoid tumour)
Translocations between chromosome 9 and 22, resulting in fusion of the BCR and ABL1 genes, can occur in a number of haematological malignancies, particularly chronic myeloid leukaemia (CML), and also acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL). The identification of this gene fusion has diagnostic, prognostic and therapeutic implications.
BCR/ABL1 PCR
Translocations between chromosome 9 and 22, resulting in fusion of the BCR and ABL1 genes, can occur in a number of haematological malignancies, particularly chronic myeloid leukaemia (CML), and also acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL). The presence of this fusion has diagnostic and therapeutic implications. The fusion gene can be detected at very low concentrations and be a marker of therapeutic response or disease progression.
CALR Screen
Mutations in the calreticulin (CALR) gene have been described in 15– 25% of patients with essential thrombocythaemia (ET) and 25–35% of patients with primary myelofibrosis (PMF). As such, these are the second most common somatic mutations in these myeloproliferative neoplasms (behind JAK2 V617F).
CBFB/MYH11 FISH
Chromosomal rearrangements affecting chromosome 16 can result in fusion of the CBFB and MYH11 genes. The CBFB-MYH11 gene fusion defines the AML subtype previously known as acute myelomonocytic leukaemia (AMML), and is often associated with abnormality of or increase in eosinophils.
Chimerism FISH
If a patient has a bone marrow transplant from a person of the opposite gender, it is possible to monitor to degree of engraftment of the donor cells by measuring the relative abundance of XX (female) and XY (male) cells in marrow or blood.
Chronic lymphocytic leuk FISH
Changes in chromosome structure and number in leukaemic cells can provide important prognostic and therapeutic information in patients with chronic lymphocytic leukaemia (CLL). A panel of probes is used to look for the most frequent abnormalities, 13q deletion, trisomy 12, ATM deletion and p53 deletion.
Eosinophilia FISH panel
A group of myeloid and lymphoid diseases associated with eosinophilia can result from aberrant tyrosine kinase expression. These related disorders are associated with either PDGFRA, PDGFRB or FGFR1 rearrangements. These rearrangements have prognostic and therapeutic implications.
ETV6/RUNX1 FISH
TEL and AML1 are rearranged by a translocation between chromosomes 12 and 21 in a subset of patients with B-cell acute lymphoblastic leukaemia (ALL). This fusion is more common in the paediatric age group. These two genes are also known as ETV6 and RUNX1 (respectively). The presence of this gene fusion has prognostic implications.
FGFR1 FISH
Gene fusions involving the FGFR1 gene and other gene partners can occur in myeloid and lymphoid neoplasms, typically with eosinophilia. Such fusions have prognostic implications.
IGH/BCL2 FISH
Gene fusions involving the IGH gene at 14q32 and BCL2 at 18q21 are common in follicular lymphomas, and can also occur in diffuse large B-cell lymphomas (DLBCL). The identification of such fusions can assist in diagnosis and classification of disease.
IGH/CCND1 FISH
Gene fusions involving the CCND1 at 11q13 and the IGH gene at 14q32 are common in mantle cell lymphoma. They can also occur in multiple myeloma. Such gene fusions have diagnostic and prognostic implications.
IGH/MAF FISH
Gene fusions involving the IGH gene at 14q32 and the MAF gene at 16q23 are seen in multiple myeloma. The identification of such fusions can assist in the diagnosis and classification of this disease.
IGH/MALT1 FISH
Gene fusions involving the IGH gene at 14q32 and MALT1 at 18q21 are frequent in several types of lymphoma. Such gene fusions have diagnostic and prognostic implications.
IGH/MYC FISH
Gene fusions involving the IGH gene at 14q32 and MYC at 8q24 are common in Burkitt lymphoma. They can also occur in other B-cell non-Hodgkin lymphomas, for example, diffuse large B-cell lymphoma (DLBCL). Less commonly, MYC can be fused with other gene partners, such as IGK and IGL. Such gene fusions have diagnostic and prognostic implications.
JAK2 screen
A specific acquired variant in the JAK2 gene (p.Val617Phe, or V617F) is common in certain myeloproliferative neoplasms. It is present in 95% of patients with polycythemia vera (PV), and approximately 50% of patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF). This test can assist in making the diagnosis of these disorders.
Karyotype (tumour)
Chromosome analysis can detect abnormalities of chromosome structure or number in malignant cells. These abnormalities can have diagnostic and prognostic implications.
KMT2A FISH
MLL (also known as KMT2A) is located at 11q23. It can undergo gene fusion with a variety of partner genes in several types of acute leukaemia. This fusion carriers prognostic implications.
Lymphoma Panel
Changes in chromosome structure and number in lymphoma cells can provide important prognostic and therapeutic information. A panel of probes is used to look for the most frequent abnormalities in lymphoma. These are the ATM deletion, 13q deletion, IGH rearrangement, TP53 deletion and MALT1 rearrangement.
MLLT3/KMT2A FISH
Chromosomal rearrangements affecting chromosome 11q23 result in fusion of the MLL gene (also known as KMT2A) with multiple different fusion partners. One of the most common fusion partners is MLLT3, located at chromosome 9p22. Presence of an MLL-MLLT3 fusion gene defines a specific AML subtype. This gene fusion is the result of a chromosomal translocation: t(9;11)(p22;q23). The identification of this gene fusion has diagnostic and prognostic implications.
Multiple hit lymphoma FISH
A B-cell lymphoma may exhibit multiple gene rearrangements involving the genes MYC and BCL2 or MYC and BCL6 (double hit), or MYC and BCL2 and BCL6 (triple hit). These rearrangements have prognostic implications.
Multiple Myeloma panel
Changes in chromosome structure and number in myeloma cells can provide important prognostic and therapeutic information. A panel of probes is used to determine risk status of the disease. High-risk indicators are IGH rearrangement (with specific partner chromosomes), TP53 deletion and 1q trisomy.
MYC FISH
Gene fusions and amplification involving the MYC gene at 8q24 are common in Burkitt lymphoma, and can occur in other B-cell non-Hodgkin lymphomas, for example, diffuse large B-cell lymphoma (DLBCL). These changes have diagnostic and prognostic implications. The most common fusion partner for MYC is IGH, although other fusion partners are possible (for example, IGK and IGL). This test will also detect amplification of MYC.
Myelodysplastic syndrome FISH
Changes in chromosome structure and number in marrow cells can provide important prognostic and therapeutic information in myelodysplastic syndrome (MDS). Deletions in the long arms of chromosomes 5,7 and 20 are the most frequent abnormalities in MDS.
PDGFRA/FIP1L1 FISH
Gene fusions involving the PDGFRA gene, typically with the FIP1L1 gene, can occur in myeloid and lymphoid neoplasms. These disorders may present as a myeloproliferative neoplasm, typically with eosinophilia. The presence of the gene fusion carries therapeutic implications.
PDGFRB FISH
Gene fusions involving the PDGFRB gene and a number of other gene partners occur in some patients with myeloproliferative neoplasms, typically with eosinophilia. This gene fusion has diagnostic and therapeutic implications.
PML/RARA FISH
Fusion of the PML and RARA defines a specific AML subtype, formerly known as acute promyelocytic leukaemia. This gene fusion is the result of a chromosomal translocation: t(15;17)(q24;q21). Identification of this fusion has diagnostic, prognostic and therapeutic implications.
RPN1/MECOM FISH
Rearrangements of chromosome 3 which result in fusion of the RPN1 and EVI1 (also known as MECOM) genes are found in a small number of patients with acute myeloid leukaemia (AML), or with therapy-related AML or myelodysplastic syndrome (MDS). These patients often have thrombocytosis. This gene fusion defines a specific AML subtype, and it carries prognostic implications.
RUNX1/RUNX1T1 FISH
Fusion of the AML1 and ETO genes defines a specific AML subtype. These two genes are also known as RUNX1 and RNX1T1 (respectively). This gene fusion is the result of a chromosomal translocation: t(8;21)(q22;q22). Identification of this fusion has prognostic implications.
TCR/IGH rearrangements
The TCR and IGH genes undergo rearrangement at the DNA level during maturation of T- and B-lymphocytes (respectively). Analysis of these genes can detect a clonal proliferation of T-cells and/or B-cells, and thereby provide diagnostic information.
TP53 FISH
TP53 is one of the genes most frequently mutated in human cancer. Deletions of the TP53 gene can be identified in some patients with chronic lymphocytic leukaemia (CLL), and this has prognostic implications.
Trisomy 12 FISH
Trisomy of chromosome 12 is the most common cytogenetic abnormality in patients with chronic lymphocytic leukaemia (CLL), and can be found in other mature B-cell neoplasms. This cytogenetic abnormality has prognostic implications.
Trisomy 8 FISH
Trisomy of chromosome 8 is a frequent, non-specific finding in several myeloid neoplasms, including acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). This cytogenetic abnormality has prognostic implications.
Oncology test (solid tumour)
ALK FISH (lung cancer)
Gene fusions involving the ALK gene and other gene partners occur in a subset of non-small cell lung cancers (NSCLC). Such fusions carry implications regarding selection of and response to therapies.
BRAF screen
Certain mutations in the BRAF gene in some solid tumours are associated with responses to therapy or the likelihood of familial disease.
EGFR FISH
Amplification of the EGFR gene, leading to overexpression, can occur in a number of tumour types. This test has diagnostic and prognostic implications in patients with glial tumours.
EGFR screen
Mutations in the EGFR (epidermal growth factor receptor) gene can guide the choice of therapy in patients with non-small cell lung cancer (NSCLC). Clinically relevant mutations occur in exons 18, 19, 20 and 21 of the gene.
Ewing sarcoma FISH
The EWSR1 probe detects breakage of this locus on chromosome 22. There are a number of possible partner genes, the most frequent being FLI1 on chromosome 11. This test has diagnostic and prognostic implications.
FOXO1 FISH
The FOXO1 (also known as FKHR) locus is rearranged in around 80% of cases of Alveolar Rhabdomyosarcoma (RMS). 60% have a PAX3-FOXO1 fusion, and 20% a PAX7-FOXO1 fusion. This test has diagnostic implications.
FUS/DDIT3 FISH
The t(12;16) translocation results in fusion of the FUS and DDIT3 genes. This test has diagnostic implications.
KRAS and NRAS screen
The presence of specific activating mutations in the KRAS and NRAS genes in certain malignancies (for example, metastatic colorectal cancer) indicates a reduced likelihood of treatment response to anti-EGFR therapy.
MDM2 FISH
The MDM2 oncogene is located on the long arm of chromosome 12. Overexpression of this gene occurs in many types of cancer. The overall frequency of MDM2 amplification in human tumours is 7%. The highest frequency is observed in soft tissue tumours (20%), osteosarcomas (16%) and oesophageal carcinomas (13%). This test has diagnostic implications.
MYCN FISH
The N-MYC (MYCN) oncogene is overexpressed in a number of tumours, such as gliomas, lung and PNET. The test has prognostic implications.
Prosigna
RNA is extracted from a small section of formalin fixed tumour tissue, and RNA molecules from each of 58 genes are counted. These numbers, together with the tumour size and number of involved nodes, are combined to generate the estimated recurrence risk and intrinsic subtype.

The test estimates the risk of distant recurrence over 10 years and defines the intrinsic subtype of the breast cancer.

PTEN FISH
The Phosphate and Tensin homologue (PTEN) gene on 10q23 is mutated in a wide range of cancers. Allelic loss is one of the most frequent events in gliomas. This test has diagnostic implications.
SS18 FISH
The t(X;18) translocation results in fusion of the SS18 gene on chromosome 18 with one of three related genes on the short arm of the X. The probe determines breakage of SS18. This test has diagnostic implications.
Oligodendroglioma FISH
Deletions of 1p and 19q are associated with tumours with oligodendroglial components. Combined alterations have been observed in up to 70% of oligodendrogliomas and 50% of mixed oligoastrocytomas. The co-deletion is due to an unbalanced translocation – t(1;19)(q10;p10). This test has prognostic implications.
USP6 FISH
The USP6 gene at 17p13 is rearranged in certain bone tumours. USP6 mutations have been identified in most cases of primary aneurysmal bone cysts (solid and cystic, including giant cell reparative granuloma of non-craniofacial bones), in nodular fasciitis and in occasional cases of myositis ossificans. This test has diagnostic implications.