Genomic Medicine

Genomic Medicine

SR NOTESTTEST COMPONENTSMETHODSPECIMEN/TRANSPORTTATCLINICAL APPLICATIONS
1BCR-ABL fusion-transcript Qualitative AnalysisQualitative detection of BCRABL genePCRBone marrow, EDTA whole blood (3ml)5 daysInitial diagnosis of patients suspected to be suffering from CML or ALL for the presence of the BCR/ABL translocation.
2BCR-ABL fusion-transcript Multiplex Qualitative AnalysisDetection of different transcriptsMultiplex qualitative PCRBone marrow, EDTA whole blood (3ml)5 daysInitial diagnosis of patients suspected to be suffering from CML or ALL for the presence of the BCR/ABL translocation having usual and uncommon transcript variants
3BCR-ABL International Scale Quantitative Analysise13a2 & e14a2 transcript detectionReal Time PCRBone marrow, EDTA whole blood (3ml)3 daysInitial diagnosis of patients suspected to be suffering from CML or ALL for the presence of the BCR/ABL translocation.
Monitoring response to TKI therapy in CML
4Minor BCR-ABLe1a2 transcript detectionReal Time PCRBone marrow, EDTA whole blood (3ml)3 daysDiagnostic workup of patients with a high probability of BCR-ABL1-positive hematopoietic neoplasms, particularly acute lymphoblastic leukemia (B-lymphoblastic leukemia), to provide a pretreatment quantitative level of BCR-ABL1 mRNA transcript if the initial diagnostic RT-PCR screen is positive
5PML-RARA α Qualitative AnalysisBCR1,BCR2,BCR3 transcript detectionReal Time PCRBone marrow, EDTA whole blood (3ml)3 daysAPL must be confirmed at the genetic level,for most cases, diagnosis is suggested by characteristic
BM morphology, immunophenotyping, and clinical
presentation. Necessary for patients who go in relapse.
6PML-RARA α Quantitative AnalysisBCR1,BCR2,BCR3 transcript detectionReal Time PCRBone marrow, EDTA whole blood (3ml)3 daysAPL must be confirmed at the genetic level,for most cases, diagnosis is suggested by characteristic
BM morphology, immunophenotyping, and clinical
presentation. Necessary for patients who go in relapse.
7JAK2 V617F mutation studyV617F mutationPCRBone marrow, EDTA whole blood (3ml)2 daysDetection of the JAK2 V617F is useful to help establish the diagnosis of MPN
8JAK2 mutation panel (Exon 12 - 15) AnalysisEXON 12-15Sanger SequencingBone marrow, EDTA whole blood (3ml)7 daysDiagnose and manage classic BCR-ABL1-negative myeloproliferative neoplasms (MPNs)
9NPM1 (Nucleophosmin) Mutation AnalysisExon 12Sanger SequencingWhole blood 3ml in EDTA vacutainer7 daysAs a prognostic indicator in patients with newly diagnosed acute myelogenous leukemia with normal karyotype and no FLT3 mutation
10FLT3 Mutation AnalysisExon 20 with ITDSanger SequencingBone marrow, EDTA whole blood (3ml)7 daysPrognostication of AML.
11CALR (Calreticulin) Mutation AnalysisExon 9Sanger SequencingBone marrow, EDTA whole blood (3ml)7 daysUse for diagnostic and prognostic information in patients with MyeloProliferative Neoplasms (MPNs) when JAK2 testing is negative.
12CEBPA mutation AnalysisSanger SequencingBone marrow, EDTA whole blood (3ml)7 daysInitial evaluation of Acute Myeloid Leukemia, both for assigning an appropriate diagnostic subclassification and as an aid for determining prognosis.
13Myeloproliferative leukemia (MPL1) mutation AnalysisExon 10Sanger SequencingBone marrow, EDTA whole blood (3ml)7 daysMay be useful when Essential Thrombocythemia or Idiopathic Myelofibrosis is suspected in JAK2 V617F negative individuals.
14ALL PCR panelMinor BCR-ABL, TEL/AML1, E2A, FISH MLL, Bone Marrow KaryotypingRT-PCRBone marrow, EDTA whole blood (3ml)7 daysRisk stratification and therapeutic management in children and adult
with newly diagnosed ALL
15AML PCR panelPML-RARA Quantitative, Inv16, AML/ETO, FISH MLL, Bone marrow KaryotypingRT-PCRBone marrow, EDTA whole blood (3ml)7 daysEvaluation of acute Myeloid Leukemia (AML) at the time of diagnosis, to assist in appropriate classification and prognosis using five translocation gene panel and karyotyping.
16AML prognostic PCR panelPML-RARA Quantitative, Inv16, AML/ETO, FLT3, NPM1, FISH MLL, Bone marrow KaryotypingRT-PCRBone marrow, EDTA whole blood (3ml)7 daysFor accurate diagnosis, prognosis and monitoring of acute myeloid leukemia
17MPL PCR PanelBCR-ABL multiplex, JAK2 PCR, JAK2 Panel, CALR, MPL1, Bone Marrow KaryotypingRT-PCRBone marrow, EDTA whole blood (3ml)7 daysThis reflex test sequentially evaluates for the common major gene mutations associated with non-BCR/ABL1-positive myeloproliferative neoplasms until a mutation is identified.
18Karyotyping- Bone MarrowAll ChromosomesCulture KaryotypingBone marrow7 daysTo diagnose congenital chromosomal abnormalities, including aneuploidy, structural abnormalities, and balanced rearrangements
19FISH for del(13q)Chromosome 13FISHSodium Heparin Blood (3ml), Bone marrow5 days13q deletion a part of CLL panel (FCLL). The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13 and 11q22-23. An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q.
20FISH for del(5q)chromosome 5FISHSodium Heparin Blood (3ml), Bone marrow5 daysThe myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3,3).
21FISH for del(7q)chromosome 7FISHSodium Heparin Blood (3ml), Bone marrow5 daysThe myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3).
22FISH for del(20q)chromosome 20FISHSodium Heparin Blood (3ml), Bone marrow5 daysThe myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3).
23FISH for detection OF E2AChromosome 1, 17 and 19FISHSodium Heparin Blood (3ml), Bone marrow5 daysAcute Lymphoblastic Leukemia (ALL) is the most common type of leukemia in children, representing almost 25 % of pediatric cancer. The majority of patients with ALL demonstrate an abnormal karyotype, either in chromosome number or as structural changes such as translocations, inversions, or deletions.
24FISH for FGFR3/IgHChromosome 4 and 14FISHSodium Heparin Blood (3ml), Bone marrow5 daysGenetic aberrations present in multiple myeloma cells play a significant role in the risk stratification and therapeutic approach in multiple myeloma patients. Chromosomal translocations affecting the IGH locus are recurrent in many types of leukemias and lymphomas.The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus.
25FISH for IgHChromosmoe 4FISHSodium Heparin Blood (3ml), Bone marrow5 daysChromosomal translocations affecting the IGH locus are recurrent in many types of lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus.
26FISH for Inv(16)chromosome 16FISHSodium Heparin Blood (3ml), Bone marrow5 daysSeveral recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasia-related features when 20% or more blood or marrow blasts are present.
27FISH for MAF/IgHFISHSodium Heparin Blood (3ml), Bone marrow5 daysGenetic aberrations present in multiple myeloma cells play a significant role in the risk stratification and therapeutic approach in multiple myeloma patients. Chromosomal translocations affecting the IGH locus are recurrent in many types of leukemias and lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus.
28FISH for MYEOV/IgHFISHSodium Heparin Blood (3ml), Bone marrow5 daysGenetic aberrations present in multiple myeloma cells play a significant role in the risk stratification and therapeutic approach in multiple myeloma patients. Chromosomal translocations affecting the IGH locus are recurrent in many types of leukemias and lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus.
29FISH for TEL/AMLFISHSodium Heparin Blood (3ml), Bone marrow5 daysA number of recurrent chromosomal abnormalities have been shown to have prognostic significance in acute lymphoblastic leukemia, especially in B-precursor ALL. Some chromosomal abnormalities, such as high hyperdiploidy and the ETV6-RUNX1 fusion, are associated with more favorable outcomes, while others, including the t(9;22), rearrangements of the KMT2A gene (chromosome 11q23), and intrachromosomal amplification of the AML1 gene (iAMP21), are associated with a worse prognosis.
30FISH for TRISOMY 12FISHSodium Heparin Blood (3ml), Bone marrow5 daysThe prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15, and deletions 13q14, 17p13, and 11q22-23. An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q.
31FISH for AML1/ETOFISHSodium Heparin Blood (3ml), Bone marrow5 daysSeveral recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasia-related features when 20% or more blood or marrow blasts are present.
32FISH for MLLFISHSodium Heparin Blood (3ml), Bone marrow5 daysA number of recurrent chromosomal abnormalities have been shown to have prognostic significance in acute lymphoblastic leukemia, especially in B-precursor ALL. Some chromosomal abnormalities, such as high hyperdiploidy and the TEL-AML1 fusion, are associated with more favorable outcomes, while others, including the t(9;22), rearrangements of the KMT2A gene (chromosome 11q23), and intrachromosomal amplification of the AML1 gene (iAMP21), are associated with a poorer prognosis.
33FISH for 11q (ATM)FISHSodium Heparin Blood (3ml), Bone marrow5 daysDetecting a neoplastic clone associated with the common chromosome abnormalities seen in patients with chronic lymphocytic leukemia (CLL) . Identifying and tracking known chromosome abnormalities in patients with CLL and tracking response to therapy.
34FISH for 17p (p53)FISHSodium Heparin Blood (3ml), Bone marrow5 daysDetecting a neoplastic clone associated with the common chromosome abnormalities seen in patients with chronic lymphocytic leukemia (CLL) . Identifying and tracking known chromosome abnormalities in patients with CLL and tracking response to therapy.
35FISH for PDGFR ALPHAFISHSodium Heparin Blood (3ml), Bone marrow5 daysIn 2008 the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues introduced a new category for myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1. Many of these cases present as a myeloproliferative neoplasm, usually with eosinophilia.
36FISH for PDGFR BETAFISHSodium Heparin Blood (3ml), Bone marrow5 daysIn 2008 the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues introduced a new category for myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB, or FGFR1. Many of these cases present as a myeloproliferative neoplasm, usually with eosinophilia.
37FISH for PML RARAFISHSodium Heparin Blood (3ml), Bone marrow5 daysSeveral recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasia-related features when 20% or more blood or marrow blasts are present.
38FISH for BCR ABLFISHSodium Heparin Blood (3ml), Bone marrow5 daysChronic myelogenous leukemia (CML) is genetically characterized by the presence of the reciprocal translocation t(9;22)(q34;q11), resulting in a BCR/ABL gene fusion on the derivative chromosome 22, called the Philadelphia (Ph) chromosome. The same translocation can also be found in acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) with some variation in the breakpoint region. Glivec (Imatinib Mesylate) treatment targeting the BCR/ABL active tyrosine kinase has become a major drug in treating CML, gastrointestinal stromal tumors, and other cancers.
39FISH for TRISOMY 8FISHSodium Heparin Blood (3ml), Bone marrow5 daysThe myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3).
40FISH- ALL Panel (Acute Lymphoblastic Leukemia)E2A, MLL, BCR-ABL, Tel/AMLFISHSodium Heparin Blood (3ml), Bone marrow5 daysIn the United States the incidence of acute lymphoblastic leukemia (ALL) is roughly 6,000 new cases per year (as of 2009), or approximately 1 in 50,000. ALL accounts for approximately 70% of all childhood leukemia cases (ages 0 to 19 years), making it the most common type of childhood cancer. Approximately 85% of pediatric cases of ALL are B-cell lineage (B-ALL) and 15% are T-cell lineage (T-ALL). It has a peak incidence at 2 to 5 years of age. The incidence decreases with increasing age, before increasing again at around 50 years of age. ALL is slightly more common in males than females. There is an increased incidence of ALL in individuals with Down syndrome, Fanconi anemia, Bloom syndrome, ataxia telangiectasia, X-linked agammaglobulinemia, and severe combined immunodeficiency. The overall cure rate for ALL in children is about 90% and about 45% to 60% of adults have long-term disease-free survival. CRLF2/IGH rearrangements are more commonly observed in patients with Down syndrome or of Hispanic descent.
41FISH - AML Panel (AcuteMyelogenous Leukemia)Inv16, PML-RARA, MLL, AML/ETOFISHSodium Heparin Blood (3ml), Bone marrow5 daysIdentify prognostically important abnormalities in newly diagnosed acute myelogenous leukemia (AML). Monitor response to therapy with specific probes (CHRFISHI) or progression of disease with probe panel. Adjunct to conventional cytogenetic studies.
42FISH - CLL Panel (Chronic Lymphocytic Leukemia)ATM/TP53, DLUEFISHSodium Heparin Blood (3ml), Bone marrow5 daysPrognostically stratify chronic lymphocytic leukemia (CLL) patients into risk groups, For individuals who have been diagnosed with CLL by clinical criteria. Lymphocytosis of greater than 5x109 cells/μL. >50% mature-appearing lymphocytes. Characteristic immunophenotype of CD5, CD19, CD20, and CD23 expression, monoclonal kappa or lambda expression, and dim surface immunoglobin expression
43FISH - MDS Panel (Myelodysplastic Syndrome)5q,7q,20qFISHSodium Heparin Blood (3ml), Bone marrow5 daysDetecting a neoplastic clone associated with the common chromosome abnormalities seen in patients with myelodysplastic syndromes or other myeloid malignancies. Evaluating specimens in which standard cytogenetic analysis is unsuccessful. Identifying and tracking known chromosome abnormalities in patients with myeloid malignancies and tracking response to therapy.
44FISH- MM Panel (Multiple Myeloma)ATM/TP53, DLUE, IGHFISHSodium Heparin Blood (3ml), Bone marrow5 daysAids in stratifying individuals with newly identified multiple myeloma (MM) into risk groups for • Prognostic counseling • Selection and sequencing of therapy
45Chimerism- STR (Short Tandem Repeat) Genotypingposttransplant monitoring by STR GenotypingPCR and Capillary ElectrophoresisEDTA whole blood (3ml)7 daysImportant clinical events in allogeneic bone marrow transplantation such as engraftment, relapse, and the effects of post-transplant therapies can be monitored on a molecular level by detecting genetic differences between recipient and donor, to help guide clinical decision making
46Beta Thalassemia (HBB)All Exons of HBBSanger SequencingEDTA Blood7 daysBeta globin gene (HBB) sequencing can be used to identify haemoglobin variants and the most common beta thalassemia mutations, including beta plus and beta zero thalassemias. It also identifies hyperunstable haemoglobin variants and dominant beta thalassemia mutations, as well as other haemoglobin variants that cannot be identified by protein methods. Some haemoglobin disorders will not be detected by beta globin gene sequencing, such as large deletional mutations and crossover events. As such, the results of this test should always be interpreted within the context of the protein studies and RBC indices.
47Factor II (G20210A) Mutation- prothrombin DeficiencyMutation G20210A of Prothrombin geneReal Time PCRWhole blood 3ml in EDTA vacutainer2 daysOrder to detect prothrombin c.*97G>A (G20210A) pathogenic variant
48Leiden Factor V (G1691A) mutation AnalysisMutation G1691A of FV geneReal Time PCRWhole blood 3ml in EDTA vacutainer2 daysFactor V Leiden mutation testing should be reserved for patients with clinically suspected thrombophilia and: 1) APC-resistance proven or suspected by a low or borderline APC-resistance ratio, or 2) a family history of factor V Leiden.
49MTHFR Mutation AnalysisExons 5 & 8 of MTHFR geneReal Time PCRWhole blood 3ml in EDTA vacutainer2 daysDirect mutation analysis for the MTHFR C677T and A1298C mutations should be reserved for patients with coronary artery disease, acute myocardial infarction, peripheral vascular artery disease, stroke, or venous thromboembolism who have increased basal homocysteine levels or an abnormal methionine-load test.
50Alpha Thalassemia (HBA) (del/dup)HBA1, HBA2, α3.7, HS-40digital PCRWhole blood 3ml in EDTA vacutainer7 daysComprehensive genetic test for detection/duplication of α thalassemia or α thalassemia trait • Detects deletional and nondeletional variants in HBA1 and HBA2.
51Sickle Cell Variants Analysis- Sickle Cell Anaemiaspecific mutationARMS PCREDTA Blood/Amniotic Fluid/ CVS7 daysSickle cell disease results in vascular occlusion and tissue ischemia, and acute or chronic organ dysfunction. Milder forms present with hemolytic anemia.
52Clinical exome sequencing.A panel of genes.NGSPreferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration. Specimen at room temperature. Also acceptable: Refrigerated. Ship in cooled container during summer months.20Clinical exome sequencing (CES) is rapidly becoming a common molecular
diagnostic test for establishing a definitive molecular diagnosis of individuals with rare genetic disorders which can allow for:
-Better understanding of the natural history/prognosis
-Targeted management (anticipatory guidance, management changes, specific therapies)
-Predictive testing of at-risk family members
-Testing and exclusion of disease in siblings or other relatives
-Recurrence risk assessment
-Reproductive decision-making
Serving as a second-tier test for patients in whom previous genetic testing for specific syndromes was negative Providing a potentially cost-effective alternative to establishing a molecular diagnosis compared to multiple independent molecular assays
53Tuberous SclerosisCoding region and certain intronic padding region of the TSC1 and TSC2 genes associated with Tuberous Sclerosis.Next-Generation SequencingPreferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration20 daysThis test is used to screen for mutations in the genes responsible for TSC. This test helps in determining the necessity for screening in other family members. In cases of a positive finding in a patient of child bearing age, Preimplantation genetic diagnosis can be performed in most cases to help conceive a child without the pathogenic mutation.
54Diamond Blackfan Anaemia PanelCoding region along with certain intronic padding region of RPL5, RPL11, RPL35A, RPS7, RPS10, RPS17, RPS19, RPS24 and RPS26 genes are associated with Diamond Blackfan Anaemia.Next-Generation SequencingPreferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration20 daysThis test is used to screen for mutations in the genes responsible for DBFAP. This test helps in determining the necessity for screening in other family members. In cases of a positive finding in a patient of child bearing age, Preimplantation genetic diagnosis can be performed in most cases to help conceive a child without the pathogenic mutation.
55BCR-ABL1 TKI/ Imatinib resistance mutation screentargeted regionsNext-Generation SequencingEDTA Blood12 daysTKI resistance mutation analysis has resulted in a significantly improved prognosis, response rate, overall survival, and patient outcome in CML patients