Clinical Genomics
| SR NO | TEST | TEST COMPONENTS | METHOD | SPECIMEN/TRANSPORT | TAT | CLINICAL APPLICATIONS |
|---|---|---|---|---|---|---|
| 1 | BCR-ABL fusion-transcript Qualitative Analysis | Qualitative detection of BCRABL gene | PCR | Bone marrow, EDTA whole blood (3ml) | 5 days | Initial diagnosis of patients suspected to be suffering from CML or ALL for the presence of the BCR/ABL translocation. |
| 2 | BCR-ABL fusion-transcript Multiplex Qualitative Analysis | Detection of different transcripts | Multiplex qualitative PCR | Bone marrow, EDTA whole blood (3ml) | 5 days | Initial 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 |
| 3 | BCR-ABL International Scale Quantitative Analysis | e13a2 & e14a2 transcript detection | Real Time PCR | Bone marrow, EDTA whole blood (3ml) | 3 days | Initial 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 |
| 4 | Minor BCR-ABL | e1a2 transcript detection | Real Time PCR | Bone marrow, EDTA whole blood (3ml) | 3 days | Diagnostic 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 |
| 5 | PML-RARA α Qualitative Analysis | BCR1,BCR2,BCR3 transcript detection | Real Time PCR | Bone marrow, EDTA whole blood (3ml) | 3 days | APL 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. |
| 6 | PML-RARA α Quantitative Analysis | BCR1,BCR2,BCR3 transcript detection | Real Time PCR | Bone marrow, EDTA whole blood (3ml) | 3 days | APL 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. |
| 7 | JAK2 V617F mutation study | V617F mutation | PCR | Bone marrow, EDTA whole blood (3ml) | 2 days | Detection of the JAK2 V617F is useful to help establish the diagnosis of MPN |
| 8 | JAK2 mutation panel (Exon 12 - 15) Analysis | EXON 12-15 | Sanger Sequencing | Bone marrow, EDTA whole blood (3ml) | 7 days | Diagnose and manage classic BCR-ABL1-negative myeloproliferative neoplasms (MPNs) |
| 9 | NPM1 (Nucleophosmin) Mutation Analysis | Exon 12 | Sanger Sequencing | Whole blood 3ml in EDTA vacutainer | 7 days | As a prognostic indicator in patients with newly diagnosed acute myelogenous leukemia with normal karyotype and no FLT3 mutation |
| 10 | FLT3 Mutation Analysis | Exon 20 with ITD | Sanger Sequencing | Bone marrow, EDTA whole blood (3ml) | 7 days | Prognostication of AML. |
| 11 | CALR (Calreticulin) Mutation Analysis | Exon 9 | Sanger Sequencing | Bone marrow, EDTA whole blood (3ml) | 7 days | Use for diagnostic and prognostic information in patients with MyeloProliferative Neoplasms (MPNs) when JAK2 testing is negative. |
| 12 | CEBPA mutation Analysis | Sanger Sequencing | Bone marrow, EDTA whole blood (3ml) | 7 days | Initial evaluation of Acute Myeloid Leukemia, both for assigning an appropriate diagnostic subclassification and as an aid for determining prognosis. | |
| 13 | Myeloproliferative leukemia (MPL1) mutation Analysis | Exon 10 | Sanger Sequencing | Bone marrow, EDTA whole blood (3ml) | 7 days | May be useful when Essential Thrombocythemia or Idiopathic Myelofibrosis is suspected in JAK2 V617F negative individuals. |
| 14 | ALL PCR panel | Minor BCR-ABL, TEL/AML1, E2A, FISH MLL, Bone Marrow Karyotyping | RT-PCR | Bone marrow, EDTA whole blood (3ml) | 7 days | Risk stratification and therapeutic management in children and adult with newly diagnosed ALL |
| 15 | AML PCR panel | PML-RARA Quantitative, Inv16, AML/ETO, FISH MLL, Bone marrow Karyotyping | RT-PCR | Bone marrow, EDTA whole blood (3ml) | 7 days | Evaluation of acute Myeloid Leukemia (AML) at the time of diagnosis, to assist in appropriate classification and prognosis using five translocation gene panel and karyotyping. |
| 16 | AML prognostic PCR panel | PML-RARA Quantitative, Inv16, AML/ETO, FLT3, NPM1, FISH MLL, Bone marrow Karyotyping | RT-PCR | Bone marrow, EDTA whole blood (3ml) | 7 days | For accurate diagnosis, prognosis and monitoring of acute myeloid leukemia |
| 17 | MPL PCR Panel | BCR-ABL multiplex, JAK2 PCR, JAK2 Panel, CALR, MPL1, Bone Marrow Karyotyping | RT-PCR | Bone marrow, EDTA whole blood (3ml) | 7 days | This reflex test sequentially evaluates for the common major gene mutations associated with non-BCR/ABL1-positive myeloproliferative neoplasms until a mutation is identified. |
| 18 | Karyotyping- Bone Marrow | All Chromosomes | Culture Karyotyping | Bone marrow | 7 days | To diagnose congenital chromosomal abnormalities, including aneuploidy, structural abnormalities, and balanced rearrangements |
| 19 | FISH for del(13q) | Chromosome 13 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | 13q 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. |
| 20 | FISH for del(5q) | chromosome 5 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | The 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). |
| 21 | FISH for del(7q) | chromosome 7 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | The 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). |
| 22 | FISH for del(20q) | chromosome 20 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | The 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). |
| 23 | FISH for detection OF E2A | Chromosome 1, 17 and 19 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Acute 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. |
| 24 | FISH for FGFR3/IgH | Chromosome 4 and 14 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Genetic 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. |
| 25 | FISH for IgH | Chromosmoe 4 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Chromosomal 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. |
| 26 | FISH for Inv(16) | chromosome 16 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Several 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. |
| 27 | FISH for MAF/IgH | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Genetic 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. | |
| 28 | FISH for MYEOV/IgH | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Genetic 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. | |
| 29 | FISH for TEL/AML | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | A 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. | |
| 30 | FISH for TRISOMY 12 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | 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. | |
| 31 | FISH for AML1/ETO | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Several 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. | |
| 32 | FISH for MLL | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | A 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. | |
| 33 | FISH for 11q (ATM) | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Detecting 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. | |
| 34 | FISH for 17p (p53) | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Detecting 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. | |
| 35 | FISH for PDGFR ALPHA | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | In 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. | |
| 36 | FISH for PDGFR BETA | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | In 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. | |
| 37 | FISH for PML RARA | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Several 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. | |
| 38 | FISH for BCR ABL | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Chronic 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 tyrosine kinase has become a major drug in treating CML, gastrointestinal stromal tumors, and other cancers. | |
| 39 | FISH for TRISOMY 8 | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | The 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). | |
| 40 | FISH- ALL Panel (Acute Lymphoblastic Leukemia) | E2A, MLL, BCR-ABL, Tel/AML | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | In 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. |
| 41 | FISH - AML Panel (AcuteMyelogenous Leukemia) | Inv16, PML-RARA, MLL, AML/ETO | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Identify 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. |
| 42 | FISH - CLL Panel (Chronic Lymphocytic Leukemia) | ATM/TP53, DLUE | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Prognostically 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 |
| 43 | FISH - MDS Panel (Myelodysplastic Syndrome) | 5q,7q,20q | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Detecting 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. |
| 44 | FISH- MM Panel (Multiple Myeloma) | ATM/TP53, DLUE, IGH | FISH | Sodium Heparin Blood (3ml), Bone marrow | 5 days | Aids in stratifying individuals with newly identified multiple myeloma (MM) into risk groups for • Prognostic counseling • Selection and sequencing of therapy |
| 45 | Chimerism- STR (Short Tandem Repeat) Genotyping | posttransplant monitoring by STR Genotyping | PCR and Capillary Electrophoresis | EDTA whole blood (3ml) | 7 days | Important 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 |
| 46 | Beta Thalassemia (HBB) | All Exons of HBB | Sanger Sequencing | EDTA Blood | 7 days | Beta 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. |
| 47 | Factor II (G20210A) Mutation- prothrombin Deficiency | Mutation G20210A of Prothrombin gene | Real Time PCR | Whole blood 3ml in EDTA vacutainer | 2 days | Order to detect prothrombin c.*97G>A (G20210A) pathogenic variant |
| 48 | Leiden Factor V (G1691A) mutation Analysis | Mutation G1691A of FV gene | Real Time PCR | Whole blood 3ml in EDTA vacutainer | 2 days | Factor 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. |
| 49 | MTHFR Mutation Analysis | Exons 5 & 8 of MTHFR gene | Real Time PCR | Whole blood 3ml in EDTA vacutainer | 2 days | Direct 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. |
| 50 | Alpha Thalassemia (HBA) (del/dup) | HBA1, HBA2, α3.7, HS-40 | digital PCR | Whole blood 3ml in EDTA vacutainer | 7 days | Comprehensive genetic test for detection/duplication of α thalassemia or α thalassemia trait • Detects deletional and nondeletional variants in HBA1 and HBA2. |
| 51 | Sickle Cell Variants Analysis- Sickle Cell Anaemia | specific mutation | ARMS PCR | EDTA Blood/Amniotic Fluid/ CVS | 7 days | Sickle cell disease results in vascular occlusion and tissue ischemia, and acute or chronic organ dysfunction. Milder forms present with hemolytic anemia. |
| 52 | Clinical exome sequencing. | A panel of genes. | NGS | Preferred 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. | 20 | Clinical 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 |
| 53 | Tuberous Sclerosis | Coding region and certain intronic padding region of the TSC1 and TSC2 genes associated with Tuberous Sclerosis. | Next-Generation Sequencing | Preferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration | 20 days | This 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. |
| 54 | Diamond Blackfan Anaemia Panel | Coding 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 Sequencing | Preferred sample EDTA Blood (3ml x 3) Amniotic Fluid/ CVS will be accepted based on clinical criteria on special consideration | 20 days | This 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. |
| 55 | BCR-ABL1 TKI/ Imatinib resistance mutation screen | targeted regions | Next-Generation Sequencing | EDTA Blood | 12 days | TKI resistance mutation analysis has resulted in a significantly improved prognosis, response rate, overall survival, and patient outcome in CML patients |
| SR NO | TEST | TEST COMPONENTS | METHOD | SPECIMEN/TRANSPORT | TAT | CLINICAL APPLICATIONS |