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Molecular genetic tests based on both DNA and RNA from tumor tissues, blood samples and cell-free tumor DNA are provided for cancers of Lung, Gastro-intestinal, Urogenital, Breast & Ovarian, Blood and Central nervous system regions. Following are the list of specific tests offered in the laboratory.

EGFR (TK Domain) Mutation screening

Order Name EGFR (Ex 18-21) Sequencing
Test Method FFPE Total nucleic acid extraction Sanger sequencing of Exon 18-21 of EGFR gene
Test Description The test should be able to identify any point mutation in the four exonic regions (from 18 to 21) including the splice site regions of the introns. While other tests could detect only certain selective mutations in the gene, our test should be able to detect any/all mutations in the regions so that any novel mutations in the region will also be reported. Also, our test should be able to detect deletions/duplications of the gene region. Also, this can detect the novel chemo-resistance mutation of EGFR (T790M).
Test Indication For Non-small cell lung cancers (NSCLC), diagnosed by histopathological examination currently have a better treatment in terms of both survival rate and quality of life index by selective Tyrosine Kinase Inhibitors which have specific activating mutations in the Tyrosine Kinase Domain of the EGFR gene. About 30% subjects with advanced stage of lung adenocarcinoma (Stage III and above) has been shown to have this type of mutations from Asian populations.
Sample Histopathology screened FFPE tumor tissue sections. From outside centers, please bring in tissue block and tissue slide for an in-house histopathology review. Histopathology review is necessary for sample adequacy.
Turn Around Time 1 week (after collection of sample)

ROS1 Fusion RT-PCR panel

Order Name ROS1 Fusion Panel RT-PCR
Test Method FFPE Total nucleic acid extraction and Multiplex Qualitative RT-PCR & Sanger sequencing
Targets ROS1 fusion transcripts 15 different break points of ROS1-SLC34A2, ROS1-CD74, ROS1-SDC4, ROS1-EZR, ROS1-LRIG3, ROS1-TPM3, ROS1-GOPC), 10 different break points of RET fusion (RET-KIF5B, RET-CCDC6, RET-NCOA, RET-TRIM33), MET (Exon 14 skipping) are checked. The amplification is compared against two controls (one Internal Control and another positive control for each set of targets.
Test Indication For Non-small cell lung cancers (NSCLC), ALK and ROS1 gene fusions are screened for prognostic and for selecting targeted chemotherapeutic management.
Sample Histopathology screened FFPE tumor tissue sections. From outside centers, please bring in tissue block and tissue slide for an in-house histopathology review. Histopathology review is necessary for sample adequacy.
TAT 1 week (after collection of sample)

EGFR T790M liquid biopsy genotyping

Order Name EGFR T790M cfDNA test
Test Method Cell-free DNA extraction and genotyping endpoint PCR
Targets EGFR T790M variant
Test Indication To assess resistance to Tyrosine Kinase Inhibitor chemotherapy and tumor evolution in NSCLC. About 1% of the EGFR mutation positive NSCLC cases, there can be resistance to Tyrosine Kinase Inhibitors such as Gefitinib. This could be due to evolution of tumor to develop rare mutant and resistant clones of cells in the tumor. This can be screened in cell-free tumor DNA in the serum of the patient. This is called liquid biopsy. We have optimized a custom-made cell-free DNA extraction technique with high yield from a low amount of whole blood sample.
Sample Whole blood sample in three (3) EDTA vacutainers.
TAT 2/3 days (after collecting the sample)

Extended RAS Sequencing

Order Name Extended RAS Sequencing (KRAS & NRAS)
Test Method Somatic gene mutation analysis by gene sequencing on DNA obtained from FFPE tumor tissue samples. Specific primers are custom synthesized, and sanger sequenced using ABI 3500® Genetic Analyzer.
Targets KRAS (Exons 2,3,4) and NRAS (Exon 2,3,4)
Test Indication Extended RAS genes, which includes exon 2, 3, and 4 of KRAS and exon 2, 3, and 4 of NRAS, are sequenced for various cancers such as Lung, colorectal, gastro-intestinal, genitourinary cancers. These three exons comprise almost all the mutations described in these two genes.
Sample Histopathology screened FFPE tumor tissue sections. From outside centers, please bring in tissue block and tissue slide for an in-house histopathology review. Histopathology review is necessary for sample adequacy.
TAT 1 week (after collection of sample)

BRAF V600E/Ksomatic genotyping

Order Name BRAF V600E/K Real-Time PCR
Test Method FFPE total nucleic acid extraction and real-time PCR for targeted mutation analysis.
Targets BRAF V600E, V600K
Test Indication BRAF mutations, V600E/K is a known driver mutation for lung, gastrointestinal, thyroid, dermatological cancers.
Sample Histopathology screened FFPE tumor tissue sections. From outside centers, please bring in tissue block and tissue slide for an in-house histopathology review. Histopathology review is necessary for sample adequacy.
TAT 1 week (after collection of sample)

BRAF Fusion Panel Multiplex RT-PCR analysis

Order Name BRAF fusion
Test Method FFPE total nucleic acid extraction and Multiplex Qualitative RT-PCR
Targets Three different KIAA1549-BRAF fusion (16:9, 15:9 & 16:11) are assessed using multiplex qualitative real-time PCR test. A housekeeping gene Internal Control is also tested along with the fusion mRNA targets.
Test Indication Pediatric medulloblastoma for prognostication and assessment.
Sample Histopathology reviewed FFPE tumor sections. If sample is from outside hospitals, please bring in tissue blocks and slide for histopathology review. Histopathology review is necessary for sample adequacy.
TAT 1 week (after collection of sample)

BRAF Fusion Panel package for Pediatric Gliomas

Order Name Pediatric Glioma Panel (BRAF fusion & V600 E/K)
Test Method FFPE total nucleic acid extraction and Multiplex Qualitative RT-PCR for fusion and real-time PCR for targeted mutation analysis.
Targets Three different KIAA1549-BRAF fusion (16:9, 15:9 & 16:11) are assessed using multiplex qualitative real-time PCR test. A housekeeping gene Internal Control is also tested along with the fusion mRNA targets.
Test Indication Pediatric medulloblastoma for prognostication and assessment.
Sample Histopathology reviewed FFPE tumor sections. If sample is from outside hospitals, please bring in tissue blocks and slide for histopathology review. Histopathology review is necessary for sample adequacy.
TAT 1 week (after collection of sample)

Microsatellite Instability Analysis (MSI-PCR)

Order Name Microsatellite Instability Analysis (MSI-PCR)
Test Method Somatic DNA extraction and Multiplex Short Tandem Repeat Fragment Analysis
Targets With three new targets as recommended by the National Cancer Care Network (NCCN) (NR21, NR24, NR27) and earlier five targets according to the Bethesda Criteria, (BAT25, BAT26, D2S123, D5S346 andD17S250) are assessed for DNA mis-match repair deficiency. Additional markers such as BAT40, MYCL are also included for low microsatellite instability somatic types. Additional details on the targets and their deterministic abilities can be obtained from our reports.
Test Indication MSI is a unique mechanism in tumour development especially for colon and endometrial cancers. The derangement in DNA mis-match repair mechanism or the “mutator phenotype” is an extensively characterized molecular pathological change in those cancers in which MSI has definite therapeutic and prognostic roles. The test directly inspect five different DNA repeat markers selected according to widely accepted criteria for Hereditary Non-Polyposis Colorectal Cancer or Lynch Syndrome (Revised Bethesda Criteria) NCCN. MSI can occur in somatic and germline cells according to the condition.
Sample Histopathology reviewed FFPE tumor tissue sections (and blocks). If sample is from outside hospitals, please bring in tissue blocks and slide for histopathology review. Histopathology review is necessary for sample adequacy.
TAT 1 week (after collection of sample)

IDH Mutation Analysis

Order Name IDH 1 & 2 (Exon 4) Sequencing
Test Method Somatic FFPE DNA extraction and Sequencing
Targets The test should be able to identify any point mutation in the Exon 4 region including the splice site regions of the introns of IDH1 and IDH2 genes. While other tests could detect only certain selective mutations in the gene, our test should be able to detect any/all mutations in the regions so that any novel mutations in the region will also be reported.
Test Indication IDH mutations has been identified as one of the best molecular marker for grading and predicting the prognosis of astrocytoma. Along with 1p19q deletion cytogenetic analysis by Fluorescent in situ Hybridization analysis, IDH1&IDH2 (Exon 4) targeted mutational scanning is also routinely done for all glioma cases. Being an oncogene, IDH mutations have less variance and Exon 4 is considered to be the most common region of mutation. Our method could identify any mutation occurring in Exon 4 region of both IDH1 and IDH2 genes. This includes the most common R132H and other specific mutations as well.
Sample Histopathology reviewed FFPE tumor tissue sections (and blocks). If sample is from outside hospitals, please bring in tissue blocks and slide for histopathology review. Histopathology review is necessary for sample adequacy.
TAT 1 week (after collection of sample)

VHL gene sequencing

Order Name VHL gene sequencing test
Test Method Germline DNA extraction & Sequencing
Targets VHL Exon 1,2,3 are sequenced using specific primers. The test should be able to identify any point mutation in the three exonic regions and the splice site regions of the introns.
Test Indication Clinically suspected cases of von Hippel-Lindau syndrome (OMIM #193300) in recurrent hemangioblastoma, renal cell carcinoma, pheochromocytoma, multi-cystic pancreas, liver or kidney, or endolymphatic sac tumor of inner ear. The human VHL is a gene located in 3p25.3 and the mutations of that gene is highly associated with the syndrome. Majority of the patients with the syndrome would have non-synonymous point mutation of the gene leading on to abnormal or absence of the VHL protein which leads to the tumor syndrome.
Sample Whole blood in 3 EDTA vacutainers. (3-5 ml)
TAT 1 week (after collection of sample)

VHL Deletion/Duplication analysis

Order Name VHL gene Deletion analysis
Test Method Germline DNA extraction &Multiple Ligation Probe Amplification (MLPA) and fragment analysis.
Targets VHL Exon 1,2,3 fragments are analyzed using MLPA.The test should be able to identify any deletions/duplications of the three exonic regions and the splice site regions of the introns.
Test Indication Clinically suspected cases of von Hippel-Lindau syndrome (OMIM #193300) in recurrent hemangioblastoma, renal cell carcinoma, pheochromocytoma, multi-cystic pancreas, liver or kidney, or endolymphatic sac tumor of inner ear. The human VHL is a gene located in 3p25.3 and the mutations of that gene is highly associated with the syndrome. Majority of the patients with the syndrome would have non-synonymous point mutation of the gene leading on to abnormal or absence of the VHL protein which leads to the tumor syndrome.
Sample Whole blood in 3 EDTA vacutainers. (3-5 ml)
TAT 1 week (after collection of sample)

AML Multi-gene Panel Test (FLT3, NPM1, CEBPA)

Order Name AML Multi-gene Panel Test (FLT3, NPM1, CEBPA)
Test Method Genomic DNA extraction, target amplification sequencing and fragment analysis
Targets Targeted sanger sequencing of FLT3 Exon 14/15 & 20, NPM1 Exon 11/12 region, and entire coding region of CEBPA gene. Fragment analysis of Internal Tandem Duplication (ITD) of FLT3, and three domains of CEBPA.
Test Indication Acute Myeloid Leukemia
Sample Whole blood sample in three (3) EDTA Vacutainers. (6-10 ml)
TAT 1 week (after sample collection)

AML Combo Package Test (Multi-gene test & Fluorescent Insitu Hybridization test for gene translocations)

Order Name AML Combo Test (Multi-Gene & FISH panel)
Test Method Genomic DNA extraction, target amplification sequencing and fragment analysis& Fluorescent In-situ Hybridization
Targets Targeted sanger sequencing of FLT3 Exon 14/15 & 20, NPM1 Exon 11/12 region, and entire coding region of CEBPA gene. Fragment analysis of Internal Tandem Duplication of FLT3, and three domains of CEBPA. This includes three translocation target analysis conducted by Cytogenetics Laboratory (BCR-ABL1, PML-RAR, inv16).
Test Indication Acute Myeloid Leukemia
Sample Whole blood sample in three (3) EDTA Vacutainers. (6-10ml)
TAT 1 week (after sample collection)

NF1 Gene Deletion/Duplication Screening

Order Name NF1Gene Deletion/Duplication screening
Test Method Multiple Ligation Probe Amplification (MLPA) and fragment analysis.
Targets The test should be able to identify any deletions/duplications of the sixty exonic regions of NF1 gene including the splice site regions of the introns.
Test Indication Neurofibromatosis type 1 (NF1) is a congenital autosomal dominant neuro-cutaneous syndrome (OMIM# 162200) characterized by occurrence of multiple typed brain tumors (meningioma, schwannoma, optic glioma), with patchy skin pigmentation and tumors, skeletal and soft tissue abnormalities.
Sample Whole blood in 2 EDTA vacutainers (3-5 ml)
TAT 1 week (after collection of sample)

NF2 Deletion Screening

Order Name NF2 Gene Deletion/Duplication screening
Test Method Multiple Ligation Probe Amplification (MLPA) and fragment analysis.
Targets The test should be able to identify any deletions/duplications of the sixty exonic regions and the splice site regions of the introns.
Test Indication Neurofibromatosis type 2 (NF2) is an autosomal dominant hereditary neurocutaneous syndrome (OMIM# 162200) characterized by occurrence of recurrent brain and spinal tumors (meningioma, schwannoma, ependymoma).
Sample Whole blood in 2 EDTA vacutainers (3-5 ml
TAT 1 week (after collection of sample)

In addition to the above, the laboratory coordinates many outsourced laboratories for services such as

  • Hereditary Breast and Ovarian Cancer screening (BRCA1 & BRCA2)
  • Germline genetic screening for all cancers by Next generation sequencing of more than 30 genes including BRCA1, BRCA2, ATM, PALB2, PTEN, CHEK2, CDK, TP53, MLH1, MSH2, MSH6, PMS2, BARD1, RAD51D, RAD51C, FANCC.
  • Quantitative real-time PCR tests for BCR-ABL1, PML-RAR, inv16 etc. for hematological cancers.
  • High-throughput mRNA expression analysis and systems biology cancer screening by Nanostring® technologies on FFPE tumor samples.
  • Custom developed drug sensitivity genotyping assays (MTHFR, DPYD, CYP2C9, CYP2D6, UGTIA1 etc.)