Facilities at the Genetics and PGT Laboratory
Our state-of-the-art laboratory offers Cytogenetic tests such as Karyotyping and FISH (fluorescence in situ hybridization) as well as Molecular Genetic tests like PCR (Polymerase Chain Reaction) for many single gene disorders.
Cytogenetic tests are carried out on suspicion of a chromosome anomaly in newborns, children, adults, the unborn child in high-risk pregnancies or an aborted fetus (products of conception). They are also carried out in patients with blood cancer or leukemia and help in their diagnosis and management. Tissue culture is done in a majority of cytogenetic tests, hence strict aseptic precautions are necessary for sample collection. Karyotyping involves the analysis of all 23 pairs of chromosomes. The rapid FISH test is used when certain specific chromosome abnormalities are suspected. We also offer FISH testing on formalin-fixed paraffin-embedded (FFPE) tumour tissue sections and FISH for bladder cancer.
Molecular tests are carried out for different single gene disorders such as Y chromosome microdeletions (30 different loci), MTHFR and Prothrombin gene mutations, beta thalassemia mutations and Periodic Fever Syndromes.
Karyotyping is a detailed analysis of chromosomes to detect abnormalities of the number or structure of chromosomes. The chromosomes are obtained from peripheral blood, bone marrow aspirates, chorionic villi, amniotic fluid and different tissues from a miscarried fetus. These tissues are cultured for short and long term duration and chromosomes are obtained. The metaphases are fixed on slides, Geimsa banded, mapped and analyzed for abnormalities. We have the Zeiss/Metasystems automated karyotyping workstations where images of the metaphases are captured, processed and stored. Numerical and structural chromosome abnormalities such as trisomies, monosomies, deletions, duplications, inversions and translocations can be detected. Chromosomal breaks also can be analyzed using special techniques.
Fluorescence in situ hybridization (FISH) is a rapid procedure to detect common chromosome abnormalities. We mainly use directly labeled commercially available FISH probes which are complementary to the region of interest on a particular chromosome. The analysis is usually done by counting coloured dots under a fluorescent microscope. The cells are pretreated and fixed on slides. The slides are dehydrated, co-denatured with an appropriate probe, hybridized, washed and mounted in antifade solution together with counterstain. The FISH signals are observed under a fluorescence microscope using appropriate filters and the images are captured and analyzed with the software.
FISH is a rapid technique to detect common aneuploidies, microdeletions and low-grade mosaicism mainly in infertility cases, prenatal diagnosis, products of conception and pediatric cases.
Common translocations, deletions, duplications in leukemia can be analysed for diagnosis and to determine response to therapy. Chromosome analysis by FISH is possible even on interphase nuclei.
Bladder cancer can be checked by FISH on urine cells.
We carry out FISH on FFPE Tumor tissue to check for HER2/neu amplification in case of breast cancer as well as for other cancers (various other genes).
Polymerase Chain Reaction (PCR) is an in vitro DNA amplification procedure that can quickly isolate and amplify a specific segment of DNA by as much as a billion fold. This involves several steps that allow a specific DNA sequence to be replicated several times and then rapidly analyzed by electrophoresis. We detect mutations like Y chromosome microdeletions by multiplex PCR in severe male factor infertility. PCR is also used in gene disorders like Beta Thalassemia, Periodic Fever Syndromes, mutation detection in the MTHFR and the Prothrombin gene.
Tests offered for infertility management:
- Blood karyotyping for individuals with infertility / Poor Obstetric outcome / Repeated Spontaneous Abortions /Repeated Implantation Failure
- Sperm DNA Fragmentation Index (DFI)
- Sperm FISH for chromosomal aneuploidy (chromosomes 13,18, 21, X, Y or any other specific chromosome if required)
- Y chromosome microdeletion detection (PCR for 30 mutations)
- FISH for SRY (sex determining region Y) deletion/translocation
- FISH on Follicular Fluid in case of IVF procedures
- FISH for detection of low grade chromosomal mosaicism on different tissues such as blood, buccal cells, urine.
- FISH for Sex Chromosome Mosaicism (Turner/Klinefelter Syndrome) from Blood /Buccal cells
- FISH for presence or absence of SRY in case of XY female or XX male
Bad Obstetric History (BOH) Panel:
- Blood karyotype with variants analysis
- Products of conception (POC) karyotype
- FISH for common chromosomal aneuploidies (13, 18, 21, X and Y) in POC
- Low-grade mosaicism detection by FISH
- FISH for Sex chromosome mosaicism (Turner/Klinefelter Syndrome)
- FISH for presence or absence of SRY in case of XY female or XX male
- MTHFR mutation analysis
- Prothrombin mutation analysis
Post natal tests:
a) Karyotyping, Microdeletion Syndromes detection:
i) Blood karyotype
ii) FISH for aneuploidy and microdeletion syndromes
- 13 & 21 and/or 18, X & Y
- Down Syndrome/Trisomy 21
- Edward Syndrome/Trisomy 18
- Patau Syndrome/Trisomy 13
- Prader Willi Syndrome
- Angelman Syndrome
- Deletion of SNRPN region
- Williams Syndrome
- DiGeorge Syndrome
- Velocardiofacial Syndrome
- Deletion 22q Syndrome /CATCH 22
- Cri-du-chat Syndrome or 5p deletion
- Wolf Hirschhorn Syndrome (WHS) or 4p deletion
- SRY deletion/translocation
- Low-grade mosaicism detection
- Sex chromosome mosaicism (Turner/Klinefelter Syndrome)
- Presence or absence of SRY in case of XY female or XX male
b) Chromosomal Breakage Studies:
Chromosome Breakage Study for
- Ataxia telangiectasia
- Fanconi’s Anemia /Chromosome stress test
- Bloom’s/Cockayne Syndrome (Sister Chromatid Exchange Analysis)
c) Periodic Fever Syndrome / Autoinflammatory Disorders testing:
- FMF Testing (MEFV gene exon 10- 29 mutations)
- FMF Testing (MEFV gene) exons 2, 5
- Crohn’s Disease (NOD2/CARD15 genes) R702W, G908R, 1007fs
- Crohn’s Disease (NOD2/CARD15 genes) exon 4 (parts 1-5)
- Blau Syndrome (NOD2/CARD15) exon 4 (parts 1-5)
- CAPS (CIAS1) exon 3 for MWS, FCAS and NOMID (parts 1 -4)
- HIDS testing (MVK) exon 9 (I268T) and exon 11 (V377I)
- TRAPS testing (TNFRSF1) exons 2, 3 (2+3), 4, 5 (4+5)
- TRAPS Testing (TNFRSF1) exons 6, 7
- DIRA (ILRN) sequencing exons 1-4
- DIRA breakpoint assay 175kb deletion
- DAD2 testing (CECR1) 9 exons
d) Other Molecular testing:
- DNA extraction and storage from different tissues.
- Beta thalassemia for 6 common Indian mutations
- Beta thalassemia for additional 14 common Indian mutations
- Beta thalassemia for 20 common Indian mutations
- HbS mutation detection for Sickle Cell Anemia
- HbE mutation detection
- MTHFR mutations C677T and A1298C
- Prothrombin Gene mutation
Prenatal Genetic Diagnosis:
Karyotyping on
- CVS
- Amniotic Fluid
- Cord Blood
FISH for
- Aneuploidies (13, 18, 21, X and Y or 13, 21 or 18, X, Y and/or 16, 22)
- Microdeletion syndrome (Uncultured cells or cultured metaphases)
Molecular testing for
- Beta-thalassemia prenatal test with VNTR analysis for maternal cell contamination
- HbS prenatal test with VNTR analysis for maternal cell contamination
- CVS cleaning
- DNA extraction with VNTR analysis for maternal cell contamination
- Maternal cell contamination check for external DNA
Hematological Malignancies:
i) Bone Marrow Karyotyping
ii) FISH for
- BCR-ABL/Philadelphia or Ph chromosome/t(9;22) for CML, AML
- BCR-ABL/Philadelphia or Ph chromosome/t(9;22) for ALL
- PML-RARA / t(15;17) / APML
- RARA breakapart rearrangement
- AML1-ETO / RUNX1T1-RUNX1 / t(8;21)
- Inversion 16 (CBFB)/t(16;16)
- Burkitt’s Lymphoma / (8q24) /(c-Myc) rearrangement
- MLL (11q23) rearrangement
- IGH (14q32) rearrangement
- Del 5q (EGR1)
- Del 7q (D7S486)
- Del 20q (20qter)
- Trisomy 8
- TEL-AML /ETV6-RUNX1 / t(12;21)
- BCL2 (Non Hodgkins Lymphoma NHL)
- RB1 (13q) deletion
- Hyper-eosinophilic syndrome (4q12) (FIP1L1-PDGFRA)
- Deletion MYB or deletion 6q
- t(1;19) or TCF3/PBX1
- t(3;3)/inversion 3/RPN1-MECOM
- t(4;14)/ IGH-FGFR3
- t(14;16) / IGH-MAF
- t(14;18)/ IGH-BCL2
- 1p loss/deletion and 1q gain /amplification
- BCL6 breakapart rearrangement
- PDGFRB breakapart rearrangement
- TRAD/14q11
- Multiple Myeloma on isolated CD138+ cells (Chr. 12, Del 13q, Del p53, Del ATM and IGH) / t(4;14) / t(14;16)
- CLL (Chr. 12, Del 13q, Del p53 and Del ATM)
- Post BMT XX/XY chimerism (Sex mismatched BMT)
Other malignancies:
FISH for
- Bladder cancer/ hematuria by Urovysion panel
- HER2/neu (ErbB2) on formalin fixed paraffin embedded (FFPE) tissue blocks for breast cancer / ovarian cancer / esophageal cancer
- FFPE (formalin fixed paraffin embedded) tissues for other cancers