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Research @ inDNA

Molecular Cytogenetics

Cytogenetics is the study of chromosomes that carry genetic information, the basic units of heredity. Chromosome disorders, a major category of genetic disease, are caused by errors in the number or structure in one or more genes, resulting in congenital malformations, developmental delay/intellectual disability, infertility and other abnormalities. In addition to the study of these disorders, cytogenetics has become an important tool in the diagnosis of patients with hematologic/oncologic disorders, and is used for disease classification, treatment decisions, and to monitor disease status and recovery.

The Molecular Cytogenetics Laboratory, a section of the Department of Molecular Pathology, includes staff members with expertise in cytogenetics and molecular genetic pathology. Together with our cytogenetics medical technologists and genetic counselor, this team is committed to providing the highest quality cytogenetic analysis available to complement your clinical practice. Accuracy, quality, reliable turnaround time, expert staff, and genetic counseling are all significant features of our program.

Cytogenetic studies include traditional techniques for neoplastic disorders, solid tumors and congenital disorders. In addition, high-resolution chromosome analysis and fluorescence in situ hybridization (FISH) are available on a variety of specimen types, including peripheral blood, bone marrow and tissue investigations. Chromosomal microarray is the latest technology to be added in our laboratory and is currently offered as a first-tier test in various pediatric indications including multiple congenital anomalies, intellectual disability and autism spectrum disorders.

Tests performed in our laboratory include standard cytogenetic analysis including preparation of karyotypes, metaphase and interphase based fluorescence in situ hybridization (FISH), and high resolution single nucleotide polymorphism oligonucleotide-based array (SNP array) analysis will be available soon.

Accredited by the NABL, ILAC and QMS, we provide the latest technology in molecular cytogenetic. We offer rapid turnaround for results and can further expedite lab tests in medically necessary cases. Our success rates consistently meet or exceed NABL standards.

In addition, our laboratory is at the forefront of developing new assays like spectral karyotyping (SKY) and bringing new tests online. We are rapidly growing group of clinical cytogenetic and molecular genetics laboratories committed to improving the quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies. The Molecular Pathology laboratories also function as core facilities for translational molecular research programs and the extraction and storage of DNA and RNA for multiple investigators. We can store and preserve pellets/specimens for future investigations.

The Molecular Cytogenetic Laboratory actively and routinely participates in the training and education of various types of students, medical residents, fellows and house staff to promote proper utilization and interpretation of molecular tests. In a climate of rapidly changing technology and increasing applications of molecular testing, these educational activities are vital to the continued success and innovation at inDNA Lifesciences Pvt. Ltd.

PCR

Molecular diagnostic assays detect nucleic acid (DNA or RNA) of infectious disease agents within test specimens. Test specimens may be swabs, fluids, blood, or tissues. A test simply designated as “PCR” is a polymerase-chain-reaction test to detect DNA and is composed of 3 basic parts:

  • Extraction of the DNA from the sample.
  • Addition of sample DNA, one set of DNA nucleotide primers and other reagents to a PCR-cycler machine for amplification of target DNA.
  • Detection of target DNA by gel-electrophoresis.

RT-PCR

RT-PCR is a reverse-transcriptase PCR test to detect RNA and is composed of the same 3 basic parts as PCR and an additional step using reverse-transcriptase enzyme to synthesize complementary DNA from the target RNA. The complementary DNA is then run in the PCR test.

Nested PCR

Nested PCR is a modification that uses 2 sets of nucleotide primers and 2 complete cycles of amplification; the second cycle of amplification further amplifies a target fragment of DNA originating within an already amplified larger target fragment of DNA. Nested PCR results in higher sensitivity than simple PCR or RT-PCR and is used for diseases that have very little target nucleic acid in tissue samples.

Real Time PCR

Real Time PCR (also called quantitative PCR) is the same as PCR except that it simultaneously amplifies and quantitates the amount of DNA after each PCR cycle. It is based on the detection and quantitation of fluorescence of a reporter dye attached to DNA probe which is specific for the amplified DNA of interest (target). The test is very specific and about 10,000 more sensitive than conventional PCR in detecting DNA.

Next Generation Sequencing

Characterizing genomic aberrations in tumors for predictive and prognostic purposes by genome sequencing has become an integral part of the precision medicine approach. The revolutionary second- or next-generation sequencing (NGS) technologies provide a viable alternative because of their massively parallel sequencing capability, which enables the simultaneous screening of multiple genes in multiple samples.

Compared with earlier genome characterization techniques, NGS technologies possess distinct advantages more suitable to addressing the challenges associated with the increasing demands for testing of multiple gene markers with lower inputs of nucleic acids. The foremost advantage of the NGS technologies is the massively parallel sequencing capability. For routine tumor sequencing, this feature facilitates simultaneous sequencing of multiple targeted genomic regions in multiple samples in the same run. This is a very important advantage that enables screening of large numbers of samples while keeping short turnaround time for timely clinical reporting.

More importantly, screening multiple markers with NGS technology requires a single input of relatively low-quantity DNA or RNA in contrast to traditional sequencing technologies, which need cumulatively larger quantities of input nucleic acid. This also decreases the overall cost of multiple-marker screening compared with the costs of low- and medium-throughput platforms. In addition, NGS is able to provide simultaneous screening of a variety of genomic aberrations such as single-nucletide variants (SNVs), multiple-nucleotide variants (MNVs), small and large insertions and deletions, and copy number variation (CNVs) of the genes. In NGS, on average, the targeted areas of interest are repeatedly sequenced hundreds and even thousands of times, providing high sensitivity and confidence for mutation detection. NGS is also quantitative as the allelic fraction of the mutation can be gleaned by the number of DNA strands with mutation in the background of strands with the wild-type sequence. These considerable advantages make NGS very desirable for routine clinical sequencing of tumors.