Hi-C Sequencing and Analysis Test
Short Name: Hi-C Sequencing
Also known as: Hi-C, Chromatin Conformation Capture Sequencing, 3D Genome Sequencing
Hi-C Sequencing and Analysis Test test available at DNA Labs India for ₹185,000. Uses Hi-C library preparation, Next-generation sequencing (Illumina), Bioinformatics analysis on Extracted DNA samples. Results in Reports are typically delivered within 10 weeks from the date of sample receipt.. Free home collection in 300+ cities across India.
🩺 Medically Reviewed By
Dr Pasupathy Arumugam
Consultant Pathologist · Reg: 21521
Last reviewed: September 7, 2026
Overview
The purpose of Hi-C sequencing is to map the 3D architecture of the genome, revealing how chromatin folds and interacts within the nucleus. This information is crucial for understanding gene regulation, identifying disease-associated chromatin interactions, and discovering novel regulatory domains. In a clinical context, Hi-C can help diagnose genetic disorders caused by structural variants that disrupt chromatin organization, and it can uncover mechanisms underlying cancer and other diseases.
- Test Code
- 6360
- CPT Code
- Not applicable
- ICD Code
- Not applicable
- Price
- ₹185,000
- Sample Type
- Extracted DNA
- Result Time
- Reports are typically delivered within 10 weeks from the date of sample receipt.
- Fasting Required
- No
- Method
- Hi-C library preparation, Next-generation sequencing (Illumina), Bioinformatics analysis
Sample Collection
No special preparation is required. However, ensure that the sample is collected in a DNAase-free tube and transported on ice to maintain DNA integrity.
Method: Blood draw or tissue biopsy (DNA extraction)
Laboratory Analysis
The sample collection involves a standard blood draw or tissue biopsy. For blood, 5-10 mL of whole blood is collected in an EDTA tube. For tissue, a biopsy is performed by a healthcare professional.
Report Delivery
The sample should be sent to the laboratory immediately. DNA extraction will be performed, and the extracted DNA will be used for Hi-C library preparation.
Timeline: Reports are typically delivered within 10 weeks from the date of sample receipt.
Patient Instructions
About This Test
Who Should Get This Test
The purpose of Hi-C sequencing is to map the 3D architecture of the genome, revealing how chromatin folds and interacts within the nucleus. This information is crucial for understanding gene regulation, identifying disease-associated chromatin interactions, and discovering novel regulatory domains. In a clinical context, Hi-C can help diagnose genetic disorders caused by structural variants that disrupt chromatin organization, and it can uncover mechanisms underlying cancer and other diseases.
How to Prepare
- Use EDTA-containing tubes for blood collection
- Avoid repeated freeze-thaw cycles
- Store at 2-8°C for up to 24 hours before processing
- For tissue samples, snap-freeze in liquid nitrogen and transport on dry ice
Doctor's Notes
Reviewed by Dr Pasupathy Arumugam — MBBS, MD (Pathology) · Reg. No. 21521
"Hi-C sequencing provides critical insights into chromatin architecture, aiding in the diagnosis of genetic disorders and cancer."
Last medically reviewed: September 7, 2026
Test Parameters & Specifications
Sample Stability
- Hemolyzed blood samples
- Clotted blood samples
- Insufficient DNA quantity (<1 µg)
- Degraded DNA (low molecular weight)
Understanding Your Results
Normal chromatin organization
No significant structural abnormalities detected; genome architecture appears typical.
Altered TAD boundaries
May indicate disruption of regulatory domains, potentially affecting gene expression and contributing to disease.
Novel enhancer-promoter loops
Could reveal new regulatory interactions that may be targeted for therapeutic intervention.
Structural variants (e.g., translocations)
May be pathogenic, especially if they disrupt gene function or regulatory elements.
Consult a clinical geneticist or oncologist if the Hi-C results reveal structural variants or chromatin abnormalities that may be associated with a genetic disorder or cancer. They can provide genetic counseling and discuss implications for management.
Limitations
- ⚠Requires high-quality, high-molecular-weight DNA
- ⚠Bioinformatics analysis is complex and may require specialized expertise
- ⚠Not a routine diagnostic test; primarily used in research or specific clinical cases
- ⚠Cost is high compared to standard genetic tests
- ⚠Interpretation may be limited by reference databases
Risks & Considerations
- ●Blood draw: minor bruising or discomfort
- ●Tissue biopsy: risk of bleeding or infection (rare)
- ●No radiation exposure involved
Interfering Factors
- ●Degraded DNA (low molecular weight)
- ●Contamination with RNA or proteins
- ●Insufficient cross-linking or digestion
- ●Low sequencing depth
- ●Batch effects in library preparation
Compare With Similar Tests
| Test | Hi-C Sequencing and Analysis | Whole Genome Sequencing (WGS) | RNA Sequencing (RNA-Seq) | ChIP-Seq | FISH (Fluorescence In Situ Hybridization) |
|---|---|---|---|---|---|
| Comparison | Hi-C Sequencing and Analysis | WGS provides DNA sequence information, while Hi-C provides 3D structure. They are complementary; Hi-C can help interpret variants in non-coding regions. | RNA-Seq measures gene expression, while Hi-C reveals regulatory interactions. Combining both can link chromatin structure to expression changes. | ChIP-Seq identifies protein-DNA interactions (e.g., transcription factors), while Hi-C maps global chromatin contacts. They can be used together to understand regulatory networks. | FISH visualizes specific chromosomal regions, but Hi-C provides genome-wide interaction maps at higher resolution. |
Frequently Asked Questions
What is Hi-C sequencing?
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Related Tests
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