Clinical-Grade WES with Expert — All Under One Roof
Whole Exome Sequencing (WES) interrogates the protein-coding regions of the genome — where over 85% of known disease-causing mutations reside — at a fraction of the cost of WGS. At CAG, we combine precision exome capture with a rigorous bioinformatics pipeline to deliver results you can trust and act on.
Whether you are a clinician diagnosing a rare paediatric disorder, a researcher characterising tumour mutations, or a pharmaceutical team screening biomarkers — our end-to-end service means you get one accountable partner, from sample to insight.
Focused on Disease-Causing Regions
WES targets the 1–2% of the genome where >85% of known disease-causing mutations reside — maximizing diagnostic yield per rupee spent.
Higher Depth, Lower Cost Than WGS
Achieve 100x–150x+ mean coverage on coding regions at a fraction of WGS cost — ideal for clinical labs, hospitals, and research institutes.
Superior Rare & De Novo Variant Detection
Deep coverage enables detection of low-frequency somatic variants, de novo mutations, and compound heterozygous hits missed by gene panels.
Actionable, Clinician-Ready Reports
ACMG/AMP-classified variants, pathogenicity scores, and interpretation summaries formatted for direct clinical or research use.
- Quality Control: FastQC, MultiQC, Trimmomatic
- Alignment: BWA-MEM2 to GRCh38 / hg19
- Variant Calling: GATK4 HaplotypeCaller, DeepVariant
- Annotation: ANNOVAR, VEP, SnpEff
- Classification: ACMG/AMP 2015 Guidelines
- Databases: ClinVar, OMIM, gnomAD, HGMD, dbSNP
- CNV Inference: XHMM, ExomeDepth
- Trio / Family-Based Joint Analysis
✦ Project Manager Assigned · Secure Data Transfer · Priority Support
Our Exome Sequencing Service Packages
Choose a plan that fits your diagnostic or research scope. All packages include raw data, QC reports, and a dedicated Project Manager.
Basic Plan
Academic researchers and general variant discovery
- Raw Data Quality Control (FastQC/MultiQC)
- Exome Capture & Reference Alignment
- SNP & InDel Variant Calling (GATK4 / DeepVariant)
- Basic Functional Annotation (ANNOVAR/SnpEff)
- Coverage & QC Statistics Report
Pro Plan
Rare diseases, Mendelian disorders, and oncology
- All Basic Plan analyses included
- ACMG/AMP Variant Classification
- Disease-specific gene panel overlays
- Pathogenicity scoring (ClinVar, OMIM, HGMD)
- Oncogene & tumour suppressor profiling
Premium Plan
Clinical diagnostics, complex cases, and advanced research
- All Pro Plan analyses included
- Trio Analysis & de novo variant detection
- CNV analysis from exome data
- Pharmacogenomics interpretation
- Publication-ready figures & pathway analysis
Supported Sequencing Platforms
Primary exome sequencing on Illumina for optimal depth and cost-efficiency — with long-read and hybrid options for complex cases.
Illumina NovaSeq
The gold standard for exome sequencing. Superior uniformity across capture regions, lowest cost per sample, and highest throughput for multi-sample projects.
PacBio & ONT
Long-read exome sequencing for difficult GC-rich regions, tandem repeats, and highly homologous genes that short-read platforms cannot resolve.
Hybrid Sequencing
Best-of-both-worlds approach: Illumina for breadth and depth, PacBio/ONT for resolving hard-to-call regions — ideal for complex clinical cases.
Not sure which platform fits your case? Our scientific team will recommend the best approach for your sample type, budget, and research question — at no cost.
Applications We Excel In
From clinical rare disease to oncology to neonatal genetics — WES delivers actionable answers across diverse medical and research domains.
Rare Genetic Disorders & Mendelian Diseases
Identify causal variants for autosomal dominant/recessive, X-linked, and mitochondrial disorders with clinical-grade confidence.
Oncology & Tumour Profiling
Detect somatic mutations, tumour mutational burden (TMB), MSI status, and germline cancer predisposition variants across all coding genes.
Trio Exome Analysis
Sequence the proband and both parents simultaneously to filter inherited variants and pinpoint de novo mutations — the most powerful diagnostic strategy.
Clinical Diagnostics & Precision Medicine
Support molecular diagnosis with ACMG-classified variant reports suitable for genetic counselling and clinical decision-making.
Pharmacogenomics & Biomarker Discovery
Identify actionable PGx variants and novel biomarkers to guide drug selection, dosing, and therapy response prediction.
Paediatric & Neonatal Genetics
Rapid, high-accuracy exome analysis for NICU and paediatric patients where a swift molecular diagnosis can directly impact clinical management.
Have a unique clinical case?
Our clinical bioinformatics team can design custom analysis pipelines for your specific diagnostic or research needs.
PhD Scientists & Clinical Geneticists at Your Service
Every exome project at CAG is handled by a team of PhD-qualified genomics scientists, certified clinical bioinformaticians, and experienced variant analysts. We don't just run pipelines — we interpret, validate, and work collaboratively to ensure every variant call meets clinical standards.
- PhD-qualified clinical geneticists on every project
- ACMG-certified variant interpretation workflow
- Peer-reviewed variant curation before report release
- Direct consultation via video call & email
Simple End-to-End Workflow
Five seamless steps from sample submission to actionable clinical or research report.
Sample Submission
Submit blood, saliva, extracted DNA, or FFPE material using our guided portal. Receive a project ID and assigned Project Manager.
Exome Capture & Library Prep
High-efficiency exome capture (Twist / Agilent SureSelect) and PCR-free library preparation for optimal uniformity and minimal bias.
Sequencing on Chosen Platform
Sequencing to target depth on your chosen platform with real-time run quality monitoring and QC checkpoints.
Bioinformatics Analysis & Interpretation
End-to-end analysis: alignment, variant calling, ACMG classification, pathway analysis, and custom downstream analyses.
Secure Data & Report Delivery
Raw FASTQ files, BAM/VCF outputs, and a detailed clinical interpretation report — delivered via secure encrypted download.
Sample Requirements
Uncertain about your sample quality? Reach out — our team will assess and advise at no cost.
Not sure which WES plan fits your case?
Our clinical bioinformatics experts will evaluate your project and recommend the right plan — with a detailed quote within 24 hours.
Frequently Asked Questions
Everything you need to know before starting your exome project.
Still have questions?
Our team responds within 2 hours on working days.
Reliable WES —
Sample to Actionable Insight
Get high-quality Whole Exome Sequencing with a dedicated Project Manager, clinical-grade variant reports, and transparent timelines — at competitive pricing for Indian researchers and institutions.
No commitment required · Response within 24 hours · Confidential