Establish a comprehensive view of the entire genome
Whole Genome Sequencing (WGS)
At Clinical Enterprise, we harness cutting-edge technology to deliver advanced whole genome sequencing services. Clinical Enterprise’s WGS services are carefully designed to cater to a wide spectrum of genomic inquiries—from detailed clinical analysis to pioneering genetic research. With precision at the core of our operations, we offer tailored sequencing solutions that empower researchers and healthcare professionals to uncover intricate genetic insights and drive significant advancements in their fields.
- Certified Quality: As a CLIA-certified, CAP-accredited, and NY CLEP-licensed laboratory, we ensure the highest standards of sequencing fidelity and data reliability.
- Comprehensive Solutions: From sample preparation to detailed bioinformatics analysis, we provide end-to-end services to accommodate a variety of genomic needs.
- Customized Analysis: We tailor data analysis to fit each project’s unique requirements with both standardized and innovative custom workflows.
Applications of Whole Genome Sequencing
Whole Genome Sequencing serves a multitude of purposes across various fields.
Comprehensive Genetic Analysis
Whole genome sequencing provides an all-encompassing view of the genome, enabling the detection of SNVs, indels, copy number variations, and structural variants. This comprehensive analysis is crucial for both clinical diagnostics and research applications, ensuring detailed genetic insights.
CLIA-Compliant Clinical Applications
Adheres to rigorous quality standards for clinical use, facilitating accurate genetic diagnosis, disease risk assessment, and personalized treatment planning. This regulatory compliance ensures the reliability and clinical utility of genomic data while meeting deadline-driven turnaround time.
Research and Discovery Tool
Powers genome-wide association studies (GWAS), functional genomics, and evolutionary biology research. Whole genome sequencing is instrumental in uncovering genetic underpinnings of diseases, drug response variability, and biodiversity.
Cost-Effective Options
Low-pass WGS offers a cost-efficient approach for genetic studies requiring lower coverage, ideal for preliminary screenings, population genetic studies, and large cohort analyses without the need for deep sequencing.
Service Offerings
Clinical Enterprise offers multiple service levels of WGS to match your needs.
CLIA-Compliant WGS
Provides 30X coverage sequencing, suitable for rigorous clinical and medical research, compliant with clinical laboratory standards.
Sample Requirements
- Sample Types: Whole Blood (WB) or saliva collected using Mawi kits.
- Volume and Concentration: A minimum of 600 ng at >12.5 ng/µL, with 1 µg recommended.
- Shipping: For WB, samples should be shipped on dry ice using overnight delivery. Saliva samples collected using the Mawi250 device can be shipped at ambient temperature.
Research Use Only WGS
Offers flexible coverage options, tailored to specific scientific inquiries and experimental needs. Low-pass WGS options available at coverage levels of 1X, 2X, and 4X.
Sample Requirements
- Sample Types: Variety of specimen types accepted providing flexibility for diverse research settings.
- Volume and Concentration: A minimum input requirement of 50 ng.
- Shipping: More flexible conditions to accommodate various research needs and sample quality. Please contact us to discuss your exact application.
Technology
Clinical Enterprise utilizes robust and cutting-edge platforms to extract, prepare, and sequence samples.
KingFisher 96 Flex
Efficient DNA extraction at several scales, suitable for medium-throughput needs.
Hamilton STAR
Highly automated extraction processes, ensuring high-quality DNA input for large-scale sequencing projects.
Qubit Fluorometer
Fast and highly accurate quantitation of DNA, RNA, and protein in less than three seconds per sample. High levels of accuracy using only 1 to 20 μL of sample, even with very dilute samples.
NovaSeq X Plus
Scalability to provide anywhere from 4 to 64 human genome samples per flow cell with as much as 16TB of data produced per run. Runs performed using 2x150bp configuration.
Advanced Workflow and Bioinformatics
Our CLIA-compliant workflows incorporate the advanced DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT platform by Illumina.
DRAGEN enhances our genetic analysis by using field-programmable gate array (FPGA) technology to accelerate key bioinformatics tasks like alignment, sorting, and variant calling. This platform allows for rapid processing of next-generation sequencing data, drastically reducing analysis time while maintaining high accuracy.
Data Management and Pre-Alignment
- Seamless integration with our workflow management software ensures efficient tracking.
- Data uploads to secure cloud services maintain integrity from the start.
- Initial sequencing metrics are reviewed to ensure quality before alignment.
Alignment
- Performed using the hg38 genome build, with data output as BAM files.
- Includes position sorting, duplicate marking, and base-quality dropoff detection (BQD).
Variant Calling
- Detailed haplotype assembly and genotyping are supported by machine learning to enhance accuracy and reduce error rates.
- Applies hard filtering to maintain high-confidence variant detection.
- VCFs are normalized to ensure accurate and concise data representation.
Outputs and Quality Control
- Outputs encompass FASTQ quality metrics, alignment metrics, and coverage metrics.
- Analysis-ready VCFs are generated for immediate clinical or research use.
- For RUO applications, we provide additional detailed analysis outputs such as Structural Variants (SVs) and Copy Number Variants (CNVs).
Reporting
- CLIA Reporting: Provides comprehensive outputs including wet bench and sequencing quality control reports, alignment files, and detailed VCFs for SNVs and InDels.
- RUO Reporting: Expanded deliverables cater to specific research needs, offering detailed analysis on Expansion Repeats, SVs, CNVs, and other complex genetic forms. Custom reports are available, which provide exhaustive information and tracking throughout the experimental process.