Our Technology

/Our Technology
Our Technology 2017-10-06T22:13:57+00:00

Our Equipment | Software Analysis

Our Equipment

Illumina HiSeq 2500

Illumina HiSeq 2500 and 4000

What it does: The HiSeq 2500 and HiSeq 4000 are both robust next generation sequencing instruments that produce large amounts of sequencing data within a matter of a few days. The HiSeq 2500, in rapid mode, can generate up to 400 million reads within 1 day and 3 hours. The HiSeq 4000 runs in High Output and can run up to 8 libraries of 300-400 millions single reads within 3.5 days.

How it is used by GMI:  The HiSeq 2500 is currently being used to run a CLIA certified clinical cancer gene panel and clinical whole exome sequencing.

GMI Equipment

Perkin-Elmer NGS Xpress

What it does:  This liquid handling instrument is a compact and easy-to-use library preparation system for automated NGS platform workflows. Its bench top design accommodates 24-NGS libraries for efficient preparations without the use of tedious manual protocols.

How it is used by GMI:  The NGS express is primarily used for library construction and magnetic bead-based cleanup steps. This automated & efficient system reduces hands-on labor for lab staff.

GMI Equipment

Qiagen QIAcube

What it does:  The Qiacube is a low-throughput robotic workstation used in extracting & purifying high quality DNA, RNA or proteins from various sources like whole blood & formalin-fixed paraffin embedded (FFPE) tissue. Its automated processing allows for increased lab productivity and standardized results. The system is based on Qiagen’s spin column technology.

How it is used by GMI:  The QIAcube extracts genomic DNA from Formalin-Fixed Paraffin Embedded tissue samples for NGS workflows.

Covaris S2 Focused-ultrasonicators

Covaris S2 Focused-ultrasonicators

What it does: The Covaris S2 Focused-ultrasonicator is a single tube system developed for sample preparation using Covaris’ patented Adaptive Focused Acoustics to deliver controlled energy to shear DNA and RNA without GC bias or thermal damage.

How it is used by GMI:  The Covaris is used for mechanical shearing of DNA to achieve a desired average target size.

Illumina cBot

Illumina cBot

What it does: The cBot is an automated system that creates clonal clusters from single molecule DNA templates and prepares them for sequencing by synthesis on the HiSeq sequencer.

How it is used by GMI:  The cBot is used for off-board cluster generation and prepares the flowcell for loading on the HiSeq.

Advanced Analytical Fragment Analyzer

Advanced Analytical Fragment Analyzer

What it does:  The Fragment Analyzer is a high-throughput system that provides sizing, quantitation, and quality control of DNA, gDNA, and RNA.  It can run up to 288 samples, resolve fragments from 10 bp to 40,000 bp, and detect input starting at 5pg/uL.

How it is used by GMI:  The Fragment Analyzer is used to provide quantitative and qualitative results for genomic DNA and libraries in the NGS workflow.

GMI Equipment

Roche LightCycler 480 II

What it does:  The LC480II is a high-throughput multi-functional genetic device system. Its real-time PCR plate platform allows gene detection, gene expression, and genetic variation analysis. This instrument performs both qualitative and quantitative detection of nucleic acids.

How it is used by GMI:  The LC480II accurately quantifies NGS libraries using its quantitative PCR technology. This step is critical for accurate loading of NGS libraries on the HiSeq 2500.

GMI Equipment

PCR workstation

What it does:  Equipped with UV light sterilization, dead-air workstations provide protection against contamination of sensitive amplification reactions, such as those used during NGS library preparation. This dead-air workstation limits sample cross-contamination and exposure of reagents to the open lab environment.

How it is used by GMI:  The PCR workstation protects reagents and master mix preparations from potential amplicon or plasmid contaminated areas during NGS workflow steps.

Agilent 2100 Bioanalyzer

Agilent 2100 Bioanalyzer

What it does: The Agilent 2100 Bioanalyzer system provides sizing, quantitation and quality control of DNA, RNA, proteins, and cells on a single platform.

How it is used by GMI:  The Bioanalyzer is used to provide quantitative and qualitative results for genomic DNA and libraries in the NGS workflow.

Software Analysis

Bioinformaticians from multiple disciplines, research groups and campuses collaborate to manage equipment-specific software, integrate data from numerous laboratory tools and apply modern analytic software pipelines. Their goal is to provide high quality genetic findings to treating physicians and their patients through Electronic Medical Records (EMRs).

Application of the equipment-specific software and data inform quality control decisions, and are used to monitor and improve laboratory techniques to produce only the highest quality sequencing data.

Modern analytic software pipelines, which include such programs as bwa, GATK and muTect are then applied to the high-quality NGS data to identify disease-related regions of interest within the genetic sample provided. Such findings are then passed to review boards, and the conclusions of these boards are incorporated into EMRs with the help of Syapse, a precision medicine data platform.