Genome-PT

CGPP-IBMC services: 

Genome Sequencing: 

- Sanger Sequencing; 

- Targeted sequencing; 

- Targeted Resequencing; 

- Small genome sequencing

- Nuclei Acid QC; 

Other services: 

- MLPA

- Fragment analysis by capillary electrophoresis;

Platform: 

- Ion Torrent Ion PGM


Equipments: 

QIAsymphony SP – DNA and RNA isolation 

QIAsymphony enables the automated sample preparation of DNA and RNA from a broad range of sample types. Genomic DNA and RNA can be purified from human whole blood human and animal tissues, formalin-fixed paraffin-embedded tissue (FFPE) and cultured cells. 


Nanodrop

Thermo Scientific™ NanoDrop 2000 are full-spectrum, UV-Vis spectrophotometers used to quantify and assess purity of DNA, RNA and protein.


QIAgility

The QIAgility is designed to perform automated PCR setup and liquid handling actions in molecular biology applications. The QIAgility uses a single-channel pipet to automate PCR setup — up to 96 PCR reactions can be set up in approximately 30 minutes. 


QIAxcel

The QIAxcel is a multicapillary electrophoresis instrument, designed to perform fast and fully automated DNA fragment analysis or qualitative and quantitative RNA analysis.


ABI 3130XL – Capillary electrophoresis 

Capillary electrophoresis (CE) is a process used to separate ionic fragments by size. In Thermo Fisher Scientific CE instrumentation, an electrokinetic injection is used to inject DNA fragments from solution and into each capillary and are separated by size based on their total charge. 

Capillary electrophoresis is the gold standard for Sanger (DNA) sequencing and fragment analysis.



NGS Workflow equipment’s: 

Qubit 

The Qubit™ 4 Fluorometer is a benchtop fluorometer that can be used for the quantitation of DNA, RNA, microRNA, and protein, as well as for the measurement of RNA integrity and quality using the highly sensitive and accurate fluorescence based Qubit™ assays. 


E-Gel® EX agarose gels  

E-Gel® EX agarose gels are pre-cast 1%, 2%, and 4% agarose gels, for use with the E-Gel® iBase™ Power System. E-Gel® EX gels have 11 wells, and a novel openable format. A proprietary fluorescent nucleic acid stain in the gel allows detection down to 1 ng/band of DNA when visualized by blue light transilluminator (excitation at 490 nm/emission at 522 nm).




TapeStation  

The 2200 TapeStation is used extensively within a range of processes, e.g. DNA sizing and quantification in the range 35 bp to 60 kbp and 5 pg/µL to 100 ng/µL and RNA library preparation for the Ion Torrent sequencing platform, or checking RNA sample integrity following extraction or after mRNA isolation. The system detects:

- Fluorescently stained double stranded DNA including genomic DNA

- Fluorescently stained total RNA (Eukaryotic and Prokaryotic)

The 4200 TapeStation system is designed to exclusively run Agilent ScreenTape kits and specified consumables. It can analyze 1 to 16 samples provided in tube strips or up to 96 samples using a well plate.


Ion OneTouch 2 System - Thermo Fisher Scientific

The Ion OneTouch 2 System performs template amplification and enrichment as part of the Ion PGM, Ion Proton, and Ion S5 and Ion S5 XL systems workflows. It provides scalable template preparation for all Ion semiconductor chips. Supports up to 400 bases on the Ion PGM™ System and up to 200 bases on the Ion Proton™ System. 




Ion Torrent PGM sequencer 

The Ion Personal Genome Machine (PGM™) sequencer sequentially floods the chip with one nucleotide after another. If a nucleotide complements the sequence of the DNA molecule in a particular micro-well, it will be incorporated and hydrogen ions are released. The pH of the solution changes in that well and is detected by the ion sensor, essentially going directly from chemical information to digital information. If there are two identical bases on the DNA strand, the voltage is double, and the chip records two identical bases. If the next nucleotide that floods the chip is not a match, no voltage change is recorded and no base is called. Because this is direct detection—no scanning, no cameras, no light—each nucleotide incorporation is measured in seconds enabling very short run times.


Bioinformatics analysis 

Once data is generated on the Ion PGM™ sequencer, it is automatically transferred to the required Torrent Server. Here data are run through signal processing and base calling algorithms that produce the DNA sequences associated with individual reads. Torrent Server hosts web pages where summarized data results can be viewed and the data themselves can be downloaded using industry-standard data formats like SFF, FASTQ, or SAM/ BAM. The Ion Torrent data can then be imported into any NGS data analysis solutions.