Genome-wide Sequencing facility
This facility is equipped with several machines for high-throughput sequencing for human whole exome (WES) and whole genome sequencing (WGS). The technique allows the characterization of an unlimited number of genetic variations for a high number of samples. Sequencing enables precise and accurate construction of the target DNA.
Sequencing by Synthesis (SBS) is a technology utilizing a chip containing thousands of wells that DNA fragments attach to for amplification by polymerase chain reaction and sequencing. The amplified DNA is read by allowing one fluorescence-labelled nucleotide to bind to the amplicon in each cycle. This method is designed for the sequencing of large genomic segments.
Some of the noteworthy equipment used for whole genome and whole exome sequencing:
- The Illumina NextSeq 500 Sequencing System – delivers high-throughput sequencing and the flexibility to carry out applications such as whole-genome, exome, or transcriptome sequencing.
- The Illumina iSeq 100 System – is ideal for small genome, targeted, and amplicon sequencing, as well as viral and microbial sequencing.
- The Illumina MiSeq System – is an integrated instrument that performs clonal amplification, genomic DNA sequencing, and data analysis with base calling, alignment, variant calling, and reporting in a single run.
- The Illumina NovaSeq – provides access to a powerful, high-throughput genomics solution for making in-house WGS or WES studies faster and more affordable. It offers output up to 6 Tb and 20B reads in < 2 days. Multiple flow cell types and read length combinations offer flexible output and run time configurations based on project needs.
Sanger sequencing is a method suitable for sequencing specific and short DNA target areas such as genes and is also used to validate results generated from the other sequencers owned by the center. A special type of PCR called chain termination PCR is used to prepare the DNA fragments for reading. In this process, a small ratio of the nucleotide bases present in the reaction mixture lack a 3’-OH group (ddNTPs), thus when a ddNTP is incorporated into a growing chain, elongation is terminated. Then, the DNA fragments of various lengths are analyzed by gel electrophoresis for sequencing. The BTC uses an automated machine that combines Sanger sequencing and gel electrophoresis.
- The Applied Biosystems 3500 Genetic Analyzer is an automated 8 and/or 24 capillary instruments designed for a wide range of sequencing and fragment analysis applications. The 3500-series instruments are the first genetic analyzers designed with a specific feature set and workflow for the Human Identification applications including de novo sequencing and resequencing (mutational profiling)—as well as SNP validation or screening
Genotyping Analysis Facility
The Genotyping Analysis by Microarray provides a comprehensive view of the genome to explore genetic variants such as single nucleotide polymorphisms (SNPs) and large structural changes in DNA among millions of markers, which help in identifying potential causative disease variants for further targeted studies
Researchers at the Center for Biotechnology are using this technology to identify regions of the human genome that contribute to disease susceptibility and phenotypes within the Arabian population, such as diabetes and cardiovascular disease.
This Microarray-based approach provides trusted performance and supports high-throughput, multiplex processing for genome-wide association studies (GWAS), variant screening, precision medicine research, and other human genotyping projects.
Some of the noteworthy equipment under this facility:
- The Illumina iScan System is a laser-based, high-resolution imaging tool for genome-wide or targeted genotyping applications, that can rapidly scan and collect large volumes of data from Illumina DNA analysis and RNA analysis high-density BeadChips.
The Genotyping Analysis by Real-time PCR offers sensitivity and specificity for detecting target nucleic acids, making it a useful and powerful technology for research applications.
This fluorescent-based method is useful for understanding disease mechanisms by comparing the expression of different genes in real-time from healthy and non-healthy samples and analyzing particular genetic variants that can lead to major changes associated with diseases.
Some of the noteworthy equipment under this facility:
- The ViiA™ 7 Real-Time PCR System combines all the qPCR features in a single high-performance instrument, with minimal well-to-well and instrument-to-instrument variation.
Other major pieces of equipment at the Center for Biotechnology for DNA processing:
MagPurix 24 Nucleic Acid Extraction System – This machine is a fully automated system for molecular biology sample preparation from a wide range of biological specimens. It oﬀers the ﬂexibility to process 1-24 samples per run simultaneously, making it ideal for laboratories requiring nucleic acid purification of small to middle sample throughputs
NanoDrop™ One Spectrophotometer – The Thermo Scientific™ NanoDrop™ One UV-Vis Spectrophotometers is developed for microvolume quantification and analysis of purified nucleic acids and a wide variety of proteins
Qsonica Sonicator (Q800R2) – Is designed for DNA and Chromatin shearing. DNA can be sheared to specific size ranges making it an ideal system for preparing samples for Next-Generation Sequencing
Fragment Analyzer – The Agilent Fragment Analyzer system is a fluorescence-based capillary electrophoresis instrument for the accurate sizing, quantification, and qualification of nucleic acids (DNA and RNA).
Veriti® Thermal Cycler – The Applied Biosystems Veriti® 96-Well Thermal Cycler with the added temperature-control technology is expected to increase the accuracy and efficiency of the polymerase chain reaction (PCR) process, providing precise control over the PCR optimization
DS-11 Series Spectrophotometer / Fluorometer – DeNovix: The DS-11 FX Series combines fluorescence, microvolume absorbance, and optional cuvette absorbance methods in a single instrument, making it ideal for rapid nucleic acid and protein quantification.
With the large production of data generated by experiments at the BTC sequencing lab, the Bioinformatics facility is responsible for the development of improved analysis and data processing methodologies for the identification of genetic variants. The facility is equipped with the computational power and the expertise needed for developing pipelines for high throughput Next Generation Sequences analysis. The facility is responsible for establishing data management and storage solutions through its BTC server and its access to the Khalif University high-performance computing resources unit. The facility also contributes towards providing continuous bioinformatics related training and workshops to the KU wider community.
Types of provided bioinformatics analysis:
o NGS and structural variation analysis
o Microarray-based data analysis
o Population genetics
o Trios and families diagnostic analysis
o HLA genotyping and analysis
Workshops and training:
The facility runs bioinformatics workshops that cover the following topics:
o From Fastq to annotated variants workshop
o Introduction to Linux for Bioinformatics
o Organized regional genomic data analysis workshops