Overview:
The mission of the Genomics Core is to provide accessible Genomics services to support medical research within HMC and Qatar. Genomics technologies and expertise aims to help dissect underlying genetic traits of diseases and conditions via techniques such as Sanger sequencing and Whole Exome Sequencing (WES).
Core Service and Technologies:
Currently it provides the following services.
1: DNA extraction
2: RNA extraction
3: QC analysis of DNA, RNA by NanoDrop 2000, Qubit 4 and 2100 Bioanalyzer
4: PCR
5: qPCR
6: Sanger sequencing
7: Whole Exome Sequencing
8: Whole Transcriptome Analysis
Once the project details have been reviewed by the Genomics Core team it will be forwarded to TRI management for scoring and approval. It is important to mention that every project must discuss cost-sharing for processing samples. All ethical, legal, regulatory approvals must have been fulfilled by the Principle Investigator (PI). It will be responsibility of PI to arrange for transport and long-term storage of sample and data. The core operates on a collaboration basis and does not charge for services, therefore core as well as the personnel who contributes to the work must be adequately acknowledged as co-authors for substantial intellectual contribution in scientific publications, posters, and presentations.
Core Technology:
- Maxwell® 16 Instrument
It is an automatic instrument which spares time and effort by removing reagent preparation, pipetting and centrifugation steps. It can extract DNA from up to 16 samples in 30 – 45 minutes making it fast and simple.
- QIAcube
It is a completely automatic instrument which can process up to 12 samples for RNA, genomic DNA, or proteins purification.
- NanoDrop 2000
It is a micro-volume spectrophotometer with fast, direct, easy measurements of DNA, RNA (A260) and protein (A280) concentrations and sample purity (260/280 ratio).
- Qubit™ 4.0
It measures DNA, RNA, and protein precisely utilizing the exceedingly sensitive fluorescence-based Qubit® quantitation assays. The dyes utilized radiate only when attached to target molecules, even in low quantities, hence reducing the impact of impurities.
- Agilent Bioanalyzer 2100
It is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells.
- Veriti™ Thermal Cycler
With the VeriFlex™ Sample Block, it can control six different thermal areas to optimize PCR conditions for a primer set with easy-to-use interface on touchscreen display.
- QuantStudio™ 12K Flex Real-Time PCR System with Accufill System
It is a highly flexible, comprehensive real-time PCR platform with easy-to-change blocks that can accommodate OpenArray® plates, TaqMan® array cards, 384-well, 96-well, and FAST 96-well plates permitting to choose the format that is right for your project.
- 3500 Series Genetic Analyzer
3500 Genetic Analyzer is fluorescence-based technique using capillary electrophoresis for DNA sequencing and fragment analysis.
- NextSeq 500
It is benchtop medium throughout sequencer which can produce up to 120 Gb data in a 29 hrs run. It can sequence amplicon panels, whole exome, transcriptome, and genome.
- GeneChip System 3000Dx v.2
Affymetrix GeneChip® System 3000Dx v.2 can be utilized for whole-transcript expression analysis, genome wide genotyping and drug metabolism/pharmacogenomics applications.
- Ion GeneStudio™ S5 Prime System with Ion Chef™ Instrument
It enables simple targeted sequencing workflows for research applications including microbial genomes, gene panels, exomes, and transcriptomes.
Team and contact details:
Dr. Gulab Sher, PhD (Head, Genomics Core Facility)
Contact details:
44390976
GSher@hamad.qa
Genomics Core Facility, Hamad Medical City, Building 320, iTRI, Doha
Select publications:
Sher et al., A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family. Eur J Med Genet. 2014 Jan;57(1):21-4. PMID: 24269551 (Impact factor: 2.368).
Sher et al., Muhammad Naeem. Molecular Diagnosis of Rare Autosomal Recessive Escobar Syndrome in a Consanguineous Pakistani Family. Genet Test Mol Biomarkers. 2018 Dec;22(12):714-718. PMID: 30461311 (Impact factor: 1.378)
Sher et al., Prevalence and Type Distribution of High-Risk Human Papillomavirus (HPV) in Breast Cancer: A Qatar Based Study. Cancers (Basel). 2020 Jun 10;12(6):1528. PMID: 32532107 (Impact factor: 6.126)
Sher et al., Epigenetic and breast cancer therapy: Promising diagnostic and therapeutic applications. Semin Cancer Biol. 2020 Aug 25;S1044-579X(20)30181-4. PMID: 32858230 (Impact factor: 11.090)
Khan S, Irfan M, Sher G et al., UGT1A1 gene mutations in Pakistani children suffering from inherited non-hemolytic unconjugated hyperbilirubinemias. Ann Hum Genet. 2013 Aug 29. PMID: 23992562 (Impact factor: 1.368)
Collaborating Institutes:
Dermatology Institute, NCCCR, Neuroscience Institute, WWRC, Qatar Metabolic Institute.
