Technology

Our technologies include:

Next Generation Sequencing (NGS) - This technology utilizes massive parallel sequencing which allows large number of genes, up to, and including the whole exome (every gene within the genome) to be analysed in one test, to identify sequence changes in patients DNA that might explain their clinical indication. For this method, our genomics lab uses high throughput systems, namely the MiSeq and NovaSeq platforms (Illumina, USA), which can accurately and reliably analyse DNA samples, within days or hours and in a cost-effective manner. NGS is used for targeted disease-gene panels, and for clinical whole exome sequencing. For more information, please see below.

Genome-wide and Exon-level microarrays - We use the Affymetrix CytoScan platform (ThermoFisher, USA) to scan patient genomes for copy number changes (deletions or duplications) that might explain their clinical presentation. The resolution of this technology can range from detecting changes in a large number of genes (chromosomal microarrays) to a small portion of one single gene (Exon arrays). In addition to copy number changes, this technology include markers (single nucleotide polymorphisms or SNPs) that can label portions of patient genomes that are identical (due to consanguinity or uniparental disomy for example) and that can be highly relevant to finding an accurate diagnosis.

Droplet Digital PCR - This is an ultrafast, high-resolution technology best suited for targeted interrogation of specific regions in our genomes, which are highly suspected to explain the patient presentation. This technology (Bio-Rad, USA) is reserved for genetic disorders with well-characterized genomic changes (such as copy number changes) that can be quickly targeted and analysed.

Fragment Analysis and Sanger Sequencing - The Genomics lab utilizes the Applied Biosystems ABI 3730 capillary electrophoresis platform (ThermoFisher, USA) to scan specific regions and/or changes in the genome undetectable by the above technologies. This includes repeat expansion disorders, specifically Fragile X syndrome, and methylation disorders such as Angelman, Prader-Willi, Beckwith- Wiedemann, and Russell-Silver syndromes. In addition, the ABI 3730 system is used to confirm sequence changes identified by NGS using Sanger sequencing methodology.

Our workflows are highly automated using state-of-the-art liquid handlers (Hamilton, Switzerland) with built-in, clinically validated standard operating procedures. This automation enables consistent, precise, and high throughput genomic testing.

Our interpretation workflows include:

Bioinformatics pipelines - The lab at Al Jalila Genomics Centre devised and clinically validated a combination of custom-made applications and commercial software packages for transforming the vast amount of data, generated by our high throughput technologies, into clinically meaningful results. Specifically, our bioinformatics pipelines can automatically analyse next generation sequencing (NGS) and genomic microarray patient data, by comparing them to the reference human genome, and then calling and annotating any changes (variants) that might be disease causing and would require manual curation by our genomic analysts. Our bioinformatics pipeline uses a host of internal and external databases to annotate each variant with several attributes, including effect on protein function or RNA splicing, allele frequency in the general population, functional and segregation data, and presence or absence in disease databases. Using this annotation and knowledge about disease mechanisms, inheritance patterns, genetic/allelic heterogeneity, phenotypic spectrum, penetrance and expressivity, our bioinformatics pipeline will then automate the prioritization of the most relevant variants in the context of patient’s clinical presentation.

Variant Interpretation pipeline - Variants prioritized through our bioinformatics pipelines will then be classified by our genomic analysts and genetic counsellors following standards and guidelines by the American College of Medical Genetics and Genomics (ACMGG). Our genomic analysts, often PhD level, are highly specialized human geneticists who will employ several tools and use their expertise in molecular genetics to understand the impact of a certain variant on protein function, and whether such impact will lead to human disease. This complex process requires an in-depth understanding of the molecular genetics of human disease, population genetics, inheritance models, and molecular biology. Available evidence about each variant will be assimilated, and then used to determine the clinical significance of each variant (whether disease causing or not) according to the ACMGG standards and guidelines.

Our genomic testing approaches include:

Whole exome sequencing - In this test, all ~20,000 coding genes will be captured, sequenced by NGS, and analyzed with a specific focus on all disease genes or genes that appear to be relevant to the patient’s clinical presentation. This is a very complex test which requires and uses patient clinical information and family history during the analysis process. Given the large number of genes and subsequent variants to be identified, it is always recommended to include parental samples (trio exome) in order to apply certain inheritance models and zoom into the more clinically relevant variants. Obtaining samples from additional family members (affected or unaffected) can be helpful in certain scenarios. In general, this test should be considered for:

▪ Complex presentations where multiple, non-overlapping features are involved

▪ Genetically heterogeneous disorders for which no genetic test is available, and/or

▪ Disorders with highly suspected genetic aetiology but exhaustive targeted genetic testing did not reveal an answer. Although the ordering process for all genetic testing should include genetic counselling, whole exome sequencing specifically required dedicated session(s) with highly skilled genetic counsellors before and after the testing is performed.

SNP-based chromosomal microarrays - This test detects large copy number changes across the whole genome and is generally recommended as a first-tier test for children with unexplained:

▪ Developmental delays

▪ Intellectual disability

▪ Multiple congenital anomalies, and/or

▪ Autism spectrum disorders

Our SNP arrays platform consists of 2.67 million markers, including 750,000 SNP probes and 1.9 million non-polymorphic probes. This high probe density ensures that all relevant disease genes have 100% coverage, with an average of 1 probe every 880 bases within all genes, and an average of 1 probe every 1,148 bases across the entire genome. Therefore, small deletions, not detectable by other low-resolution platforms, can be easily identified using our system.

Targeted NGS disease panels - The Al Jalila Genomics Centre designed and validated next generation sequencing approaches for targeted sequencing and analysis of a defined set of genes known to cause a particular disease. Using a targeted analysis approach, curated gene lists are used to capture the relevant genes for analysis. Alternatively, we offer an exome slice approach where the healthcare provider can select which genes are to be analysed allowing for customizable gene panels for individual patients. The advantage of the exome slice approach is that it allows for fast and cost-effective reflex testing of other gene sets or the whole exome for the non-diagnostic cases.

Targeted disease panels generally have faster turnaround time at a reduced cost, and alleviate the possibility of detecting variants or changes not related to the patient phenotype (so-called incidental or secondary findings) often encountered in whole exome sequencing or any other genome-wide testing. However, targeted gene panels should be ordered when there is a strong clinical suspicion for a particular genetic disease caused a single or a group of genes.

Al Jalila Genomics Centre now offers targeted NGS panels for a spectrum of paediatric disorders and syndromes across multiple specialties, including Neurology and Neurodevelopment, Pulmonary, Hearing loss, Gastroenterology, Orthopaedics, Endocrinology, Nephrology, Rheumatology and Metabolism.

For our NGS-based tests, we will ensure adequate coverage of the relevant genes (≥99% of targeted regions at ≥10X coverage). All clinically relevant variants will be Sanger confirmed before reporting.