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2. Genetic Testing

In this video Sanjeev Bhaskar Lead Clinical Bioinformatician describes the role of the bioinformatician in the Congenital Cataract case study
The service that we provide within MCGM is to mainly look at bilateral congenital cataract. And that screens for variants across 114 genes, which is distributed across about 1,450 regions that have been associated to bilateral congenital cataract. But what’s interesting about this particular case is that although we screen for sporadic cases and we look for an autosomally dominant, recessive, and x-linked inheritance patterns, this particular case was not necessarily what was relevant for the primary purpose of the panel but for juvenile onset, which is actually quite interesting because that’s actually what we also expected the panel to offer is to also look at other ocular malformations.
And quite often when we have referrals for this testing, we expect clinicians to provide us with family history, or at least to provide us with some kind of clinical diagnosis to allow us to then look at which of the 114 genes are relevant. Of course, when you have a presentation like in this case, which is supposed to be an autosomally recessive kind of characteristics, we are looking for a homozygous event or a compound heterozygous event happening.
Once we have managed to collate all that data in relation to the variant, we then look at published evidence to suggest is there any prior evidence to suggest it’s been seen previously. And we look at population frequencies. So we resource a lot of information that’s been done for instance in the ExAc projects, or looking at the 1,000 projects, or looking at dbSNP, as well. But more important that we found to be a very powerful tool is to look at our own in-house data to filter out information that might be just background polymorphisms.

In this video, provided by Manchester Centre for Genomic Medicine, Sanjeev Bhaskar Group Lead Clinical Bioinformatician at the Manchester Centre for Genomic Medicine describes the role of the bioinformatician and clinical genetic scientist in the analysis of this case.

He outlines the process of mapping all the short next generation sequencing reads to the human reference genome to piece the them back together and then how these reads are annotated to see where there are differences in comparison to the reference sequence. Finally he discusses how this data is then analysed and interpreted to determine which variant is likely to be responsible for causing the cataract in the two boys.

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Clinical Bioinformatics: Unlocking Genomics in Healthcare

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