Use of whole genome sequencing to determine genetic basis of suspected mitochondrial disorders: cohort study, 2021, Schon et al.

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Use of whole genome sequencing to determine genetic basis of suspected mitochondrial disorders: cohort study

Abstract
Objective To determine whether whole genome sequencing can be used to define the molecular basis of suspected mitochondrial disease.

Design Cohort study.

Setting National Health Service, England, including secondary and tertiary care.

Participants 345 patients with suspected mitochondrial disorders recruited to the 100 000 Genomes Project in England between 2015 and 2018.

Intervention Short read whole genome sequencing was performed. Nuclear variants were prioritised on the basis of gene panels chosen according to phenotypes, ClinVar pathogenic/likely pathogenic variants, and the top 10 prioritised variants from Exomiser. Mitochondrial DNA variants were called using an in-house pipeline and compared with a list of pathogenic variants. Copy number variants and short tandem repeats for 13 neurological disorders were also analysed. American College of Medical Genetics guidelines were followed for classification of variants.

Main outcome measure Definite or probable genetic diagnosis.

Results A definite or probable genetic diagnosis was identified in 98/319 (31%) families, with an additional 6 (2%) possible diagnoses. Fourteen of the diagnoses (4% of the 319 families) explained only part of the clinical features. A total of 95 different genes were implicated. Of 104 families given a diagnosis, 39 (38%) had a mitochondrial diagnosis and 65 (63%) had a non-mitochondrial diagnosis.

Conclusion Whole genome sequencing is a useful diagnostic test in patients with suspected mitochondrial disorders, yielding a diagnosis in a further 31% after exclusion of common causes. Most diagnoses were non-mitochondrial disorders and included developmental disorders with intellectual disability, epileptic encephalopathies, other metabolic disorders, cardiomyopathies, and leukodystrophies. These would have been missed if a targeted approach was taken, and some have specific treatments.
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On the subject of mitochondrial dysfunction, does anyone have a view on the possible usefulness of this just published work on whole genome sequencing by the MRC Mitochondrial Biology Unit and Departments of Clinical Neuroscience and Medical Genetics at Cambridge?

Whole genome sequencing increases diagnosis of rare disorders by nearly a third
https://www.cam.ac.uk/research/news...esearch&utm_medium=social&utm_source=linkedin

I'm far out of my depth, but I wonder if this team could swap notes with Decode ME?

 

Obvious person to alert is @Simon M but there may be others.

Think the recent video update from Chris Ponting mentioned that the ME/CFS GWAS study (DecodeME) could eventually move to whole genome sequencing study i.e. using the DecodeME samples (correct?).

 

whole genome sequencing remains very expensive at around £1000 per person. Decodeme only has funding to investigate DNA differences at close to million locations in the genome, which is very different. It plans to store part of the saliva sample (where people give consent) for future whole genome sequencing if it can secure funding in future. So this isn't relevant just yet but whole genome sequencing costs will continue to fall and hopefully, this is one for the future.

 

Thanks very much for this reply - useful to know.

 

I recall a twitter thread relatively recently discussing a new paper from whole exome sequencing, looking for the contribution of rare variants in collapsed gene models. I recall that the conclusions were that there were no significants hits for ME, which when combined with the lack of evidence from the common variant screens showed that the power of ~2000 patients was simply not high enough.

I'm guessing the utility in doing whole genome sequencing with low power would be to cover rare variants in the remaining non coding genome?

 

my understanding is that rare variants almost always occur in the coding region (i.e. affecting the protein that is made, not the quantity of the protein). This is because such protein-coding variants often have large effects. Most variants that turn up in GWAS are in non-coding regions and have small effects.

There's a reason it's like this. If the protein coding variant is common enough to show up in a GWAS, it probably only has a negligible effect (many protein coding variants don't affect function). If there was a common protein coding variants that made a real difference in ME/CFS, we would almost certainly know about it by now.

 

That's really interesting. So you might expect protein coding mutations to be fairly binary most of the time - either total loss of function or synonymous/little change. Whereas non coding region mutations have a continuous effect ie eQTLs. I imagine this can get very complicated very quickly, but I guess the SNPs interact with each other too in a way that's not necessarily linear.

Does this mean then that whole genome sequencing is not really worthwhile in your opinion? I suppose it would only serve to fill in any SNPs that aren't included on the chips. Maybe there's other uses too like looking at indels and other chromosome level changes.

 

not exactly. Many changes will be synonyms (changes in DNA sequence that either lead to the same amino acid being specified) or a similar one in non-critical parts of the protein. RARE variants won't necessarily be complete loss of function, but they are likely to have a significant loss of function if they are going to be of any significance.

one of the reasons for doing whole genome sequencing is to find rare variants that are worth including on GWAS chips. The other reason is that the rare variants themselves are more powerful biological clues because they are in protein coding regions.

Just to recap common versus rare variants:
— common variants are laid to have only a small effect and be in non-coding regions (so they affect the amount of protein produced but not the protein itself). Because they are small effect they have a negligible effect on risk for an individual. Their real value is that if particular genes or biological pathways (or tissue types) keep showing up for the same disease in a GWAS, that then becomes a valuable biological clue about what might be causing the illness.
— Rare variants are different. They are likely to affect the protein that is made and affect its function. As such, they not only allow to have a significant effect on the risk for an individual (and may even largely explain why they got sick), but also provide stronger biological clues). But they are very hard to find. They can show up in very large GWAS, but are also often found threefold in sequencing.