Whole Exome Sequencing Is the Preferred Strategy to Identify the Genetic Defect in Patients With a Probable or Possible Mitochondrial Cause 2018

pattismith

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fgene-09-00400.pdf

Frontiers | Whole Exome Sequencing Is the Preferred Strategy to Identify the Genetic Defect in Patients With a Probable or Possible Mitochondrial Cause | Genetics (frontiersin.org)

Mitochondrial pathogenic variants can be found in the mitochondrial DNA (mtDNA) or in any of the 1,500 nuclear genes with a mitochondrial function.

We have performed a two-step next-generation sequencing approach in a cohort of 117 patients, mostly children, in whom a mitochondrial disease-cause could likely or possibly explain the phenotype.

A total of 86 patients had a mitochondrial disorder, according to established clinical and biochemical criteria.

The other 31 patients had neuromuscular symptoms, where in a minority a mitochondrial genetic cause is present, but a non-mitochondrial genetic cause is more likely.

All patients were screened for pathogenic variants in the mtDNA and, if excluded, analyzed by whole exome sequencing (WES).

We identified causative pathogenic variants in the mtDNA in 20% of the patient-cohort, and in nuclear genes in 49%, implying an overall yield of 68%.

We identified pathogenic variants in mitochondrial and non-mitochondrial genes in both groups with, obviously, a higher number of mitochondrial genes affected in mitochondrial disease patients.

Furthermore, we show that 31% of the disease-causing genes in the mitochondrial patient group were not included in the MitoCarta database, and therefore would have been missed with MitoCarta based gene-panels.

We conclude that WES is preferable to panel-based approaches for both groups of patients, as the mitochondrial gene-list is not complete and mitochondrial symptoms can be secondary.

Also, clinically and genetically heterogeneous disorders would require sequential use of multiple different gene panels.

We conclude that WES is a comprehensive and unbiased approach to establish a genetic diagnosis in these patients, able to resolve multi-genic disease-causes.
 

pattismith

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If you've had a WES performed, I wonder if anything useful can be done with that information.
I suppose once you have the WES, you need a special analyse of your result to screen for the genes involved in mitochondrial function.

The age of disease onset in the cohort varied from birth to approximately 50 years old. As 77% of our patients was below 18 years at the age of diagnosis we used the mitochondrial disease criteria (MDC) for children (Morava et al., 2006).

The MDC include clinical signs and symptoms (max 4 points), metabolic abnormalities and neuroimaging (max 4 points) and histologic anomalies (max 4 points). Score 1: mitochondrial disorder unlikely; score 2 to 4: possible mitochondrial disorder; score 5 to 7: probable mitochondrial disorder; score 8 to 12: definite mitochondrial disorder.

In group I patients were included, in whom the diagnosis of a mitochondrial disease was probable or definite (MDC > 5).

Patients not meeting these MD-criteria (MDC < 5, group 2) had neuromuscular symptoms that are not specific for mitochondrial disease, but in which a mitochondrial genetic cause has been identified in a minority of cases.

All parents were unaffected.
1626673003250.png
 

hapl808

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Had most of those tests done including acylcarnitine and lactate and pyruvate. All seemed normal I believe. WES did not find anything unusual, but my understanding is that's highly dependent on what they're looking for.
 
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Had most of those tests done including acylcarnitine and lactate and pyruvate. All seemed normal I believe. WES did not find anything unusual, but my understanding is that's highly dependent on what they're looking for.
Not really WES looks in the whole exomes (85% of all possible mutations i think), you don't look for a specific mutation. WGS is better and now accessible.
 

Learner1

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If you've had a WES performed, I wonder if anything useful can be done with that information.
It certainly can - it found 4 specific problems that require treatment.
Had most of those tests done including acylcarnitine and lactate and pyruvate. All seemed normal I believe. WES did not find anything unusual, but my understanding is that's highly dependent on what they're looking for.
There have found a limited number of mito mutations,they are finding new ones all the time.

And, it's possible to have no known mito SNPs, but have a secondary mito dysfunction due to environmental factors like infections, toxins, drugs, etc.
 

hapl808

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The company that ran my WES offers one re-run without extra cost. It's been a couple years so maybe new things have been identified and I'll try to run it again. Mine found nothing reportable. My understanding (talking to geneticists) is that there is more information in the WES that could be shared, but they limit their analysis to certain things depending on the company.
 

Learner1

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The company that ran my WES offers one re-run without extra cost. It's been a couple years so maybe new things have been identified and I'll try to run it again. Mine found nothing reportable. My understanding (talking to geneticists) is that there is more information in the WES that could be shared, but they limit their analysis to certain things depending on the company.
That can be useful, though running mine didn't turn up primary mito disease. However getting my data loaded into Enlis helped me find genes that significantly impact health (like hemochromatosis, a clotting disorder, and high cancer risk). Worth knowing about.
 

hapl808

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I'll have to look into Enlis. As I recall, the data was kind of huge - I never received the raw exome data. I've loaded 23&Me into various services, but I think the WES panel was several gigabytes.
 

Learner1

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I'll have to look into Enlis. As I recall, the data was kind of huge - I never received the raw exome data. I've loaded 23&Me into various services, but I think the WES panel was several gigabytes.
Enlis has a page that explains which file formats you need to load into their software. You do an upload to them, they massage your data, and then you can use their application to browse through it. There are different kinds of filters that you can use to find disease causing genes. I was able to load both 23andMe and GeneDX files.
 

pattismith

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The first question, is when to suspect mitochondrial dysfunction?

This 2021 study is from MELAS patients (genetic mitochondrial disease)

Circulating markers of NADH-reductive stress correlate with mitochondrial disease severity

JCI136055.v1.pdf (dm5migu4zj3pb.cloudfront.net)
We validated 20 analytes (1 protein, 19 metabolites) that distinguish patients with MELAS from controls.

The collection includes classic (lactate, alanine) and more recently identified (GDF-15, α-hydroxybutyrate) mitochondrial markers.

By mining untargeted mass-spectra we uncovered 3 less well-studied metabolite families: N-lactoyl-amino acids, β-hydroxy acylcarnitines, and β-hydroxy fatty acids.

Many of these 20 analytes correlate strongly with established measures of severity, including Karnofsky status, and mechanistically, nearly all markers are attributable to an elevated NADH/NAD+ ratio, or NADH-reductive stress.

Our work defines a panel of organelle function tests related to NADH-reductive stress that should enable classification and monitoring of mitochondrial disease.
 
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