SequenceME genetic study - from Oxford Nanopore Technologies, the University of Edinburgh and Action for ME

[paolo]

Is there a description of the population to be used as a comparison for the SV data generated by SequenceME from ME/CFS patients? I think the reference population may be the one described here, which includes 189 subjects of European ancestry genotyped by Oxford Nanopore.

Same question for the methylation data.

This question may already have been answered elsewhere.

 

[paolo]

Is there a description of the population to be used as a comparison for the SV data generated by SequenceME from ME/CFS patients? I think the reference population may be the one described here, which includes 189 subjects of European ancestry genotyped by Oxford Nanopore.

Same question for the methylation data.

This question may already have been answered elsewhere.

Oxford Nanopore is currently sequencing 50k UK Biobank participants, with completion by the end of 2026 (R). So this is probably the answer to my question.

 

[Hoopoe]

This is the first study of its kind, right? Meaning, no one has ever done a long read sequencing study on a large group of patients with the same diagnosis, right?

Is this study a speculative search where it's not clear what will happen, or is it more a case of long read sequencing being expected to be worth doing once prices come down and ME/CFS happens to be the first condition with a big long read sequencing study?

My understanding the advantage of long read sequencing is that it can detect structural variants that can be missed with short read sequencing. Do we know that structural variants are important in other diseases with similar prevalence?

The thought that with this study we're setting out to explore the unknown is exciting.

 

[Andy]

This is the first study of its kind, right? Meaning, no one has ever done a long read sequencing study on a large group of patients with the same diagnosis, right?

I believe that 9k ME/CFS (or Long Covid) samples would be the largest whole genome sequencing study on one specific condition. There have been larger studies looking at things like multiple forms of cancer or multiple individual conditions.

Is this study a speculative search where it's not clear what will happen, or is it more a case of long read sequencing being expected to be worth doing once prices come down and ME/CFS happens to be the first big long read sequencing study?

We (the SequenceME&LC team) believe that the DecodeME results provide strong enough evidence for genetic involvement to make SequenceME&LC worthwhile, in order to pin down the exact details of that genetic involvement.

My understanding the advantage of long read sequencing is that it can detect structural variants that can be missed with short read sequencing. Do we know that structural variants are important in other diseases with similar prevalence?

I don't know about similar prevalence but yes, structural variants are important in many other diseases.