The man who does not make his own tools does not make his own sculpture.

Irving Stone, The Agony and The Ecstasy

An analysis of the UK Biobank database carried out by Neale’s Lab pointed out a significant correlation between a region of chromosome 13 and females with self-reported Chronic Fatigue Syndrome (see this blog post). This result was further analyzed in a subsequent paper in which it was suggested that the causal variant within this region may be rs7337312 (position 13:41353297:G:A on reference genome GRCh37, forward strand) (Dibble J. et al. 2020). It is included in a regulatory region of gene SLC25A15, which encodes mitochondrial ornithine transporter I, and the potential biological effects of this variant have been discussed in the aforementioned study. I made an attempt at my own discussion of this variant (here).

It is not unusual for a GWAS study to associate a trait with a long sequence of variants belonging to the same chromosome and in a close physical relationship one with the other, due to high linkage disequilibrium often present between variants close to one another (see this blog post). Several methods have been developed in the last years to further refine the association and find the variant that causes the disease and drives the association of its nearby SNPs. These methods are based on both purely mathematical considerations and on the analysis of the known consequences of the variants, and we refer to them by the evocative name of fine-mapping (Schaid DJ et al. 2018).

I tried to develop my own method and software for a purely mathematical approach to fine-mapping and I applied it to the region associated with ME/CFS in females, and I found variant rs11147812 (13:41404706:T:C on h19) as the most likely causal one. The detailed discussion of the method I followed and the scripts I wrote are available here for download. It might be noted that this variant belongs to a genetic entity (pseudogene TPTE2P5) that harbors variants that have been strongly associated with the following hematic parameters (see GWAS catalog).

The alternative allele of rs11147812 has been reported to increase (effect size > 0) the expression of gene SLC25A15 in fat (see this page) with a p value of 2.85\cdot10^{-20}. Since the alternative variant is less frequent in patients than in controls, the prediction is that we have a reduced expression of SLC25A15 in fat, in female CFS patients.

Diastolic blood pressure (reduction)Evangelou E et al. 2018
Blood volume occupied by platelets (increase)Astle WG et al. 2016
Basophil count (decrease)Masahiro K et al. 2018
Table. Significant associations between traits and variants of TPTE2P5.

Note. The header image shows the convergence of the linear method used by my script for fine-mapping the region on chromosome 13. The detailed discussion of the method I followed and the scripts I wrote are available here for download.


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