Chr15 54.5M-55.5M
Methodology
To narrow the DecodeME1 GWAS-1 signal, I fine-mapped the hit on chromosome 15 using SUSIE2. The parameters of my SUSIE runs were the same as for the chromosome 1 locus.
Results
Each of the 4 SUSIE runs produced a single credible set containing identical variants, as illustrated by the following UpSet plot:
Here is a plot of the SUSIE results for the \(L=10\) case. It is representative of the other runs.
Compare to the other loci, the SUSIE credible set at this locus is relatively concentrated on a single variant: a G \(\to\) A substitution at GRCh37 position 55158922 on chromosome 15.
The detailed results for the \(L=10\) run are below.
Variant List (L=10)
| cs | CHR | POS | EA | NEA | alpha | mu | PIP |
|---|---|---|---|---|---|---|---|
| L1 | 15 | 55158922 | G | A | 0.194239 | 0.022945 | 0.194239 |
| L1 | 15 | 55156405 | G | T | 0.0154931 | 0.0210618 | 0.0154931 |
| L1 | 15 | 55156404 | C | T | 0.0135511 | 0.0209574 | 0.0135511 |
| L1 | 15 | 55159801 | G | A | 0.00887744 | -0.020624 | 0.00887744 |
| L1 | 15 | 55159342 | C | T | 0.00869299 | 0.0206073 | 0.00869299 |
| L1 | 15 | 55159715 | A | G | 0.00865026 | 0.0206034 | 0.00865026 |
| L1 | 15 | 55160462 | T | C | 0.00863258 | -0.0206018 | 0.00863258 |
| L1 | 15 | 55155938 | AT | A | 0.00843442 | -0.0205833 | 0.00843442 |
| L1 | 15 | 55159757 | G | A | 0.00842407 | 0.0205823 | 0.00842407 |
| L1 | 15 | 55159554 | A | G | 0.00833134 | 0.0205735 | 0.00833134 |
| L1 | 15 | 55159908 | G | C | 0.00817564 | 0.0205585 | 0.00817564 |
| L1 | 15 | 55159130 | T | G | 0.00777701 | 0.0205186 | 0.00777701 |
| L1 | 15 | 55160802 | G | A | 0.00777479 | 0.0205184 | 0.00777479 |
| L1 | 15 | 55159862 | C | A | 0.00776098 | 0.0205169 | 0.00776098 |
| L1 | 15 | 55151145 | G | A | 0.00763584 | 0.020504 | 0.00763584 |
| L1 | 15 | 55160634 | G | C | 0.00750143 | -0.0204898 | 0.00750143 |
| L1 | 15 | 55150810 | T | A | 0.00749837 | 0.0204894 | 0.00749837 |
| L1 | 15 | 55160787 | G | A | 0.00747256 | 0.0204867 | 0.00747256 |
| L1 | 15 | 55162470 | A | T | 0.00741571 | 0.0204806 | 0.00741571 |
| L1 | 15 | 55150181 | A | G | 0.00739617 | -0.0204785 | 0.00739617 |
| L1 | 15 | 55158509 | G | C | 0.00729678 | 0.0204676 | 0.00729678 |
| L1 | 15 | 55160980 | G | A | 0.00719136 | 0.020456 | 0.00719136 |
| L1 | 15 | 55154962 | C | A | 0.00714397 | 0.0204507 | 0.00714397 |
| L1 | 15 | 55152971 | A | C | 0.00713734 | 0.0204499 | 0.00713734 |
| L1 | 15 | 55156363 | T | C | 0.00703595 | 0.0204385 | 0.00703595 |
| L1 | 15 | 55150505 | G | C | 0.00699785 | -0.0204341 | 0.00699785 |
| L1 | 15 | 55154631 | C | CA | 0.0069904 | -0.0204333 | 0.0069904 |
| L1 | 15 | 55150921 | T | A | 0.00688969 | 0.0204216 | 0.00688969 |
| L1 | 15 | 55150420 | T | C | 0.00688722 | -0.0204213 | 0.00688722 |
| L1 | 15 | 55158137 | A | G | 0.00686915 | 0.0204192 | 0.00686915 |
| L1 | 15 | 55160781 | C | T | 0.00683767 | 0.0204155 | 0.00683767 |
| L1 | 15 | 55161542 | G | A | 0.00681783 | 0.0204132 | 0.00681783 |
| L1 | 15 | 55150740 | A | AG | 0.00675653 | -0.020406 | 0.00675653 |
| L1 | 15 | 55150236 | C | T | 0.00673402 | -0.0204033 | 0.00673402 |
| L1 | 15 | 55150220 | G | A | 0.00673402 | -0.0204033 | 0.00673402 |
| L1 | 15 | 55155773 | T | A | 0.00672354 | -0.020402 | 0.00672354 |
| L1 | 15 | 55150483 | T | A | 0.00671521 | -0.020401 | 0.00671521 |
| L1 | 15 | 55150469 | T | C | 0.00671521 | -0.020401 | 0.00671521 |
| L1 | 15 | 55150258 | C | T | 0.00667991 | -0.0203968 | 0.00667991 |
| L1 | 15 | 55156322 | G | C | 0.00667471 | 0.0203962 | 0.00667471 |
| L1 | 15 | 55150596 | G | A | 0.00660857 | -0.0203882 | 0.00660857 |
| L1 | 15 | 55149993 | T | C | 0.00657418 | -0.020384 | 0.00657418 |
| L1 | 15 | 55150322 | A | C | 0.00656919 | 0.0203834 | 0.00656919 |
| L1 | 15 | 55157158 | C | T | 0.00656767 | 0.0203832 | 0.00656767 |
| L1 | 15 | 55141309 | A | G | 0.00648876 | -0.0203735 | 0.00648876 |
| L1 | 15 | 55155165 | T | C | 0.00641002 | -0.0203636 | 0.00641002 |
| L1 | 15 | 55155416 | G | A | 0.00639977 | -0.0203623 | 0.00639977 |
| L1 | 15 | 55156382 | T | TTTGA | 0.00639849 | 0.0203622 | 0.00639849 |
| L1 | 15 | 55155884 | G | A | 0.0063085 | -0.0203508 | 0.0063085 |
| L1 | 15 | 55154548 | T | C | 0.00630743 | -0.0203506 | 0.00630743 |
| L1 | 15 | 55163453 | A | T | 0.00630585 | 0.0203504 | 0.00630585 |
| L1 | 15 | 55163164 | A | G | 0.00623856 | 0.0203418 | 0.00623856 |
| L1 | 15 | 55153845 | A | T | 0.00621276 | -0.0203385 | 0.00621276 |
| L1 | 15 | 55140913 | C | T | 0.00620837 | 0.0203379 | 0.00620837 |
| L1 | 15 | 55156259 | T | C | 0.00620357 | 0.0203373 | 0.00620357 |
| L1 | 15 | 55153804 | A | G | 0.00615213 | -0.0203306 | 0.00615213 |
| L1 | 15 | 55142936 | G | A | 0.00614562 | -0.0203297 | 0.00614562 |
| L1 | 15 | 55155311 | A | G | 0.00613643 | -0.0203285 | 0.00613643 |
| L1 | 15 | 55154217 | A | G | 0.00612682 | -0.0203272 | 0.00612682 |
| L1 | 15 | 55158666 | C | G | 0.00612348 | 0.0203268 | 0.00612348 |
| L1 | 15 | 55153408 | T | C | 0.00610903 | 0.0203249 | 0.00610903 |
| L1 | 15 | 55152773 | A | G | 0.00604668 | -0.0203166 | 0.00604668 |
| L1 | 15 | 55142784 | T | C | 0.00600083 | -0.0203105 | 0.00600083 |
| L1 | 15 | 55153652 | G | A | 0.00599989 | 0.0203104 | 0.00599989 |
| L1 | 15 | 55141109 | C | G | 0.00594218 | 0.0203026 | 0.00594218 |
| L1 | 15 | 55155203 | C | T | 0.00590906 | 0.020298 | 0.00590906 |
| L1 | 15 | 55155588 | G | A | 0.00585259 | -0.0202903 | 0.00585259 |
| L1 | 15 | 55155488 | G | A | 0.00584117 | 0.0202887 | 0.00584117 |
| L1 | 15 | 55155705 | A | G | 0.00578881 | -0.0202814 | 0.00578881 |
| L1 | 15 | 55141411 | G | C | 0.00572153 | -0.020272 | 0.00572153 |
| L1 | 15 | 55155621 | C | A | 0.00566069 | -0.0202633 | 0.00566069 |
| L1 | 15 | 55142751 | C | A | 0.00561426 | -0.0202567 | 0.00561426 |
| L1 | 15 | 55164204 | T | C | 0.00557786 | 0.0202514 | 0.00557786 |
| L1 | 15 | 55179674 | T | A | 0.00552171 | 0.0202432 | 0.00552171 |
| L1 | 15 | 55142885 | T | A | 0.00539448 | -0.0202244 | 0.00539448 |
| L1 | 15 | 55157598 | C | A | 0.00530939 | 0.0202115 | 0.00530939 |
| L1 | 15 | 55139964 | G | A | 0.00524553 | -0.0202017 | 0.00524553 |
| L1 | 15 | 55139771 | C | CA | 0.0050837 | -0.0201762 | 0.0050837 |
| L1 | 15 | 55142175 | T | C | 0.00505264 | -0.0201712 | 0.00505264 |
| L1 | 15 | 55142417 | C | CA | 0.00504953 | -0.0201707 | 0.00504953 |
| L1 | 15 | 55161311 | A | G | 0.00488197 | 0.0201433 | 0.00488197 |
| L1 | 15 | 55139544 | A | C | 0.00488022 | -0.020143 | 0.00488022 |
| L1 | 15 | 55142359 | T | C | 0.00487064 | -0.0201414 | 0.00487064 |
| L1 | 15 | 55142285 | G | A | 0.00484012 | -0.0201363 | 0.00484012 |
| L1 | 15 | 55169774 | A | T | 0.00479019 | 0.0201279 | 0.00479019 |
| L1 | 15 | 55139224 | A | G | 0.00471216 | -0.0201145 | 0.00471216 |
| L1 | 15 | 55139290 | C | G | 0.00470535 | -0.0201133 | 0.00470535 |
| L1 | 15 | 55152652 | A | G | 0.00461872 | 0.0200982 | 0.00461872 |
| L1 | 15 | 55139155 | G | A | 0.00451411 | -0.0200795 | 0.00451411 |
| L1 | 15 | 55163547 | A | G | 0.00450927 | -0.0200786 | 0.00450927 |
| L1 | 15 | 55170143 | T | C | 0.00450508 | -0.0200778 | 0.00450508 |
| L1 | 15 | 55140017 | G | A | 0.0044235 | -0.0200629 | 0.0044235 |
| L1 | 15 | 55165540 | T | C | 0.00427123 | -0.0200343 | 0.00427123 |
| L1 | 15 | 55139377 | T | A | 0.00425802 | -0.0200318 | 0.00425802 |
| L1 | 15 | 55170256 | A | G | 0.00425796 | -0.0200317 | 0.00425796 |
| L1 | 15 | 55184544 | G | A | 0.00424669 | 0.0200296 | 0.00424669 |
| L1 | 15 | 55139200 | G | C | 0.00422039 | -0.0200245 | 0.00422039 |
| L1 | 15 | 55139422 | G | A | 0.00421633 | -0.0200237 | 0.00421633 |
| L1 | 15 | 55139887 | T | C | 0.00391255 | -0.0199624 | 0.00391255 |
| L1 | 15 | 55170268 | C | T | 0.00390411 | 0.0199607 | 0.00390411 |
| L1 | 15 | 55165718 | C | G | 0.00374692 | -0.0199269 | 0.00374692 |
| L1 | 15 | 55167006 | C | T | 0.00361574 | 0.0198976 | 0.00361574 |
| L1 | 15 | 55171011 | C | T | 0.00358585 | 0.0198907 | 0.00358585 |
| L1 | 15 | 55165263 | G | C | 0.00352309 | 0.0198762 | 0.00352309 |
| L1 | 15 | 55165574 | A | C | 0.00346833 | -0.0198632 | 0.00346833 |
| L1 | 15 | 55177426 | A | G | 0.00311969 | 0.0197757 | 0.00311969 |
| L1 | 15 | 55144960 | T | C | 0.00275204 | -0.0196715 | 0.00275204 |
| L1 | 15 | 55150442 | C | T | 0.00270635 | -0.0196575 | 0.00270635 |
| L1 | 15 | 55144812 | C | T | 0.00266382 | -0.0196443 | 0.00266382 |
| L1 | 15 | 55146363 | A | C | 0.00266234 | -0.0196439 | 0.00266234 |
| L1 | 15 | 55146375 | T | A | 0.00266234 | -0.0196439 | 0.00266234 |
| L1 | 15 | 55148502 | C | A | 0.00257041 | -0.0196145 | 0.00257041 |
| L1 | 15 | 55144024 | T | C | 0.00255165 | -0.0196084 | 0.00255165 |
| L1 | 15 | 55149334 | C | G | 0.00251331 | -0.0195957 | 0.00251331 |
| L1 | 15 | 55148611 | A | G | 0.00248078 | -0.0195849 | 0.00248078 |
| L1 | 15 | 55146427 | T | C | 0.00246719 | 0.0195803 | 0.00246719 |
| L1 | 15 | 55146437 | C | T | 0.00246719 | 0.0195803 | 0.00246719 |
| L1 | 15 | 55146428 | A | AT | 0.00246719 | 0.0195803 | 0.00246719 |
| L1 | 15 | 55146430 | C | G | 0.00246719 | 0.0195803 | 0.00246719 |
| L1 | 15 | 55146419 | A | G | 0.00246711 | 0.0195802 | 0.00246711 |
| L1 | 15 | 55146422 | A | G | 0.00246711 | 0.0195802 | 0.00246711 |
| L1 | 15 | 55149475 | A | G | 0.00246539 | -0.0195796 | 0.00246539 |
| L1 | 15 | 55144410 | A | T | 0.00246278 | -0.0195788 | 0.00246278 |
| L1 | 15 | 55148803 | G | A | 0.00244612 | -0.0195731 | 0.00244612 |
| L1 | 15 | 55156790 | A | C | 0.0024296 | 0.0195674 | 0.0024296 |
| L1 | 15 | 55149391 | C | T | 0.00241855 | -0.0195636 | 0.00241855 |
| L1 | 15 | 55146402 | T | A | 0.00241219 | -0.0195614 | 0.00241219 |
| L1 | 15 | 55143693 | C | T | 0.00240553 | -0.0195591 | 0.00240553 |
| L1 | 15 | 55147758 | G | A | 0.00239269 | -0.0195546 | 0.00239269 |
| L1 | 15 | 55148142 | A | C | 0.00236545 | -0.019545 | 0.00236545 |
| L1 | 15 | 55144342 | A | G | 0.00236339 | -0.0195443 | 0.00236339 |
| L1 | 15 | 55149415 | C | T | 0.00235917 | -0.0195428 | 0.00235917 |
| L1 | 15 | 55144927 | A | G | 0.00235142 | -0.01954 | 0.00235142 |
| L1 | 15 | 55148017 | C | T | 0.00234663 | -0.0195383 | 0.00234663 |
| L1 | 15 | 55145552 | C | CA | 0.00234551 | -0.0195379 | 0.00234551 |
| L1 | 15 | 55148332 | G | A | 0.00232851 | -0.0195318 | 0.00232851 |
| L1 | 15 | 55149268 | G | C | 0.00231774 | -0.0195279 | 0.00231774 |
| L1 | 15 | 55143433 | G | A | 0.00231069 | -0.0195253 | 0.00231069 |
| L1 | 15 | 55146202 | A | G | 0.0023089 | -0.0195247 | 0.0023089 |
| L1 | 15 | 55144589 | C | T | 0.00230817 | -0.0195244 | 0.00230817 |
| L1 | 15 | 55144447 | A | T | 0.00230358 | -0.0195227 | 0.00230358 |
| L1 | 15 | 55143681 | C | T | 0.00226321 | -0.0195079 | 0.00226321 |
| L1 | 15 | 55143755 | T | C | 0.00225717 | -0.0195057 | 0.00225717 |
| L1 | 15 | 55143666 | G | A | 0.00225665 | -0.0195055 | 0.00225665 |
| L1 | 15 | 55142858 | A | C | 0.00224818 | -0.0195023 | 0.00224818 |
| L1 | 15 | 55144666 | G | A | 0.00224718 | -0.0195019 | 0.00224718 |
| L1 | 15 | 55149211 | T | C | 0.00223003 | -0.0194955 | 0.00223003 |
| L1 | 15 | 55144181 | G | C | 0.00222661 | -0.0194942 | 0.00222661 |
| L1 | 15 | 55143399 | C | G | 0.00221813 | -0.019491 | 0.00221813 |
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Genetics Delivery Team, Thibaud Boutin, Andrew D Bretherick, Joshua J Dibble, Esther Ewaoluwagbemiga, Emma Northwood, Gemma L Samms, Veronique Vitart, Project, Cohort Delivery Team, Øyvind Almelid, and others. Initial findings from the DecodeME genome-wide association study of myalgic encephalomyelitis/chronic fatigue syndrome. medRxiv, pages 2025–08, 2025. URL: https://www.medrxiv.org/content/10.1101/2025.08.06.25333109v1. ↩
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Gao Wang, Abhishek Sarkar, Peter Carbonetto, and Matthew Stephens. A simple new approach to variable selection in regression, with application to genetic fine mapping. Journal of the Royal Statistical Society Series B: Statistical Methodology, 82(5):1273–1300, 2020. URL: https://academic.oup.com/jrsssb/article/82/5/1273/7056114. ↩