{"users":[{"id":660,"username":"Ofure_U","name":"Ofure Ubah","avatar_template":"/user_avatar/isgw-forum.colorado.edu/ofure_u/{size}/627_2.png","trust_level":0},{"id":486,"username":"JamesHart","name":"Jimmy Hart","avatar_template":"/letter_avatar_proxy/v4/letter/j/f07891/{size}.png","primary_group_name":"2025-Participants","flair_name":"2025-Participants","flair_group_id":46,"trust_level":0},{"id":311,"username":"l.yengo","name":"Loic Yengo","avatar_template":"/letter_avatar_proxy/v4/letter/l/a9adbd/{size}.png","primary_group_name":"Faculty","flair_name":"Faculty","flair_group_id":41,"trust_level":3},{"id":708,"username":"kristen","name":"Kristen","avatar_template":"/letter_avatar_proxy/v4/letter/k/c4cdca/{size}.png","trust_level":3},{"id":7,"username":"davide","name":"David Evans","avatar_template":"/letter_avatar_proxy/v4/letter/d/258eb7/{size}.png","primary_group_name":"Faculty","flair_name":"Faculty","flair_group_id":41,"moderator":true,"trust_level":4},{"id":727,"username":"Kristien_vdWalt","name":"Kristien van der Walt","avatar_template":"/user_avatar/isgw-forum.colorado.edu/kristien_vdwalt/{size}/625_2.png","trust_level":0},{"id":6,"username":"anonymous","name":"anonymous","avatar_template":"/letter_avatar_proxy/v4/letter/a/8491ac/{size}.png","trust_level":3},{"id":579,"username":"helenl","name":"Helen","avatar_template":"/letter_avatar_proxy/v4/letter/h/b5ac83/{size}.png","trust_level":1},{"id":526,"username":"jeongah.lee","name":"","avatar_template":"/user_avatar/isgw-forum.colorado.edu/jeongah.lee/{size}/624_2.png","trust_level":0},{"id":550,"username":"bastien.rioux","name":"Bastien Rioux","avatar_template":"/letter_avatar_proxy/v4/letter/b/f9ae1b/{size}.png","trust_level":1},{"id":625,"username":"jense180","name":"Lily","avatar_template":"/letter_avatar_proxy/v4/letter/j/ea5d25/{size}.png","trust_level":1},{"id":658,"username":"dmitrk02","name":"DmitryK","avatar_template":"/letter_avatar_proxy/v4/letter/d/8edcca/{size}.png","trust_level":1}],"primary_groups":[{"id":46,"name":"2025-Participants"},{"id":41,"name":"Faculty"}],"flair_groups":[{"id":46,"name":"2025-Participants","flair_url":null,"flair_bg_color":"","flair_color":""},{"id":41,"name":"Faculty","flair_url":null,"flair_bg_color":"","flair_color":""}],"topic_list":{"can_create_topic":false,"filter":"latest","more_topics_url":"/c/isg-workshops-2026/28?page=1","per_page":30,"top_tags":[{"id":3,"name":"r","slug":"r"},{"id":2,"name":"openmx","slug":"openmx"},{"id":14,"name":"sem","slug":"sem"},{"id":1,"name":"gcta","slug":"gcta"},{"id":9,"name":"genomicsem","slug":"genomicsem"},{"id":8,"name":"plink","slug":"plink"}],"topics":[{"fancy_title":"Cross-Ancestry eQTL","id":922,"title":"Cross-Ancestry eQTL","slug":"cross-ancestry-eqtl","posts_count":5,"reply_count":2,"highest_post_number":5,"image_url":null,"created_at":"2026-06-29T23:33:57.561Z","last_posted_at":"2026-07-12T21:10:34.026Z","bumped":true,"bumped_at":"2026-07-12T21:10:34.026Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Thanks for the fantastic lectures. I had previously asked this question during the lecture but need a reiteration including helpful resources as I am new to this kind of analysis “Is it correct practice to conduct eQTL a&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":43,"like_count":2,"has_summary":false,"last_poster_username":"Ofure_U","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest","description":"Original Poster, Most Recent Poster","user_id":660,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Recent Poster","user_id":486,"primary_group_id":46,"flair_group_id":46},{"extras":null,"description":"Recent Poster","user_id":311,"primary_group_id":41,"flair_group_id":41}]},{"fancy_title":"Liability scale h2 from meta-analysis data","id":835,"title":"Liability scale h2 from meta-analysis data","slug":"liability-scale-h2-from-meta-analysis-data","posts_count":3,"reply_count":1,"highest_post_number":3,"image_url":null,"created_at":"2026-06-09T21:00:47.537Z","last_posted_at":"2026-06-17T18:09:57.518Z","bumped":true,"bumped_at":"2026-06-17T18:09:57.518Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"In the video on the munge() function, it was mentioned that for meta-analyses nEff needed to be calculated as the sum of nEff from each contributing sample rather than an overall nEff based on overall case/control preval&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":34,"like_count":2,"has_summary":false,"last_poster_username":"JamesHart","category_id":35,"op_like_count":1,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":708,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":486,"primary_group_id":46,"flair_group_id":46}]},{"fancy_title":"MR QC - how can strand issues for palindromic SNPs happen with modern genotyping?","id":847,"title":"MR QC - how can strand issues for palindromic SNPs happen with modern genotyping?","slug":"mr-qc-how-can-strand-issues-for-palindromic-snps-happen-with-modern-genotyping","posts_count":4,"reply_count":2,"highest_post_number":4,"image_url":null,"created_at":"2026-06-10T06:21:33.561Z","last_posted_at":"2026-06-16T18:28:29.947Z","bumped":true,"bumped_at":"2026-06-16T18:28:29.947Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"In the first video about sensitivity analysis for Mendelian Randomization, it mentions that people often exclude palindromic SNPs because of the possibility of strand issues (but that sometimes things like allele frequen&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":33,"like_count":0,"has_summary":false,"last_poster_username":"davide","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":708,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":7,"primary_group_id":41,"flair_group_id":41}]},{"fancy_title":"FastMAP or meta-analysing fine-mapping statistics","id":920,"title":"FastMAP or meta-analysing fine-mapping statistics","slug":"fastmap-or-meta-analysing-fine-mapping-statistics","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-12T14:15:26.525Z","last_posted_at":"2026-06-12T14:15:26.581Z","bumped":true,"bumped_at":"2026-06-12T14:15:26.581Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hi, \nThank you for the very helpful fine-mapping lectures!! I am interested in applying the FastMAP tool to combine cohort-specific fine-mapping results, but I was unable to find the tool/publication on a quick google se&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":31,"like_count":0,"has_summary":false,"last_poster_username":"Kristien_vdWalt","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":727,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"PIP Thresholds","id":919,"title":"PIP Thresholds","slug":"pip-thresholds","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:52:52.694Z","last_posted_at":"2026-06-11T22:52:52.738Z","bumped":true,"bumped_at":"2026-06-11T22:52:52.738Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"What is the PIP cut-off for reliable causal? \n\nReplying to “What is the PIP cut-off for reliable causal?”: \n\n0.9 is usually people use, which basically translates to: 10% of the variants with PIP&gt;0.9 are expected to be f&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":19,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Fine-Mapping Window Size","id":917,"title":"Fine-Mapping Window Size","slug":"fine-mapping-window-size","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:50:46.827Z","last_posted_at":"2026-06-11T22:50:46.881Z","bumped":true,"bumped_at":"2026-06-11T22:50:46.881Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"In the prerecorded videos Ran suggested using a 3MB window around the lead variant, but I’ve also seen pipelines use 1Mb or even 500kb. How should we think about what window size is best to use? \n\nReplying to “In the pre&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":27,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Computing In-Sample LD for Large Cohorts","id":916,"title":"Computing In-Sample LD for Large Cohorts","slug":"computing-in-sample-ld-for-large-cohorts","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:50:09.995Z","last_posted_at":"2026-06-11T22:50:10.043Z","bumped":true,"bumped_at":"2026-06-11T22:50:10.043Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"What is the best approach for computing in-sample LD for a larger cohort (+100.000), without it being very computationally intensive? \n\nReplying to “What is the best approach for computing in-sample …”: \n\nGreat question &hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":17,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Non-Additive Effects, cis-QTLs, and trans-QTLs","id":915,"title":"Non-Additive Effects, cis-QTLs, and trans-QTLs","slug":"non-additive-effects-cis-qtls-and-trans-qtls","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:49:38.853Z","last_posted_at":"2026-06-11T22:49:38.929Z","bumped":true,"bumped_at":"2026-06-11T22:49:38.929Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"I was wondering if you could go over how we define the types of effects we expect. More concretely (And I don’t have a good biological rationale for this) would we expect different types of effect - i.e. trans QTL having&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":24,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Credible Sets and Number of Causal Variants","id":913,"title":"Credible Sets and Number of Causal Variants","slug":"credible-sets-and-number-of-causal-variants","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:49:02.260Z","last_posted_at":"2026-06-11T22:49:02.311Z","bumped":true,"bumped_at":"2026-06-11T22:49:02.311Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"How do you decide how many SNPs to allow in your credible set? I see that we can manual set that # \n\nReplying to “How do you decide how many SNPs to allow in your c…”: \n\nYou may be looking at the number of causal variant&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":17,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"External LD Matrices and Fine-Mapping","id":912,"title":"External LD Matrices and Fine-Mapping","slug":"external-ld-matrices-and-fine-mapping","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:47:12.477Z","last_posted_at":"2026-06-11T22:47:12.529Z","bumped":true,"bumped_at":"2026-06-11T22:47:12.529Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"If you don’t have access to the within-sample LD matrix (e.g., using 23andMe sum stats), how can you control for false positives generated by using an external LD matrix. \nFor example: \nEuropean 23andMe GWAS sum stats \nL&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":16,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Minor Alleles, QQ Plots, and Practical Answers","id":911,"title":"Minor Alleles, QQ Plots, and Practical Answers","slug":"minor-alleles-qq-plots-and-practical-answers","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:46:39.881Z","last_posted_at":"2026-06-11T22:46:39.929Z","bumped":true,"bumped_at":"2026-06-11T22:46:39.929Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Two questions: \nI noticed males were coded as 0 and females were coded a 1. Isn’t this opposite of the most frequent way this is coded? \nIs the answer for Q14 also incorrect? the answer is listed as 4,189,956 cis, 35,789&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":13,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Functional Annotation of Highly Correlated Traits","id":910,"title":"Functional Annotation of Highly Correlated Traits","slug":"functional-annotation-of-highly-correlated-traits","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:45:29.912Z","last_posted_at":"2026-06-11T22:45:29.962Z","bumped":true,"bumped_at":"2026-06-11T22:45:29.962Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"If you have a genetic correlation between two traits (let’s say 0.9) that have a strong correlation from LDSC regression - is it possible and worth doing functional annotation of these traits to see if they differ biolog&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":16,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Environmental Effects and G×E in QTL Analyses","id":909,"title":"Environmental Effects and G×E in QTL Analyses","slug":"environmental-effects-and-gxe-in-qtl-analyses","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T22:44:57.608Z","last_posted_at":"2026-06-11T22:44:57.659Z","bumped":true,"bumped_at":"2026-06-11T22:44:57.659Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"how do we model environmental effects or gene–environment interactions in the QTL analyses, it is the same as looking into key covariates such as age, sex, ancestry principal components , thank \n\nReplying to “how do we m&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":14,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Multi-cohort fine mapping approach","id":908,"title":"Multi-cohort fine mapping approach","slug":"multi-cohort-fine-mapping-approach","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T21:01:02.823Z","last_posted_at":"2026-06-11T21:01:02.866Z","bumped":true,"bumped_at":"2026-06-11T21:01:02.866Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Question about multi-cohort fine mapping as taught at the end of the video on Statistical fine-mapping part 2: would a joint modeling approach be expected to be more accurate than the combining approach, and if so, why? &hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":19,"like_count":0,"has_summary":false,"last_poster_username":"helenl","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":579,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Weighted Mode Estimates","id":907,"title":"Weighted Mode Estimates","slug":"weighted-mode-estimates","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T16:06:09.509Z","last_posted_at":"2026-06-11T16:06:09.559Z","bumped":true,"bumped_at":"2026-06-11T16:06:09.559Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"How was that weighted mode estimate picked from all the other estimates that the function output? Smallest standard error? \n\nReplying to “How was that weighted mode estimate picked from al…”: \n\nSorry I understand what yo&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":17,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"MR Across Ancestries","id":905,"title":"MR Across Ancestries","slug":"mr-across-ancestries","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T16:05:35.496Z","last_posted_at":"2026-06-11T16:05:35.555Z","bumped":true,"bumped_at":"2026-06-11T16:05:35.555Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"do MR results translate well to other ancestries? is there a way to avaluate that? \nhttps://www.researchsquare.com/article/rs-6091701/v1 \n\nReplying to “do MR results translate well to other ancestries? …”: \n\nIn general, &hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":16,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Exposure Strength and Instrument Quality","id":904,"title":"Exposure Strength and Instrument Quality","slug":"exposure-strength-and-instrument-quality","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T16:04:47.199Z","last_posted_at":"2026-06-11T16:04:47.250Z","bumped":true,"bumped_at":"2026-06-11T16:04:47.250Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Is there a certain minimum SNP heritabilty required for the exposure? Or minimum VAF for a SNP? \n\nReplying to “Is there a certain minimum SNP heritabilty require…”: \n\nThe strength of the exposure-SNP association the key &hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":20,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"InSIDE Assumption","id":903,"title":"InSIDE Assumption","slug":"inside-assumption","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T16:03:26.720Z","last_posted_at":"2026-06-11T16:03:26.767Z","bumped":true,"bumped_at":"2026-06-11T16:03:26.767Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"is there a test to see if the InSIDE assumption holds? If the assumption is that the SNP-exposure effects aren’t correlated with the SNP-outcome effects can’t we just test that empirically? \n\nReplying to “is there a test&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":15,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Wald Ratio P-values and Standard Errors","id":901,"title":"Wald Ratio P-values and Standard Errors","slug":"wald-ratio-p-values-and-standard-errors","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T16:02:53.837Z","last_posted_at":"2026-06-11T16:02:53.890Z","bumped":true,"bumped_at":"2026-06-11T16:02:53.890Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"I might miss something but how to get p value and SE for a Wald ratio (Q9) \n\nReplying to “I might miss something but how to get p value and …”: \n\nbeta/SE ~ Z(0,1) \n\nReplying to “I might miss something but how to get p va&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":15,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Requirements for MR Exposures","id":900,"title":"Requirements for MR Exposures","slug":"requirements-for-mr-exposures","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T16:02:21.510Z","last_posted_at":"2026-06-11T16:02:21.557Z","bumped":true,"bumped_at":"2026-06-11T16:02:21.557Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"You have reviewed the requirements for SNPs, but what are the requirements for exposures? Do they need to be certain types of traits? \n\nReplying to “You have reviewed the requirements for SNPs, but w…”: \n\nHere’s a nice a&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":19,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Colocalisation vs MR-Egger Intercept","id":899,"title":"Colocalisation vs MR-Egger Intercept","slug":"colocalisation-vs-mr-egger-intercept","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T15:48:35.809Z","last_posted_at":"2026-06-11T15:48:35.859Z","bumped":true,"bumped_at":"2026-06-11T15:48:35.859Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"How should we interpret an MR result that shows strong colocalisation but also a significant MR-Egger intercept? Thanks. \n\nReplying to “How should we interpret an MR result that shows st…”: \n\ncolocalisation suggests that&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":21,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Pleiotropy and MR Assumptions","id":898,"title":"Pleiotropy and MR Assumptions","slug":"pleiotropy-and-mr-assumptions","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T15:47:57.202Z","last_posted_at":"2026-06-11T15:47:57.249Z","bumped":true,"bumped_at":"2026-06-11T15:47:57.249Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Does the pliatropy (I can’t spell) concern influence the second assumption as well (i.e. no SNP influences on confounders)? Thanks :slightly_smiling_face: \n\nReplying to “Does the pliatropy (I can’t spell) concern influen&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":14,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"MR Assumption 3 (Exclusion Restriction)","id":896,"title":"MR Assumption 3 (Exclusion Restriction)","slug":"mr-assumption-3-exclusion-restriction","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T15:47:22.441Z","last_posted_at":"2026-06-11T15:47:22.487Z","bumped":true,"bumped_at":"2026-06-11T15:47:22.487Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"By third assumption, you mean SNP marginally not associated with outcome? \n\nReplying to “By third assumption, you mean SNP marginally not …”: \n\nMarginally, it is expected to be associated (via the exposure variable). But&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":13,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Multiple Exposures in MR","id":895,"title":"Multiple Exposures in MR","slug":"multiple-exposures-in-mr","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T15:46:04.085Z","last_posted_at":"2026-06-11T15:46:04.146Z","bumped":true,"bumped_at":"2026-06-11T15:46:04.146Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"How is it possible to model 2SMR with multiple traits or outcomes? \n\nReplying to “How is it possible to model 2SMR with multiple tra…”: \n\nIf you want to include multiple exposures you can (under certain assumptions) use &hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":14,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Ascertainment Bias and Mendelian Randomization Assumptions","id":894,"title":"Ascertainment Bias and Mendelian Randomization Assumptions","slug":"ascertainment-bias-and-mendelian-randomization-assumptions","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T15:45:21.579Z","last_posted_at":"2026-06-11T15:45:21.632Z","bumped":true,"bumped_at":"2026-06-11T15:45:21.632Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Would ascertainment bias affect the assumption of the random segregation of alleles? \n\nReplying to “Would ascertainment bias affect the assumption of …”: \n\nI would say no- ascertainment bias wouldn’t affect random segreg&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":12,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Fine-mapping strategy in a difficult meta-analysis setting","id":893,"title":"Fine-mapping strategy in a difficult meta-analysis setting","slug":"fine-mapping-strategy-in-a-difficult-meta-analysis-setting","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-11T15:00:55.292Z","last_posted_at":"2026-06-11T15:00:55.340Z","bumped":true,"bumped_at":"2026-06-11T15:00:55.340Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"I would like to get advice on how to deal with the following scenario. \nScenario \n\n\nI have GWAS summary statistics from a large meta-analysis of mixed-ancestry cohorts (multi-ancestry meta-GWAS). \n\n\nI do not have access &hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":20,"like_count":0,"has_summary":false,"last_poster_username":"jeongah.lee","category_id":37,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":526,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Random effects IVW analysis","id":892,"title":"Random effects IVW analysis","slug":"random-effects-ivw-analysis","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2026-06-10T15:20:32.862Z","last_posted_at":"2026-06-11T11:14:58.576Z","bumped":true,"bumped_at":"2026-06-11T11:14:58.576Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Is there an advantage to use the random-effects version of IVW in MR? Would you use it as a primary analysis vs the fixed effect?","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":27,"like_count":0,"has_summary":false,"last_poster_username":"davide","category_id":36,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":550,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":7,"primary_group_id":41,"flair_group_id":41}]},{"fancy_title":"RCode for doing biometric moderation?","id":883,"title":"RCode for doing biometric moderation?","slug":"rcode-for-doing-biometric-moderation","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2026-06-10T14:17:29.782Z","last_posted_at":"2026-06-10T20:37:04.591Z","bumped":true,"bumped_at":"2026-06-10T20:37:04.591Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"I am interested in testing whether a biometric moderation model in which genetic influences on personality vary as a function of relationship satisfaction provides a better fit to the data than a model without moderation&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":37,"like_count":1,"has_summary":false,"last_poster_username":"dmitrk02","category_id":32,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":625,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":658,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Problems and Assumptions of LDSC h²","id":891,"title":"Problems and Assumptions of LDSC h²","slug":"problems-and-assumptions-of-ldsc-h","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-10T14:29:10.744Z","last_posted_at":"2026-06-10T14:29:10.793Z","bumped":true,"bumped_at":"2026-06-10T14:29:10.793Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Does h2 from LDSC have similar problems with h2 from HE regression/GREML (e.g., Shared environmental effects, population stratification, MAF and LD heterogeneity)? \n\nReplying to “Does h2 from LDSC have similar problems w&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":16,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":35,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Sample Overlap in LDSC","id":890,"title":"Sample Overlap in LDSC","slug":"sample-overlap-in-ldsc","posts_count":1,"reply_count":0,"highest_post_number":1,"image_url":null,"created_at":"2026-06-10T14:27:53.565Z","last_posted_at":"2026-06-10T14:27:53.614Z","bumped":true,"bumped_at":"2026-06-10T14:27:53.614Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"If they’re not independent samples for LDSC, could there be bias from sample overlap? \n\nReplying to “If they’re not independent samples for LDSC, could…”: \n\nSample overlap only bias the intercept. The slope of the regres&hellip;","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags":[],"tags_descriptions":{},"views":13,"like_count":0,"has_summary":false,"last_poster_username":"anonymous","category_id":35,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_vote":false,"posters":[{"extras":"latest single","description":"Original Poster, Most Recent Poster","user_id":6,"primary_group_id":null,"flair_group_id":null}]}]}}