# Downstream analysis with genomic data **URL:** https://isgw-forum.colorado.edu/c/downstream-anslysis-genomic-data/27.md [Latest](https://isgw-forum.colorado.edu/latest.md) · [Categories](https://isgw-forum.colorado.edu/categories.md) · [Tags](https://isgw-forum.colorado.edu/tags.md) --- ## [About the Downstream analysis with genomic data category](https://isgw-forum.colorado.edu/t/about-the-downstream-analysis-with-genomic-data-category/456)
**Author:** [@matthew\_keller](https://isgw-forum.colorado.edu/u/matthew_keller)\ **Replies:** 0
Downstream analysis that use whole-genome data, such as LD score regression, GREML, Genomic SEM, Mendelian randomization, etc. --- ## [Apakah layanan GoPay 24 jam?](https://isgw-forum.colorado.edu/t/apakah-layanan-gopay-24-jam/945)
**Author:** [@Quan](https://isgw-forum.colorado.edu/u/Quan)\ **Replies:** 0\ **Last updated:** [October 17, 2026, 9:54am UTC](https://isgw-forum.colorado.edu/t/apakah-layanan-gopay-24-jam/945 "2026-10-17T09:54:56Z")
Ya, layanan "Gopay’ 24 jam melalui (+62.857.6990.8715) WhatsApp dapat diakses 24/7 jam, memungkinkan Anda mendapatkan bantuan dan informasi. --- ## [Nomor Call Center Gopay](https://isgw-forum.colorado.edu/t/nomor-call-center-gopay/939)
**Author:** [@Quan](https://isgw-forum.colorado.edu/u/Quan)\ **Replies:** 0\ **Last updated:** [October 17, 2026, 9:41am UTC](https://isgw-forum.colorado.edu/t/nomor-call-center-gopay/939 "2026-10-17T09:41:46Z")
GoPay kini memiliki nomor WhatsApp resmi 62 857-6990-8715. resmi yang terverifikasi dapat diakses 24/7 jam. --- ## [Palindromic SNPS](https://isgw-forum.colorado.edu/t/palindromic-snps/926)
**Author:** [@jameeberg](https://isgw-forum.colorado.edu/u/jameeberg)\ **Replies:** 0\ **Last updated:** [July 6, 2026, 12:56pm UTC](https://isgw-forum.colorado.edu/t/palindromic-snps/926 "2026-07-06T12:56:36Z")
Hi, All, I would like to make a note of when it is necessary to remove palindromic SNPs from analyses downstream of GWAS. For these analyses, the effect allele and reference alleles are always annotated. It seems it is… --- ## [Resources for learning about Structural Equation Modeling (SEM)](https://isgw-forum.colorado.edu/t/resources-for-learning-about-structural-equation-modeling-sem/836)
**Author:** [@bml](https://isgw-forum.colorado.edu/u/bml)\ **Replies:** 0\ **Last updated:** [June 10, 2026, 12:24am UTC](https://isgw-forum.colorado.edu/t/resources-for-learning-about-structural-equation-modeling-sem/836 "2026-06-10T00:24:10Z")
Re-posting a question that I and another person had during a live practical session. What resources would you recommend to learn about SEM, for folks new to this? --- ## [Question about SNP-heritability and alleles in PLINK](https://isgw-forum.colorado.edu/t/question-about-snp-heritability-and-alleles-in-plink/755)
**Author:** [@Shal](https://isgw-forum.colorado.edu/u/Shal)\ **Replies:** 0\ **Last updated:** [June 2, 2026, 10:55am UTC](https://isgw-forum.colorado.edu/t/question-about-snp-heritability-and-alleles-in-plink/755 "2026-06-02T10:55:34Z")
Hi Loic, Thank you again for the wonderful session yesterday. I have a question about heritability. When we have a large sample size, is it standard practice to use PLINK to estimate SNP-heritability in a set of unrela… --- ## [LDSC for rG -\> Neff or N](https://isgw-forum.colorado.edu/t/ldsc-for-rg-neff-or-n/724)
**Author:** [@JamesHart](https://isgw-forum.colorado.edu/u/JamesHart)\ **Replies:** 1\ **Last updated:** [April 21, 2026, 12:29pm UTC](https://isgw-forum.colorado.edu/t/ldsc-for-rg-neff-or-n/724 "2026-04-21T12:29:06Z")
Hi everyone! Does it matter if you use N effective or N total, when running LDSC for cross trait rG? I’m aware it will impact heritability estimates but not sure if only worried about rG. --- ## [LD proxies for TwoSampleMR](https://isgw-forum.colorado.edu/t/ld-proxies-for-twosamplemr/725)
**Author:** [@JamesHart](https://isgw-forum.colorado.edu/u/JamesHart)\ **Replies:** 2\ **Last updated:** [August 24, 2025, 7:13pm UTC](https://isgw-forum.colorado.edu/t/ld-proxies-for-twosamplemr/725 "2025-08-24T19:13:08Z")
Hi everyone! Does anyone have a nice guide for adding in LD proxies for missing SNPs in outcome GWAS for use in two sample mr? Thanks so much! --- ## [Asking a theoretical question about LDSC](https://isgw-forum.colorado.edu/t/asking-a-theoretical-question-about-ldsc/726)
**Author:** [@xueyingqin](https://isgw-forum.colorado.edu/u/xueyingqin)\ **Replies:** 3\ **Last updated:** [June 26, 2025, 3:24pm UTC](https://isgw-forum.colorado.edu/t/asking-a-theoretical-question-about-ldsc/726 "2025-06-26T15:24:29Z")
Hi Professors, I would like to ask a question about LDSC. Since bivariate LDSC could calculate genetic correlation between two traits X and Y, I don’t know whether it is correct to understand the genetic correlation in … --- ## [Multivariate GWAS with GenomicSEM](https://isgw-forum.colorado.edu/t/multivariate-gwas-with-genomicsem/650)
**Author:** [@rcupertino](https://isgw-forum.colorado.edu/u/rcupertino)\ **Replies:** 0\ **Last updated:** [August 15, 2024, 9:46pm UTC](https://isgw-forum.colorado.edu/t/multivariate-gwas-with-genomicsem/650 "2024-08-15T21:46:56Z")
Hi, I’m trying to run a multivariate GWAS using GenomicSEM. I munged the sumstats, did ldsc and I’m having error with the function sumstats, see below: files ← c(“ftnd\_wave3\_meta\_analysis\_summary\_stats.all\_chr.eur.txt”… --- ## [Transmitted and non-transmitted alleles](https://isgw-forum.colorado.edu/t/transmitted-and-non-transmitted-alleles/644)
**Author:** [@michek18](https://isgw-forum.colorado.edu/u/michek18)\ **Replies:** 0\ **Last updated:** [April 23, 2024, 12:33am UTC](https://isgw-forum.colorado.edu/t/transmitted-and-non-transmitted-alleles/644 "2024-04-23T00:33:10Z")
Hi, I’ve been revisiting the lecture on “Estimating Intergenerational Transmission” by Jared Balbona. I am confused about the influence of paternal and maternal Familial Environment (FE; Fp and Fm). Based on Jared’s exa… --- ## [MR with SEM](https://isgw-forum.colorado.edu/t/mr-with-sem/634)
**Author:** [@rcupertino](https://isgw-forum.colorado.edu/u/rcupertino)\ **Replies:** 2\ **Last updated:** [March 8, 2024, 11:37pm UTC](https://isgw-forum.colorado.edu/t/mr-with-sem/634 "2024-03-08T23:37:27Z")
@davide mention today about MR with SEM. Is there any recommended material on that? --- ## [Bottoms Up vs Top Down GWAS](https://isgw-forum.colorado.edu/t/bottoms-up-vs-top-down-gwas/528)
**Author:** [@JD3874](https://isgw-forum.colorado.edu/u/JD3874)\ **Replies:** 1\ **Last updated:** [March 10, 2023, 11:47pm UTC](https://isgw-forum.colorado.edu/t/bottoms-up-vs-top-down-gwas/528 "2023-03-10T23:47:30Z")
We talked about the the issues behind not being able to replicate GWAS results, issues with linkage disequilibrium, etc. Is it possible to bypass LD and improve replication accuracy by performing GWAS or a variation … --- ## [Significant negative heritability in LDSC](https://isgw-forum.colorado.edu/t/significant-negative-heritability-in-ldsc/522)
**Author:** [@Giaco](https://isgw-forum.colorado.edu/u/Giaco)\ **Replies:** 2\ **Last updated:** [March 10, 2023, 10:26pm UTC](https://isgw-forum.colorado.edu/t/significant-negative-heritability-in-ldsc/522 "2023-03-10T22:26:17Z")
I wondered whether someone could help me understand negative (and significant) h2snp estimates (estimated via either LDSC or stratified LDSC). And if there is some good reference on how to deal with them. Many thanks! … --- ## [Ancestry admixtures and ld scores](https://isgw-forum.colorado.edu/t/ancestry-admixtures-and-ld-scores/514)
**Author:** [@docherty.anna](https://isgw-forum.colorado.edu/u/docherty.anna)\ **Replies:** 1\ **Last updated:** [March 10, 2023, 5:31pm UTC](https://isgw-forum.colorado.edu/t/ancestry-admixtures-and-ld-scores/514 "2023-03-10T17:31:44Z")
OK, 2 questions. I have an African American ancestry GWAS meta-analysis and used cov-adjusted LD scores from UKBB AFR to run LDSC. The attenuation ratio was high. Thinking that gnomAD might better fit the ancestry admixt… --- ## [Backing out effective sample size](https://isgw-forum.colorado.edu/t/backing-out-effective-sample-size/523)
**Author:** [@Andrew\_Grotzinger](https://isgw-forum.colorado.edu/u/Andrew_Grotzinger)\ **Replies:** 0\ **Last updated:** [March 10, 2023, 4:58pm UTC](https://isgw-forum.colorado.edu/t/backing-out-effective-sample-size/523 "2023-03-10T16:58:35Z")
Hi everyone, There were several questions yesterday that centered around how to get the appropriate effective sample size for various situations (e.g., when analyzing GWAS data with related individuals, for case/control… --- ## [PRS vs Mendelian Randomisation](https://isgw-forum.colorado.edu/t/prs-vs-mendelian-randomisation/521)
**Author:** [@salahudeen\_mirza](https://isgw-forum.colorado.edu/u/salahudeen_mirza)\ **Replies:** 1\ **Last updated:** [March 9, 2023, 5:18pm UTC](https://isgw-forum.colorado.edu/t/prs-vs-mendelian-randomisation/521 "2023-03-09T17:18:56Z")
Hi everyone, I was wondering aside from the methodological difference what the major theory difference would be in using a PRS vs MR approach to understand exposure outcome association. For example if we take the example… --- ## [Copy code for LDSC practical](https://isgw-forum.colorado.edu/t/copy-code-for-ldsc-practical/518)
**Author:** [@Andrew\_Grotzinger](https://isgw-forum.colorado.edu/u/Andrew_Grotzinger)\ **Replies:** 0\ **Last updated:** [March 8, 2023, 8:52pm UTC](https://isgw-forum.colorado.edu/t/copy-code-for-ldsc-practical/518 "2023-03-08T20:52:26Z")
cp -r /faculty/andrew/LDSC\_Practical\_2023 .