General Information

Data visualization and download of summary statistics of GWAS of nuMoM2b traits (Human genome: GRCh38)

---

Guidelines

1. Trait Description

- Incorporate as many genetically related pregnancy traits as possible, excluding trisomy and self-reported race traits;

- Traits were filtered based on the above flowchart, resulting in 479 “original traits” used. There are more “traits” than “original traits” because one nominal “original trait” is recoded to multiple “one vs. rest” variables. For instance, PEgHTN_7 indicates 7 vs. sum(1 to 6), where 7 is the testing level and sum(1 to 6) is the reference level. The filters applied used total sample size, not ancestry specific sample size;

- Certain variables were measured at multiple visit: _v1 indicates visit 1 (6-13 weeks), _v2 indicates visit 2 (16-21 weeks), and _v3 indicates visit 3 (22-29 weeks);

- Check n_EUR, n_AFR and n_AMR to determine if the corresponding GWAS is available for the specific trait and sample size. If N/A is displayed, the corresponding GWAS is unavailable. When the GWAS is available, input the trait into the GWAS Manhattan Plot to obtain GWAS results.




2. GWAS Manhattan Plot

- Visualize and download GWAS results, only SNPs with P-value<0.05 are stored in the database;

- Trait ~ SNP + maternal age + distance to median maternal age + PC1:PC10 for continuous and ordered categorical traits, BETA is effect size;

- logit(P(Trait=1)) ~ SNP + maternal age + distance to median maternal age + PC1:PC10 for binary traits, including recoded “one vs. rest” variables, BETA is log(OR);

- In Meta results, column “Direction” indicates the effect directions of Europeans, Africans, and Admixed Americans. For example, ?+? indicates positive effect only in Africans, and Europeans and Admixed Americans are missing; --? indicates consistent negative effects of Europeans and Africans, and Admixed Americans are missing; +++ indicates all ancestry groups have consistent positive effects.




3. PheWAS Plot

- Visualize and download PheWAS results, if one is interested in a specific SNP’s associations with all pregnancy traits.

- In Meta results, column “Direction” indicates the effect directions of Europeans, Africans, and Admixed Americans. Same description as above.

---

How to cite

Yan, Q., Guerrero, R.F., Khan, R.R., Surujnarine, A.A., Wapner, R.J., et al. (2023). Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b. Genetics 225

---

Contact Information

Qi Yan - qy2253@cumc.columbia.edu

---

Download all results

EUR (90Gb)     AFR (137Gb)     AMR (78Gb)     Meta (163Gb)

---