Genome-wide association mapping of quantitative traits in NMRI outbred mice

Description

Our genome wide assoication study using 288 outbred NMRI mice was performed to map loci influencing HDL cholesterol, systolic blood pressure, triglyceride levels, glucose, and urinary albumin-to-creatinine ratios. Tail-cuff blood pressure was measured in 8-week-old mice, and systolic blood pressure (SBP), diastolic blood pressure (DPB) and mean arterial pressure (MAP) was calculated. Once the mice were 10-weeks-old, urine samples were collected, and urinary albumin and creatinine concentrations were measured. A series of mouse albumin standards was also quantified. Blood samples were obtained from each mouse and measurement of total cholesterol (CHL), HDL cholesterol (HDL), triglycerides (TG), and glucose (GLU) performed. Genomic DNA samples were genotyped using the Mouse Diversity Genotyping Array (Yang et al. 2009). For further details see Zhang et al. 2011.

Reference

Genome-Wide Association Mapping of Quantitative Traits in Outbred Mice
Zhang W, Korstanje R, Thaisz J, Staedtler F, Harttman N, Xu L, Feng M, Yanas L, Yang H, Valdar W, Churchill GA, DiPetrillo K.
G3 (Bethesda). 2012 Feb;2(2):167-74. PMCID: PMC3284324 [ Full Text ]

Datasets


Phenotype

pheno_raw.csv
288 animals with 8 phenotypes: systolic blood pressure (SBP), diastolic blood pressure (DPB), mean arterial pressure (MAP), urinary albumin-to-creatinine ratios (ACR), HDL cholesterol (HDL), total cholesterol (CHL), triglycerides (TRI) and glucose (GLU).
The PedNum column represents animal IDs.

Genotype

snps.dat.collapsed.csv
44,428 SNPs from 288 animals.
The genotypes are coded as 0, 0.5 and 1 corresponding to AA, AB and BB genotypes, respectively.
The description of columns are as follows:
1. chr: chr ID
2. mb37: base pair position (NCBI Build 37)
3. medianPos (median of base pair positions for the identical SNPs in the 2Mb interval)
4. probeset_id,
5. 292: Animal IDs e.g. X301 corresponds to the animal 301 in the phenotype data