An integrated in silico gene mapping strategy in inbred mice

Abstract

In recent years in silico analysis of common laboratory mice has been introduced and subsequently applied, in slightly different ways, as a methodology for gene mapping. Previously we have demonstrated some limitation of the methodology due to sporadic genetic correlations across the genome. Here, we revisit the three main aspects that affect in silico analysis. First, we report on the use of marker maps: we compared our existing 20,000 SNP map to the newly released 140,000 SNP map. Second, we investigated the effect of varying strain numbers on power to map QTL. Third, we introduced a novel statistical approach: a cladistic analysis, which is well suited for mouse genetics and has increased flexibility over existing in silico approaches. We have found that in our examples of complex traits, in silico analysis by itself does fail to uniquely identify quantitative trait gene (QTG)-containing regions. However, when combined with additional information, it may significantly help to prioritize candidate genes. We therefore recommend using an integrated work flow that uses other genomic information such as linkage regions, regions of shared ancestry, and gene expression information to obtain a list of candidate genes from the genome.

Figure 1.—

Comparison between the 20K map (top, A and B) and the 140K map (bottom, A and B). (A) Points represent the association between the albinism phenotype and individual SNPs. Colors represent different chromosomes. Tyrosinase is located on chromosome 7. (B) Points represent the association between the albinism phenotype and haplotypes of length 3 using cladistic analysis. Colors represent different chromosomes. Tyrosinase is located on chromosome 7.

Figure 1.—

Comparison between the 20K map (top, A and B) and the 140K map (bottom, A and B). (A) Points represent the association between the albinism phenotype and individual SNPs. Colors represent different chromosomes. Tyrosinase is located on chromosome 7. (B) Points represent the association between the albinism phenotype and haplotypes of length 3 using cladistic analysis. Colors represent different chromosomes. Tyrosinase is located on chromosome 7.

Figure 2.—

Comparison between the 20K map (top, A and B) and the 140K map (bottom, A and B). (A) Points represent the association between the albinism phenotype and individual SNPs along chromosome 7. The position of the tyrosinase gene is represented by a red line. (B) Points represent the association between the albinism phenotype and haplotypes of length 3 using cladistic analysis along chromosome 7. The position of the tyrosinase gene is represented by a red line.

Figure 2.—

Comparison between the 20K map (top, A and B) and the 140K map (bottom, A and B). (A) Points represent the association between the albinism phenotype and individual SNPs along chromosome 7. The position of the tyrosinase gene is represented by a red line. (B) Points represent the association between the albinism phenotype and haplotypes of length 3 using cladistic analysis along chromosome 7. The position of the tyrosinase gene is represented by a red line.

Figure 3.—

Comparison between the 20K map (top, A and B) and the 140K map (bottom, A and B). (A) Points represent the association between the blindness phenotype and individual SNPs along chromosome 5. The position of the pde6b gene is represented by a red line. (B) Points represent the association between the blindness phenotype and haplotypes of length 3 using cladistic analysis along chromosome 5. The position of the pde6b gene is represented by a red line.

Figure 3.—

Comparison between the 20K map (top, A and B) and the 140K map (bottom, A and B). (A) Points represent the association between the blindness phenotype and individual SNPs along chromosome 5. The position of the pde6b gene is represented by a red line. (B) Points represent the association between the blindness phenotype and haplotypes of length 3 using cladistic analysis along chromosome 5. The position of the pde6b gene is represented by a red line.

Figure 4.—

Cladistic analysis based on a 10-SNP haplotype. Similar haplotypes are merged into groups and a test for association is performed at each level of the tree. Missing data are allowed as illustrated here.“〈NA〉” indicates missing genotype.

Figure 5.—

Comparison of the different algorithms in estimating gene position in a Mendelian trait. (A) P-value distribution using a single-marker analysis (S140). (B) Cladistic analysis with a 3-SNP haplotype (C140.3). (C) Cladistic analysis with a 10-SNP haplotype (C140.10). (D) Cladistic analysis of length 100 kb (C140.sli). (E) C140.3 after applying a smoother. (F) C140.10 after applying a smoother. (G) C140.sli after applying a smoother. The x-axis represents the base-pair position along chromosome 7; the underlying gene for albinism, tyrosinase, is situated at 74.5 Mb.

Figure 5.—

Comparison of the different algorithms in estimating gene position in a Mendelian trait. (A) P-value distribution using a single-marker analysis (S140). (B) Cladistic analysis with a 3-SNP haplotype (C140.3). (C) Cladistic analysis with a 10-SNP haplotype (C140.10). (D) Cladistic analysis of length 100 kb (C140.sli). (E) C140.3 after applying a smoother. (F) C140.10 after applying a smoother. (G) C140.sli after applying a smoother. The x-axis represents the base-pair position along chromosome 7; the underlying gene for albinism, tyrosinase, is situated at 74.5 Mb.

Figure 6.—

Comparison of the different algorithms in estimating gene position in a complex trait. (A) P-value distribution using a single-marker analysis (S140). (B) Cladistic analysis with a 3-SNP haplotype (C140.3). (C) Cladistic analysis with a 10-SNP haplotype (C140.10). (D) Cladistic analysis of length 100 kb (C140.sli). (E) C140.3 after applying a smoother. (F) C140.10 after applying a smoother. (G) C140.sli after applying a smoother. The x-axis represents the base-pair position along chromosome 1; one contributing gene for cholesterol, ApoA2, is situated at 171.3 Mb and is represented by a vertical line.

Figure 6.—

Comparison of the different algorithms in estimating gene position in a complex trait. (A) P-value distribution using a single-marker analysis (S140). (B) Cladistic analysis with a 3-SNP haplotype (C140.3). (C) Cladistic analysis with a 10-SNP haplotype (C140.10). (D) Cladistic analysis of length 100 kb (C140.sli). (E) C140.3 after applying a smoother. (F) C140.10 after applying a smoother. (G) C140.sli after applying a smoother. The x-axis represents the base-pair position along chromosome 1; one contributing gene for cholesterol, ApoA2, is situated at 171.3 Mb and is represented by a vertical line.

Figure 7.—

An integrated strategy for narrowing down the genome to a list of candidate genes. Integrated work flow brings in information from linkage analysis, IBD blocks, in silico analysis, and gene expression to obtain a short list of candidate genes. This example is based on the cholesterol trait.