Non-parametric Linkage Analysis
4.7.4.1
I have viewed the npl on chromosome 20 and all other chromosomes in general then focused on the region of interest in family #1 (described in 4.7.1.2).
4.7.4.1.1 Npl for chromosome 20 and others
The maximum multipoint npl LOD score for chromosome 20 is 2.04, at a region closed to the P-Telomere, but upstream from the region of the interest in family #1. Another region with LOD score of 2.00 downstream from the region of interest in family #1.
Three SNPs have single point LODs >2.0 and they are; rs2327790 at 33.25 cM with LOD score of 2.7, rs1028846 at 29.01cM and rs1535487 at 41.86cM, both provide LOD score of and 2.4. Further 23 SNPs have LODs > 1.0 (out of 58 SNPs) at the same region of maximum multipoint LOD score (Figure 4.13). That has supported the region identified in multipoint analysis.
In addition the maximum LOD scores on other chromosomes were between 0.12 & 0.17 among chromosomes 1, 9, 10, 11, 13, 15 & 22, while maximum LOD scores on chromosomes 2, 3, 8 & X were 0.67, 0.59, 0.84 & 0.97 respectively. In addition maximum LOD scores between 0.21 and 0.31were obtained on chromosomes 4, 14, 16, 18 & 21. In contrast only chromosome 5 showed maximum LOD score of <0.0, while maximum LOD scores of < 0.1 were obtained for chromosomes 6, 7, & 12 & 19, as seen in (Figure 4.14).
4.7.4.1.2 Analysis at the region of interest in family #1
The region of interest in family #1 (described in 4.7.1.2) was focused on and the npl multipoint analysis of the merge data of family #1 & #2 showed LOD score of 2.0 among the whole region (Figure 4.13).
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Figure 4.14; Graph showing the maximum and minimum LOD scores (of all chromosomes), obtained by non- parametric linkage analysis on merge data of family #1 and family #2. All chromosomes showed maximum LOD score <1.00, except chromosomes 17 & 20 where the maximum LOD scores are <2 and >2 respectively. Figure 4.13; Graph showing regional plot of chromosome 20 comparing LOD scores obtained using multi- point non-parametric linkage (npl), (blue solid line) and single point npl (red dots), for the merged data of family #1 & #2. The maximum LOD score was 2.04, at a region close to the P-Telomere of the chromosome, but upstream from (20p12.3-p11.23, where family #1 showed maximum LOD). Another region with LOD score of 2 was obtained at a region downstream from (20p12.3-p11.23). Single point analysis supported multipoint with LODs >2.0 and higher ( 2.7 at 33.3cM and 2.4 at 29.01cM and 41.86cM).
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Parametric Linkage Analysis (Dominant)
4.7.4.2
I have observed the npl on chromosome 20 and all other chromosomes in general then focused on the region of interest in family #1 (described in 4.7.1.2).
4.7.4.2.1 Dominant analysis for chromosome 20 and others
The maximum dominant (multipoint) LOD score for chromosome 20 is 2.3, at a region closed to the P-Telomere, but upstream the region of the interest in family #1.
Sixteen SNPs have single point LODs > 1.1 (one of which was 1.9), and further 7 SNPs have LODs 6 (out of 58 SNPs) at the same region of multipoint high LOD (Figure 4.13). That has supported the region identified in multipoint Analysis.
In addition only 7 chromosomes showed maximum LODs > 0.0. These were 2, 3, 4, 16, 17, 20 & X, with chromosome 20 the highest in all with LOD 2.3. (Figure 4.16) Show the maximum and minimum Dominant LODs on each chromosome.
4.7.4.2.2 Analysis at the region of interest in family #1
I have focused more on the region of interest in family #1 (described in 4.7.1.2), and the dominant multipoint analysis of the merged data of family #1 & #2, showed maximum LOD scores of 0.5 among the whole region as seen in (Figure 4.15).
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Figure 4.15; Graph showing regional plot of chromosome 20 comparing LOD scores obtained using multi-point dominant (blue solid line) and single point dominant (red dots), for the merged data of family #1 & #2. The maximum LOD score was 2.3, at a region close to the P-Telomere of the chromosome, but upstream from (20p12.3-p11.23, where maximum LOD obtained in family #1), and was supported by single- point npl in which the maximum npl LOD score was 1.9 & below.
Figure 4.16; Graph showing the maximum and minimum LOD scores (of all chromosomes), obtained by dominant linkage analysis on merge data of family #1 and family #2. All chromosomes showed maximum LOD score <1.00, except chromosome 20 where the maximum LOD scores is 2.3 which is higher than what obtained by the data of family #1 only
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4.8 Conclusion
In view of the family history and phenotypic similarity in family #1 and family #2, I hypothesized that genetic variants in both families would be similar and thus analysed the only available DNA sample of family #2 (from 6 individuals). By analysing these few individuals, the main target was to look at the region of interest in family #1 (between 20p12.3 and 20p11.23). My intention was to add the LOD scores for the two families; however the analysis of family #2 at that region did not support those for family #1. In fact the findings had a negative impact since adding the LOD scores reduced that obtained in family #1 alone. Examining the two GWLA data sets (of family #1 and family #2) across chromosomes on other than the target region have shown no significant findings with maximum LODs of 0.90 in npl, 0.89 in Dominant analysis and < 0.5 in recessive analyses.
Specifically, performing GWLA on the merged data of both families has decreased the maximum npl LODs (from 3.01 in family #1 only) to 2.0, at that region of interest. However, single point npl has shown a maximum LOD score of 2.7 at rs2327790 (33.25 cM), and 2.4 at 2 NSPs; rs1028846 (29.01) and rs1535487 (41.86). The gene at the region with LOD score of 2.7 (rs2327790 at 33.25 cM) is TASP1 (Taspase Threonine Aspartase, 1), encodes a protein required for the maintenance of HOX gene expression. The gene at the region with LOD score of 2.4 (rs1028846 at 29.01cM) is BTBD3, which is the last gene in the list of the 10 genes in family #1. The second gene in the region with LOD score of 2.4 (rs1535487 at 41.86 cM) is SLC24A3, described as solute carrier family 24 and encodes sodium/calcium transporter, a member of the family of K(+)-dependent Na(+)/Ca(2+) exchangers [268]. Same findings obtained in dominant analysis on chromosome 20, as the maximum LOD for family #1 only was 2.03, but for the data of both families it was 2.3, at a region closed to the P- Telomere, but upstream the region of the interest in family #1.
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