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Measuring Haplotype Rarity

Cross-comparability across marker sets

Again with Taylor data only, we investigated the question of whether the measurement systems were consistent across marker sets, Did haplotypes score the same at different numbers of markers? It was, of course, possible to look at only the 50% who had results for all marker sets.

At first glance, scores seemed inconsistent across the marker sets. However, correlation coefficients were mostly high, ranging from a low of 0.179 to a high of 0.998. The least significance observed  was p=0.0123[1] (Wheaton: 25 vs. 67).

Table  11
Comparability Across Marker Sets<
n= 196 Wheaton Ratio Deviation
12
mkrs
37
mkrs
12
mkrs
37
mkrs
12
mkrs
37
mkrs
12 markers   * 0.665   * 0.680   * 0.755
25 markers 0.731 0.931 0.703 0.984 0.998 0.695
37 markers 0.665   * 0.680   * 0.755   *
67 markers 0.233 0.265 0.285 0.341 0.695 0.923

  Significance
12 markers   * =0.001   * <.0001   * <.0001
25 markers <.0001 <.0001 <.0001 <.0001 <.0001 <.0001
37 markers <.0001   * <.0001   * <.0001 <.0001
67 markers 0.001 =0.0002 <.0001 <.0001 <.0001   *

Rank Correlation

Haplotypes were ranked by scores for each marker set in each of the three methods and then the rankings were compared.

As to rank correlation, correlation coefficients ranged from 0.181 to 0.9384 and least significance was p=0.0113.

Table 12
Cross-comparability of Rankings,
n= 196 Wheaton Ratio Deviation
12 mkrs 37 mkrs 12 mkrs 37 mkrs 12 mkrs 37 mkrs
12 markers   * 0.588   * 0.662   * 0.211
25 markers 0.685 0.890 0.759 0.938 0.776 0.210
37 markers 0.588   * 0.662   * 0.181 0.249
67 markers 0.214 0.316 0.285 0.324 0.211   *
Significance
12 markers   * <0.0001   * <0.0001   * =0.011
25 markers <0.0001 <0.0001 <0.0001 <0.0001 <0.0001 =0.001
37 markers <0.0001   * <0.0001   * =0.011   *
67 markers =0.0027 <.0001 <0.0001 <0.0001 =0.003 =0.0004

Comment: While the correlations are significant, at least some is due to inclusion of smaller marker sets within larger; the 67-marker set includes the 37-, as does 37- include 25-, etc. It is specifically not suggested that scores for markers 1-12 are related to scores for markers 13-25, 26-37 or 38-67. We suspect that scores for markers 1-12 will not correlate with 13-25, etc.

Summary

There is some limited comparability across the four marker sets, due largely to the inclusion of smaller sets within larger.