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If, ultimately, the claims-reporting requirement for Medicare Advantage plans is not enforced, this may limit the value of linkages like the one described in this paper.
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The R2 value of linkage disequilibrium was calculated for all possible marker pairs within each chromosome.
To detect the small-effect QTL, the threshold value of linkage was set as P = 0.05 (Chi-square test).
To identify these potential small-effect QTL, we reanalyzed the data using a lower threshold value of linkage (P = 0.05).
Most of these genomic regions did not reach a genome-wide significant threshold value of linkage, with P values between 0.05 and 0.001 [ 1- 5].
This suggests that there must be other susceptibility genes whose contributions were not big enough to reach the stringent significance threshold value of linkage analysis.
In the case of a sufficiently large positive value of linkage disequilibrium (D' > 0.9), the polarization mark is assigned to 1, whereas in the case of a sufficiently large negative linkage disequilibrium (D' < -0.9) the polarization mark is assigned to -1.
However, Cia2 contributed to only 16% of the phenotype variations, indicating that there should be some small-effect QTL whose contributions to CIA were not big enough to reach the significant threshold value of linkage.
We also performed similar calculations assuming that the interaction was observed at a nearby noncausal locus H with minor allele frequency p B = 0.2 and the maximum value of linkage disequilibrium r between alleles at the disease susceptibility locus G.
There are algebraic restrictions on the range of r (10), and the maximum value of linkage disequilibrium between alleles at G and H when p B = 0.2 depends on the value of p A: When p A = 0.1, maximum r = 0.44; when p A = 0.25, maximum r = 0.75; and when p A = 0.4, maximum r = 0.37.
In this study we assess the importance of these differences by analysing birth cohorts in DIN and GPRD to: (i) compare the volume of recording of prescribing and diagnostic codes in DIN and GPRD (both overall and by examining variation between practices); (ii) examine the value of linkage for identifying explicitly the reason for prescribing.
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