Abstract
The transmission disequilibrium test (TDT) has been employed to map disease susceptibility loci (DSL), while being immune to the problem of population admixture. The customary TDT test (TDTD) was developed for affected child(ren) and their parents and was most often applied to case-parent trios. Recently, the TDT has been extended to the situations when (1) parents are not available but affected and nonaffected sibs from each family are available, (2) unrelated control-parent trios are available for combined analyses with case-parent trios (TDTDC), and (3) large pedigrees. For many diseases, affected children in the case-parent trios enlisted into the TDTD have unaffected sibs who can be recruited. We present an extension of the TDT by effectively incorporating one unaffected sib of each of the affected children in the case-parent trios into a single analysis (TDTDS, where DS denotes discordant sib pairs). We have developed a general analytical method for computing the statistical power of the TDTDS under any genetic model, the accuracy of which is validated by computer simulations. We compare the power of the TDTD, TDTDS under a range of parameter space and genetic models. We find that the TDTDS is generally more powerful than the TDTDC and TDTD, particularly when the disease is prevalent (>30%) in the population. The relative power of the TDTD and the TDTDS largely depends upon the allele frequencies and genetic effects at the DSL, whereas the recombination rate, the degree of linkage disequilibrium, and the marker allele frequencies have little effect. Importantly, the TDTDS not only may be more powerful, it also has the advantage of being able to test for segregation distortion that may yield false linkage/association in the TDTD.
| Original language | English |
|---|---|
| Pages (from-to) | 451-461 |
| Number of pages | 11 |
| Journal | Human Genetics |
| Volume | 110 |
| Issue number | 5 |
| DOIs | |
| State | Published - May 2002 |
| Externally published | Yes |
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All Science Journal Classification (ASJC) codes
- Genetics(clinical)
- Genetics
Cite this
Transmission disequilibrium test with discordant sib pairs when parents ae available. / Deng, Hong Wen; Chen, Wei Min; Recker, Robert R.
In: Human Genetics, Vol. 110, No. 5, 05.2002, p. 451-461.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Transmission disequilibrium test with discordant sib pairs when parents ae available
AU - Deng, Hong Wen
AU - Chen, Wei Min
AU - Recker, Robert R.
PY - 2002/5
Y1 - 2002/5
N2 - The transmission disequilibrium test (TDT) has been employed to map disease susceptibility loci (DSL), while being immune to the problem of population admixture. The customary TDT test (TDTD) was developed for affected child(ren) and their parents and was most often applied to case-parent trios. Recently, the TDT has been extended to the situations when (1) parents are not available but affected and nonaffected sibs from each family are available, (2) unrelated control-parent trios are available for combined analyses with case-parent trios (TDTDC), and (3) large pedigrees. For many diseases, affected children in the case-parent trios enlisted into the TDTD have unaffected sibs who can be recruited. We present an extension of the TDT by effectively incorporating one unaffected sib of each of the affected children in the case-parent trios into a single analysis (TDTDS, where DS denotes discordant sib pairs). We have developed a general analytical method for computing the statistical power of the TDTDS under any genetic model, the accuracy of which is validated by computer simulations. We compare the power of the TDTD, TDTDS under a range of parameter space and genetic models. We find that the TDTDS is generally more powerful than the TDTDC and TDTD, particularly when the disease is prevalent (>30%) in the population. The relative power of the TDTD and the TDTDS largely depends upon the allele frequencies and genetic effects at the DSL, whereas the recombination rate, the degree of linkage disequilibrium, and the marker allele frequencies have little effect. Importantly, the TDTDS not only may be more powerful, it also has the advantage of being able to test for segregation distortion that may yield false linkage/association in the TDTD.
AB - The transmission disequilibrium test (TDT) has been employed to map disease susceptibility loci (DSL), while being immune to the problem of population admixture. The customary TDT test (TDTD) was developed for affected child(ren) and their parents and was most often applied to case-parent trios. Recently, the TDT has been extended to the situations when (1) parents are not available but affected and nonaffected sibs from each family are available, (2) unrelated control-parent trios are available for combined analyses with case-parent trios (TDTDC), and (3) large pedigrees. For many diseases, affected children in the case-parent trios enlisted into the TDTD have unaffected sibs who can be recruited. We present an extension of the TDT by effectively incorporating one unaffected sib of each of the affected children in the case-parent trios into a single analysis (TDTDS, where DS denotes discordant sib pairs). We have developed a general analytical method for computing the statistical power of the TDTDS under any genetic model, the accuracy of which is validated by computer simulations. We compare the power of the TDTD, TDTDS under a range of parameter space and genetic models. We find that the TDTDS is generally more powerful than the TDTDC and TDTD, particularly when the disease is prevalent (>30%) in the population. The relative power of the TDTD and the TDTDS largely depends upon the allele frequencies and genetic effects at the DSL, whereas the recombination rate, the degree of linkage disequilibrium, and the marker allele frequencies have little effect. Importantly, the TDTDS not only may be more powerful, it also has the advantage of being able to test for segregation distortion that may yield false linkage/association in the TDTD.
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U2 - 10.1007/s00439-002-0675-9
DO - 10.1007/s00439-002-0675-9
M3 - Article
VL - 110
SP - 451
EP - 461
JO - Human Genetics
JF - Human Genetics
SN - 0340-6717
IS - 5
ER -