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. 2000:663-74.
doi: 10.1142/9789814447331_0064.

An analytic solution to single nucleotide polymorphism error-detection rates in nuclear families: implications for study design

D Gordon  1 , S M Leal, S C Heath, J Ott
Affiliations

An analytic solution to single nucleotide polymorphism error-detection rates in nuclear families: implications for study design

D Gordon et al. Pac Symp Biocomput. 2000.

Abstract

Recently, there has been increased interest in using Single Nucleotide Polymorphisms (SNPs) as a method for detecting genes for complex traits. SNPs are diallelic markers that have the potential to be inexpensively produced using chip technology. It has been suggested that SNPs will be beneficial in study designs that utilize trio data (father, mother, child). In our previous work, we calculated the probability of detecting Mendelian errors at a SNP locus for a trio randomly selected from a population in Hardy-Weinberg equilibrium. The highest error-detection rate was 30%. Here we investigate the error-detection rate when additional sibs are genotyped. We define an error to be a change from a 1 allele to a 2 allele, or vice versa. Typing one additional sib increases the detection rate on average by 10-13%. Typing two additional sibs increases the detection rate on average by 14-19%. The increase in the detection rate is dependent on the allele frequencies. Equal allele frequencies produce the lowest detection rates, independent of true error rates and number of offspring genotyped. Typing additional siblings not only improves error-detection rates, but can also provide additional linkage information. In order to increase linkage information and error-detection rates, at least two additional siblings should be ascertained when available.

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Figures

Figure 1.
Figure 1.
Error-Detection Rate for quartets as function of allele frequency and true error rate
Figure 2.
Figure 2.
Error-Detection Rate for quintets as function of allele frequency and true error rate
See this image and copyright information in PMC

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References

    1. Risch N, Merikangas K, Science 273, 1516 (1996) - PubMed
    1. Wang DG et al., Science 280, 1077 (1998) - PubMed
    1. Falk CT, Rubinstein P, Ann Hum Genet 51, 227 (1987) - PubMed
    1. Spielman RS, McGinnis RE, Ewens WJ, Am J Hum Genet 52(3), 506 (1993) - PMC - PubMed
    1. Spielman RS, Ewens WJ, Am J Hum Genet 59(5), 983 (1996) - PMC - PubMed

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