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The effect of selective sampling on mapping quantitative trait loci

N J Camp1, A Bansal

  • 1Section of Molecular Medicine, University of Sheffield, UK.

Genetic Epidemiology
|January 1, 1997
PubMed
Summary
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Selective sampling in sib pairs for quantitative traits (Q1) showed similar genome screen results to all pairs, but reduced power for detecting quantitative trait loci (QTLs). False positive rates remained comparable across methods.

Area of Science:

  • Genetics
  • Statistical Genetics
  • Genomic Analysis

Background:

  • Quantitative trait locus (QTL) detection is crucial for understanding complex traits.
  • Selective sampling strategies aim to increase efficiency in genetic studies.
  • The impact of selective sampling on genome-wide linkage analysis requires careful evaluation.

Purpose of the Study:

  • To compare the effectiveness of selective sampling criteria (SC1, SC2) against analyzing all sib pairs (ALL) for QTL detection.
  • To assess the impact of selective sampling on linkage analysis power and false positive rates for a simulated quantitative trait (Q1).

Main Methods:

  • Utilized 773 sib pairs from GAW10, applying two selective sampling criteria (SC1, SC2) and analyzing all pairs (ALL).
  • Performed whole genome screens across 10 data replicates for each sampling criterion.

Related Experiment Videos

  • Conducted fine screens on suggestive linkage regions and validated findings in an independent replicate.

    • Main Results:

    • Genome screen results were broadly similar across ALL, SC1, and SC2, with stricter selection yielding lower maxima and more erratic lod scores.
    • The major QTL on chromosome 5 (22% variance) was detected in 6/10 replicates with ALL, and 4/10 with SC1/SC2.
    • A minor QTL on chromosome 8 (0.5% variance) was detected in only one replicate using SC1; false positive rates were comparable, but power decreased with selective sampling.

    Conclusions:

    • Selective sampling did not substantially alter coarse genome screen results but reduced power for detecting QTLs, potentially due to initial sample size limitations.
    • False positive rates were similar across selective and non-selective sampling methods.
    • Further investigation with larger sample sizes is warranted to optimize selective sampling strategies in genetic studies.