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Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
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Epistasis detectably alters correlations between genomic sites in a narrow parameter window
Gabriele Pedruzzi1, Igor M Rouzine1
1Sorbonne Université, Institute de Biologie Paris-Seine, Laboratoire de Biologie Computationelle et Quantitative, LCQB, Paris, France.
Plos One
|June 1, 2019
Summary
Epistasis and linkage cause correlations in allele frequencies, known as linkage disequilibrium (LD). This study models their interaction, finding epistasis detection improves with stronger recombination, but fundamental restrictions exist for identifying true genetic interactions.
Area of Science:
- Genomics
- Population Genetics
- Evolutionary Biology
Background:
- Genomic sites interact due to epistasis (non-multiplicative allele effects) and physical linkage.
- Epistasis and linkage create correlations in allele frequencies (linkage disequilibrium, LD), influenced by recombination.
Purpose of the Study:
- To model and compare the contributions of epistasis and linkage to LD in an adapting population.
- To understand the relative sensitivity of epistasis and linkage to recombination.
- To identify fundamental restrictions in detecting true genetic interactions.
Main Methods:
- Modeling an adapting population with mutation, selection, epistasis, and genetic drift.
- Utilizing haplotype-based measures of LD for epistatic and non-epistatic pairs.
- Analyzing optimal detection percentages and false positive rates in population samples.
Main Results:
- True epistatic interactions are detectable within specific genomic and temporal windows, especially with strong recombination.
- Shared ancestry can create stochastic LD, masking epistasis in non-interacting pairs, particularly in smaller populations.
- Epistasis detection improves as linkage effects diminish faster than epistasis with increased recombination.
Conclusions:
- Epistasis's contribution to locus association can be isolated by averaging haplotype frequencies across multiple populations.
- Fundamental limitations exist for detecting true genetic interactions in DNA sequence datasets.
- Recombination plays a crucial role in distinguishing between epistasis and linkage effects.
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