Multiple haplotype reconstruction from allele frequency data

Pelizzola, Marta; Behr, Merle; Li, Housen; Munk, Axel; Futschik, Andreas

doi:10.1038/s43588-021-00056-5

Cited by 9 publications

(18 citation statements)

References 53 publications

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“…Additional results for Gaussian noise with standard deviation 0.05 are reported in Figure A.8 in the Appendix, which confirm the findings from Figure 2. Further, we compared our posterior mean estimates with those obtained by the frequentist method from [15]. We found the accuracy of both approaches to be very close.…”

Section: Randomly Generated S and ωmentioning

confidence: 88%

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Bayesian linear models with unknown design over finite alphabets

Wang

Futschik

Dutta

2022

Preprint

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Our topic is the reconstruction of the unknown matricesSandωfor the multivariate linear modelY=Sω+εunder the assumption that the entries ofSare drawn from the finite alphabet 𝔄 = 0, 1 andωis a weight matrix. While a frequentist method has recently been proposed for this purpose, a Bayesian approach seems also desirable. We therefore provide a new hierarchical Bayesian method for this inferential task. Our approach provides estimates of the posterior that may be used to quantify uncertainty. Since matching permutations in bothSandωlead to the same reconstructionSω, we introduce an order-preserving shrinkage prior to establish identifiability with respect to permutations.

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Section: Randomly Generated S and ωmentioning

confidence: 88%

“…• ω init : The initialization of ω is obtained using the method provided by [15], the details of this algorithm can be found in the supplementary information (algorithm 2).…”

Section: Posterior Computation For Finite Alphabet Design Initializat...mentioning

confidence: 99%

Bayesian linear models with unknown design over finite alphabets

Wang

Futschik

Dutta

2022

Preprint

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“…In order to apply haplotype based tests, we focus on relatively short genomic windows such that the haplotypes are not affected by recombination and their frequency changes can be followed over time. In [17] the window size for various organisms is provided such that the impact of recombination can be assumed negligible, which may be used as a guideline. We demonstrate that haplotype based tests are more powerful than traditional SNP based approaches for E&R experiments when the number of haplotypes is small to moderate.…”

Section: Discussionmentioning

confidence: 99%

“…. respectively by ranking the normalised differences in frequency change over time and test the hypothesis: (17) as long as the previous null hypothesis is rejected. The method of normalisation, the N e computation, and the testing procedure are analogous as before.…”

Section: Testing For the Number Of Selected Haplotypesmentioning

confidence: 99%

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Haplotype based testing for a better understanding of the selective architecture

Chen

Pelizzola

Futschik

2022

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The identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here we provide a new testing approach that uses haplotype frequencies instead of allele frequencies. With this approach, less multiple testing correction is needed, which leads to tests with higher power, especially when the number of candidate haplotypes is small or moderate. Another advantage is that haplotype frequencies can often be recovered with less noise than SNP frequencies, especially under pool sequencing. For a larger number of haplotypes, we investigate methods to combine them to a moderate number of haplotype subsets. The use of haplotypes also permits a better understanding of selective signatures. For this purpose, we propose post hoc tests for the selected haplotypes and differences between their selection coefficients. Using both simulated and real data sets, we illustrate the performance and benefits of our proposed test statistics.

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