Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

BioRxiv : the Preprint Server for Biology
Paul D BlischakAndrea D Wolfe

Abstract

Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty--ADU), which complicates the calculation of important quantities such as allele frequencies. Here we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high throughput sequencing data in the form of read counts.We bridge the gap from data collection (using restriction enzyme based techniques [e.g., GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package POLYFREQS and demonstrate its use with two example analyses that investigate (i) levels of expected and observed hetero...Continue Reading

Related Concepts

Alleles
Guillain-Barre Syndrome
Restriction Mapping
Computer Software
Evaluation
Simulation
Single Nucleotide Polymorphism
Comparative Genomic Analysis
Analysis
Population Group

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.