title: Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data.
abstract: Next-generation sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the human leukocyte antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population genomics analyses, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the single-nucleotide polymorphisms (SNPs) reported by 1000G (phase I) at five HLA genes (HLA-A, -B, -C, -DRB1, and -DQB1). We take advantage of the availability of HLA Sanger sequencing of 930 of the 1092 1000G samples and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls in HLA genes are incorrect and that allele frequencies are estimated with an error greater than ±0.1 at approximately 25% of the SNPs in HLA genes. We found a bias toward overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates and discuss the outcomes of including those sites in different kinds of analyses. Because the HLA region is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity.
authors: Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090 São Paulo, SP, Brazil.
authors: Débora Y C
authors: DY
authors: Brandt
authors: Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090 São Paulo, SP, Brazil.
authors: Vitor R C
authors: VR
authors: Aguiar
authors: Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090 São Paulo, SP, Brazil.
authors: Bárbara D
authors: http://orcid.org/0000-0001-7676-9367
authors: BD
authors: Bitarello
authors: Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090 São Paulo, SP, Brazil.
authors: Kelly
authors: K
authors: Nunes
authors: Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors: Jérôme
authors: J
authors: Goudet
authors: Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090 São Paulo, SP, Brazil diogo@ib.usp.br.
authors: Diogo
authors: http://orcid.org/0000-0002-7155-5674
authors: D
authors: Meyer
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D005787:Gene Frequency; D005828:Genetics, Population; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D005838:Genotype; D006680:HLA Antigens / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans
chemical_list: D006680:HLA Antigens
keywords: 1000 Genomes; HLA; NGS; mapping bias