title: Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data.
abstract: Analyses investigating low frequency variants have the potential for explaining additional genetic heritability of many complex human traits. However, the natural frequencies of rare variation between human populations strongly confound genetic analyses. We have applied a novel collapsing method to identify biological features with low frequency variant burden differences in thirteen populations sequenced by the 1000 Genomes Project. Our flexible collapsing tool utilizes expert biological knowledge from multiple publicly available database sources to direct feature selection. Variants were collapsed according to genetically driven features, such as evolutionary conserved regions, regulatory regions genes, and pathways. We have conducted an extensive comparison of low frequency variant burden differences (MAF<0.03) between populations from 1000 Genomes Project Phase I data. We found that on average 26.87% of gene bins, 35.47% of intergenic bins, 42.85% of pathway bins, 14.86% of ORegAnno regulatory bins, and 5.97% of evolutionary conserved regions show statistically significant differences in low frequency variant burden across populations from the 1000 Genomes Project. The proportion of bins with significant differences in low frequency burden depends on the ancestral similarity of the two populations compared and types of features tested. Even closely related populations had notable differences in low frequency burden, but fewer differences than populations from different continents. Furthermore, conserved or functionally relevant regions had fewer significant differences in low frequency burden than regions under less evolutionary constraint. This degree of low frequency variant differentiation across diverse populations and feature elements highlights the critical importance of considering population stratification in the new era of DNA sequencing and low frequency variant genomic analyses.
authors.affiliation: Center for Human Genetic Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America ; Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America.
authors.forename: Carrie B
authors.initials: CB
authors.lastname: Moore
authors.affiliation: Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America.
authors.forename: John R
authors.initials: JR
authors.lastname: Wallace
authors.affiliation: Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Wolfe
authors.affiliation: Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America.
authors.forename: Alex T
authors.initials: AT
authors.lastname: Frase
authors.affiliation: Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Pendergrass
authors.affiliation: Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Weiss
authors.affiliation: Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America.
authors.forename: Marylyn D
authors.initials: MD
authors.lastname: Ritchie
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D055106:Genome-Wide Association Study; D016045:Human Genome Project; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics