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Title: Defining window-boundaries for genomic analyses using smoothing spline techniques

Journal Article · · Genetics Selection Evolution (Online)
 [1];  [2];  [3];  [4];  [3]
  1. Univ. of California, Davis, CA (United States). Dept. Plant Sciences.
  2. Univ. of Wisconsin, Madison, WI (United States). Dept. of Animal Sciences and Dept. of Biostatistics and Medical Information.
  3. Univ. of Wisconsin, Madison, WI (United States). Dept. of Agronomy and Dept. of Energy Great Lakes Bioenergy Research Center.
  4. Univ. of Wisconsin, Madison, WI (United States). Dept. of Animal Sciences, Dept. of Biostatistics and Medical Information and Dept. of Dairy Science.
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High-density genomic data is often analyzed by combining information over windows of adjacent markers. Interpretation of data grouped in windows versus at individual locations may increase statistical power, simplify computation, reduce sampling noise, and reduce the total number of tests performed. However, use of adjacent marker information can result in over- or under-smoothing, undesirable window boundary specifications, or highly correlated test statistics. We introduce a method for defining windows based on statistically guided breakpoints in the data, as a foundation for the analysis of multiple adjacent data points. This method involves first fitting a cubic smoothing spline to the data and then identifying the inflection points of the fitted spline, which serve as the boundaries of adjacent windows. This technique does not require prior knowledge of linkage disequilibrium, and therefore can be applied to data collected from individual or pooled sequencing experiments. Moreover, in contrast to existing methods, an arbitrary choice of window size is not necessary, since these are determined empirically and allowed to vary along the genome.

Research Organization:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
FC02-07ER64494
OSTI ID:
1184786
Journal Information:
Genetics Selection Evolution (Online), Vol. 47, Issue 1; ISSN 1297-9686
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 55 works
Citation information provided by
Web of Science

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Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population journal July 2017
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A Nested Mixture Model for Genomic Prediction Using Whole-Genome SNP Genotypes report January 2016
Drosophila simulans : A Species with Improved Resolution in Evolve and Resequence Studies journal May 2017
Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data journal February 2019
Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation journal April 2017
Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data journal November 2019
GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity journal April 2019
QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection journal July 2019
Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans journal December 2018
Functional models in genome-wide selection journal October 2019
Genome-wide association study on legendre random regression coefficients for the growth and feed intake trajectory on Duroc Boars journal May 2015
Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle journal January 2019
Demographic history and genomics of local adaptation in blue tit populations posted_content May 2020
Parasitism drives host genome evolution: Insights from the Pasteuria ramosa - Daphnia magna system : BRIEF COMMUNICATION journal March 2017
The genomic basis of adaptation to calcareous and siliceous soils in Arabidopsis lyrata text January 2018
The genomic basis of adaptation to calcareous and siliceous soils in Arabidopsis lyrata journal December 2018
The identification of novel regions for reproduction trait in Landrace and Large White pigs using a single step genome-wide association study journal December 2018
Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations journal September 2017
A nested mixture model for genomic prediction using whole-genome SNP genotypes journal March 2018
Linkage disequilibrium clustering‐based approach for association mapping with tightly linked genomewide data journal May 2018
Genomic regions influencing intramuscular fat in divergently selected rabbit lines journal November 2019
Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle journal April 2019
Exploring Evolutionary Relationships Across the Genome Using Topology Weighting journal March 2017
Exploring evolutionary relationships across the genome using topology weighting journal January 2017
Genome-wide genetic structure and differentially selected regions among Landrace, Erhualian, and Meishan pigs using specific-locus amplified fragment sequencing journal August 2017
Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia journal June 2018
Application of a Bayesian dominance model improves power in quantitative trait genome-wide association analysis journal January 2017

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