Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads

Ehsan Motazedi, Chris Maliepaard, Richard Finkers, Richard Visser, Dick De Ridder*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.

Original languageEnglish
Article number335
JournalFrontiers in Genetics
Volume10
Issue numberMAR
DOIs
Publication statusPublished - 16 Apr 2019

Fingerprint

Polyploidy
Haplotypes
Alleles
Genotype
Population
Tetraploidy
Pedigree
Solanum tuberosum
Chromosomes

Keywords

  • Estimation
  • Family
  • Haplotype
  • Polyploid
  • Sequence data

Cite this

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title = "Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads",
abstract = "DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.",
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Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads. / Motazedi, Ehsan; Maliepaard, Chris; Finkers, Richard; Visser, Richard; De Ridder, Dick.

In: Frontiers in Genetics, Vol. 10, No. MAR, 335, 16.04.2019.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads

AU - Motazedi, Ehsan

AU - Maliepaard, Chris

AU - Finkers, Richard

AU - Visser, Richard

AU - De Ridder, Dick

PY - 2019/4/16

Y1 - 2019/4/16

N2 - DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.

AB - DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.

KW - Estimation

KW - Family

KW - Haplotype

KW - Polyploid

KW - Sequence data

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