ArticleFrontiers in genetics2019
Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 19 citations in OpenAlex.
- Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing.BMC plant biology · 2025Article
- Imputef: imputation of polyploid genotype classes and allele frequencies.BMC genomics · 2025Article
- Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers.G3 (Bethesda, Md.) · 2025Article
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- The Contribution ofInternational journal of molecular sciences · 2022Review
- Genetic polyploid phasing from low-depth progeny samples.iScience · 2022Article
- Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species.Frontiers in plant science · 2022Review
- Apple whole genome sequences: recent advances and new prospects.Horticulture research · 2019Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.