Evidence map›Paper›PMID 32668004›Full record

ArticleMolecular biology and evolution2020

Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes.

Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, John M Chater, Le Zhang, Julong Wei, Yuan-Ming Zhang, Chenwu Xu, Wei-De Zhong and 8 more

Open access · hybridAbstract readComparative StudyEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
2.2field-weighted citation impact, top 12% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed, 21 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors at 5 institutions in 2 countries.

Ruidong LiDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Han QuDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Jinfeng ChenDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Shibo WangDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
John M ChaterDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Le ZhangGraduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA.
Julong WeiDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Yuan-Ming ZhangStatistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
Chenwu XuJiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China.
Wei-De ZhongDepartment of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China.
Jianguo ZhuDepartment of Urology, Guizhou Provincial People's Hospital, Guizhou, China.
Jianming LuDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Yuanfa FengDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Weiming ChenDepartment of Urology, Guizhou Provincial People's Hospital, Guizhou, China.
Renyuan MaDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Sergio Pietro FerranteDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Mikeal L RooseDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
Zhenyu JiaDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.
University of California, Riverside · USGuangzhou Medical University · CNGuizhou Provincial People's Hospital · CNHuazhong Agricultural University · CNYangzhou University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor's chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

Indexed as

Genetic TechniquesGerm CellsHaplotypesSoftwareChromosomesHumansRecombination, GeneticZea mayschromosome-length haplotypeevolutionary geneticsgametequantitative geneticsrecombination

Identifiers

PMID32668004
PMCPMC7743722
OpenAlexW3042988589

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

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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.