ArticleNature biotechnology2014
Whole-genome haplotyping using long reads and statistical methods.
Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers, 1 of them a synthesis that pooled it.
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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.
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.
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Who cites it
109 citing papers in PubMed, 1 synthesis or guideline pooled it, 183 citations in OpenAlex.
- Pooled it
- Article
- Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points.Nature protocols · 2025Review
- MethPhaser: methylation-based long-read haplotype phasing of human genomes.Nature communications · 2024Article
- Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method.Scientific reports · 2024Article
- Review
- A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- Review
- DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution.Nature genetics · 2022Article
- Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics modelPeerJ · 2022Article
- Reconstruction of evolving gene variants and fitness from short sequencing reads.Nature chemical biology · 2021Article
- Article
- Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer.Communications biology · 2021Article
- SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.BMC bioinformatics · 2021Article
- Understanding three-dimensional chromatin organization in diploid genomes.Computational and structural biotechnology journal · 2021Review
- Nucleic Acids Analysis.Science China. Chemistry · 2021Review
- UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution.Nature communications · 2020Article
- A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues.Molecular ecology resources · 2020Article
- A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle.Genes · 2020Article
49 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
The rapid growth of sequencing technologies has greatly contributed to our understanding of human genetics. Yet, despite this growth, mainstream technologies have not been fully able to resolve the diploid nature of the human genome. Here we describe statistically aided, long-read haplotyping (SLRH), a rapid, accurate method that uses a statistical algorithm to take advantage of the partially phased information contained in long genomic fragments analyzed by short-read sequencing. For a human sample, as little as 30 Gbp of additional sequencing data are needed to phase genotypes identified by 50× coverage whole-genome sequencing. Using SLRH, we phase 99% of single-nucleotide variants in three human genomes into long haplotype blocks 0.2-1 Mbp in length. We apply our method to determine allele-specific methylation patterns in a human genome and identify hundreds of differentially methylated regions that were previously unknown. SLRH should facilitate population-scale haplotyping of human genomes.
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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.