ArticleNucleic acids research2012
Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
What it found
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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
60 citing papers in PubMed, 127 citations in OpenAlex.
- Graph-based deep reinforcement learning for haplotype assembly with Ralphi.Genome research · 2025Article
- Genotype imputation from low-coverage WGS using haplotype reference panels in cultivated strawberry.BMC genomics · 2025Article
- Direct inference of haplotypes from sequencing data.Bioinformatics advances · 2025Article
- DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering.Briefings in bioinformatics · 2024Article
- Pairwise comparative analysis of six haplotype assembly methods based on users' experience.BMC genomic data · 2023Article
- New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads.Life science alliance · 2023Article
- A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Phased Genome Assemblies.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Benchmarking phasing software with a whole-genome sequenced cattle pedigree.BMC genomics · 2022Article
- HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes.BMC bioinformatics · 2021Article
- SpecHap: a diploid phasing algorithm based on spectral graph theory.Nucleic acids research · 2021Article
- Ranbow: A fast and accurate method for polyploid haplotype reconstruction.PLoS computational biology · 2020Article
- A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle.Genes · 2020Article
- CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline.F1000Research · 2020Article
- Minimum error correction-based haplotype assembly: Considerations for long read data.PloS one · 2020Article
- Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing.Nature communications · 2019Article
- Application of Chaotic Laws to Improve Haplotype Assembly Using Chaos Game Representation.Scientific reports · 2019Article
- Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes.Bioinformatics (Oxford, England) · 2019Article
- Next-Generation Sequencing Strategies.Cold Spring Harbor perspectives in medicine · 2019Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.
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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.