ArticleGenome research2016
Direct chromosome-length haplotyping by single-cell sequencing.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 67 citations in OpenAlex.
- Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq.Nucleic acids research · 2026Article
- Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor.Nucleic acids research · 2025Article
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- Article
- Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype.Nature genetics · 2024Article
- Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.Plant communications · 2024Article
- Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.Genome biology · 2024Article
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq.Cell discovery · 2024Article
- Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.bioRxiv : the preprint server for biology · 2024Article
- Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- Functional analysis of structural variants in single cells using Strand-seq.Nature biotechnology · 2023Article
- The variation and evolution of complete human centromeres.bioRxiv : the preprint server for biology · 2023Article
- Gaps and complex structurally variant loci in phased genome assemblies.Genome research · 2023Article
- Genome-Wide Analysis of Rare Haplotypes Associated with Breast Cancer Risk.Cancer research · 2023Article
- Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq.Cell genomics · 2023Article
- Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges.Methods in molecular biology (Clifton, N.J.) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid genomes along the entire length of all chromosomes. We demonstrate this by building a complete haplotype for a HapMap individual (NA12878) at high accuracy (concordance 99.3%), without using generational information or statistical inference. By use of this approach, we mapped all meiotic recombination events in a family trio with high resolution (median range ∼14 kb) and phased larger structural variants like deletions, indels, and balanced rearrangements like inversions. Lastly, the single-cell resolution of Strand-seq allowed us to observe loss of heterozygosity regions in a small number of cells, a significant advantage for studies of heterogeneous cell populations, such as cancer cells. We conclude that Strand-seq is a unique and powerful approach to completely phase individual genomes and map inheritance patterns in families, while preserving haplotype differences between single cells.
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What OpenQuestion holds
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.