ArticleNature genetics2014
Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.
Article in Nature genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed.
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.Life (Basel, Switzerland) · 2026Article
- Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework.Nature communications · 2025Article
- Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS + .Genome biology · 2025Article
- Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation.BMC genomics · 2025Article
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
- Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq.Nature cell biology · 2024Article
- Single-nucleus chromatin landscape dataset of mouse brain development and aging.Scientific data · 2024Article
- Fusobacterium nucleatum infection modulates the transcriptome and epigenome of HCT116 colorectal cancer cells in an oxygen-dependent manner.Communications biology · 2024Article
- Epigenomic tomography for probing spatially defined chromatin state in the brain.Cell reports methods · 2024Article
- Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution.Nature protocols · 2024Review
- Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis.Trends in genetics : TIG · 2024Review
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- High-capacity sample multiplexing for single cell chromatin accessibility profiling.BMC genomics · 2023Article
- Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer.Military Medical Research · 2023Review
- Microfluidics-free single-cell genomics with templated emulsification.Nature biotechnology · 2023Article
- Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.Nature biotechnology · 2023Article
- Article
- FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing.Genome biology · 2023Article
- Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing.Methods in molecular biology (Clifton, N.J.) · 2023Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
Abstract
Haplotype-resolved genome sequencing enables the accurate interpretation of medically relevant genetic variation, deep inferences regarding population history and non-invasive prediction of fetal genomes. We describe an approach for genome-wide haplotyping based on contiguity-preserving transposition (CPT-seq) and combinatorial indexing. Tn5 transposition is used to modify DNA with adaptor and index sequences while preserving contiguity. After DNA dilution and compartmentalization, the transposase is removed, resolving the DNA into individually indexed libraries. The libraries in each compartment, enriched for neighboring genomic elements, are further indexed via PCR. Combinatorial 96-plex indexing at both the transposition and PCR stage enables the construction of phased synthetic reads from each of the nearly 10,000 'virtual compartments'. We demonstrate the feasibility of this method by assembling >95% of the heterozygous variants in a human genome into long, accurate haplotype blocks (N50 = 1.4-2.3 Mb). The rapid, scalable and cost-effective workflow could enable haplotype resolution to become routine in human genome sequencing.
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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.