ArticleNature biotechnology2017
Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.
Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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.
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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
27 citing papers in PubMed, 61 citations in OpenAlex.
- Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.Life (Basel, Switzerland) · 2026Article
- 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
- Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method.Scientific reports · 2024Article
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing.Genome biology · 2023Article
- A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Rapid and sensitive single-cell RNA sequencing with SHERRY2.BMC biology · 2022Article
- Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis.The Journal of pathology · 2022Review
- Features and applications of haplotypes in crop breeding.Communications biology · 2021Review
- Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Modular barcode beads for microfluidic single cell genomics.Scientific reports · 2021Article
- Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content.iScience · 2021Article
- stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads.Frontiers in genetics · 2021Article
- Long-read human genome sequencing and its applications.Nature reviews. Genetics · 2020Review
- A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data.Molecular biology and evolution · 2020Article
- Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.Genome research · 2020Article
- High throughput barcoding method for genome-scale phasing.Scientific reports · 2019Article
- Accurate Tracking of the Mutational Landscape of Diploid Hybrid Genomes.Molecular biology and evolution · 2019Article
Corrections and comments
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Authors and funding
19 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Haplotype-resolved genome sequencing promises to unlock a wealth of information in population and medical genetics. However, for the vast majority of genomes sequenced to date, haplotypes have not been determined because of cumbersome haplotyping workflows that require fractions of the genome to be sequenced in a large number of compartments. Here we demonstrate barcode partitioning of long DNA molecules in a single compartment using "on-bead" barcoded tagmentation. The key to the method that we call "contiguity preserving transposition" sequencing on beads (CPTv2-seq) is transposon-mediated transfer of homogenous populations of barcodes from beads to individual long DNA molecules that get fragmented at the same time (tagmentation). These are then processed to sequencing libraries wherein all sequencing reads originating from each long DNA molecule share a common barcode. Single-tube, bulk processing of long DNA molecules with ∼150,000 different barcoded bead types provides a barcode-linked read structure that reveals long-range molecular contiguity. This technology provides a simple, rapid, plate-scalable and automatable route to accurate, haplotype-resolved sequencing, and phasing of structural variants of the genome.
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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.