ArticleProceedings of the National Academy of Sciences of the United States of America2013
Whole-genome haplotyping by dilution, amplification, and sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- TELLBASE: a novel tool of TELL-seq barcode-assisted scaffold assembler for bacterial genomes.Briefings in bioinformatics · 2025Article
- Chimera: The spoiler in multiple displacement amplification.Computational and structural biotechnology journal · 2023Review
- Retrospective Genotyping and Whole Genome Sequencing of a Canine Parvovirus Outbreak in Bangladesh.Pathogens (Basel, Switzerland) · 2021Article
- Determination of complete chromosomal haplotypes by bulk DNA sequencing.Genome biology · 2021Article
- SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.BMC bioinformatics · 2021Article
- Fully Phased Sequence of a Diploid Human Genome DeterminedG3 (Bethesda, Md.) · 2020Article
- TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads.GigaScience · 2020Article
- Next-Generation Sequencing Strategies.Cold Spring Harbor perspectives in medicine · 2019Review
- ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing.International journal of molecular sciences · 2019Article
- Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia.European journal of human genetics : EJHG · 2019Article
- Long range haplotyping of paired-homologous chromosomes by single-chromosome sequencing of a single cell.Scientific reports · 2018Article
- An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.Bioinformatics (Oxford, England) · 2018Article
- 3C-PCR: a novel proximity ligation-based approach to phase chromosomal rearrangement breakpoints with distal allelic variants.Human genetics · 2018Article
- Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy.Nucleic acids research · 2017Article
- Recent Advances in Experimental Whole Genome Haplotyping Methods.International journal of molecular sciences · 2017Review
- Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.Nature biotechnology · 2017Article
- HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.Genome research · 2017Article
- International Standards for Genomes, Transcriptomes, and Metagenomes.Journal of biomolecular techniques : JBT · 2017Review
- Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification.International journal of molecular sciences · 2017Article
- An accurate clone-based haplotyping method by overlapping pool sequencing.Nucleic acids research · 2016Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Standard whole-genome genotyping technologies are unable to determine haplotypes. Here we describe a method for rapid and cost-effective long-range haplotyping. Genomic DNA is diluted and distributed into multiple aliquots such that each aliquot receives a fraction of a haploid copy. The DNA template in each aliquot is amplified by multiple displacement amplification, converted into barcoded sequencing libraries using Nextera technology, and sequenced in multiplexed pools. To assess the performance of our method, we combined two male genomic DNA samples at equal ratios, resulting in a sample with diploid X chromosomes with known haplotypes. Pools of the multiplexed sequencing libraries were subjected to targeted pull-down of a 1-Mb contiguous region of the X-chromosome Duchenne muscular dystrophy gene. We were able to phase the Duchenne muscular dystrophy region into two contiguous haplotype blocks with a mean length of 494 kb. The haplotypes showed 99% agreement with the consensus base calls made by sequencing the individual DNAs. We subsequently used the strategy to haplotype two human genomes. Standard genomic sequencing to identify all heterozygous SNPs in the sample was combined with dilution-amplification-based sequencing data to resolve the phase of identified heterozygous SNPs. Using this procedure, we were able to phase >95% of the heterozygous SNPs from the diploid sequence data. The N50 for a Yoruba male DNA was 702 kb whereas the N50 for a European female DNA was 358 kb. Therefore, the strategy described here is suitable for haplotyping of a set of targeted regions as well as of the entire genome.
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