title: Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.
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.
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Sasan
authors.initials: S
authors.lastname: Amini
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Pushkarev
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Lena
authors.initials: L
authors.lastname: Christiansen
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Emrah
authors.initials: E
authors.lastname: Kostem
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Tom
authors.initials: T
authors.lastname: Royce
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Casey
authors.initials: C
authors.lastname: Turk
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Natasha
authors.initials: N
authors.lastname: Pignatelli
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Adey
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Jacob O
authors.initials: JO
authors.lastname: Kitzman
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Kandaswamy
authors.initials: K
authors.lastname: Vijayan
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Mostafa
authors.initials: M
authors.lastname: Ronaghi
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Steemers
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D016000:Cluster Analysis; D004247:DNA / Q000235:genetics; D005260:Female; D015723:Gene Library; D015894:Genome, Human; D023281:Genomics; D006239:Haplotypes; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D019895:Transposases / Q000235:genetics
chemical_list: D004247:DNA; D019895:Transposases