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San Diego, CA, United States

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. © 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. Source

Illumina | Date: 2015-03-31

The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which permit the sequential determination of nucleotide sequences in two distinct and separate regions on complementary strands of the double-stranded polynucleotide template. The two regions for sequence determination may or may not be complementary to each other.

Illumina | Date: 2015-08-07

Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.

Fluidic cartridge including a liquid container having a reservoir configured to hold a liquid. The liquid container includes an interior surface. The fluidic cartridge also includes a transfer tube that extends from the interior surface to a distal end. The distal end includes a fluidic port that is in flow communication with the reservoir through the transfer tube. The transfer tube has a piercing segment that includes the distal end. The fluidic cartridge also includes a movable seal that is engaged to the piercing segment of the transfer tube and configured to slide along the piercing segment from a closed position to a displaced position during a mating operation. The movable seal blocks flow of the liquid through the fluidic port when in the closed position. The piercing segment extends through the movable seal when in the displaced position.

Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.

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