Vanadis Diagnostics

Pixelgen Technologies Ab

Filip Karlsson

Olof John Ericsson

Carl Oscar Fredrik Dahl

Fredrik Roos

Simon Fredriksson

Provided herein is probe system comprising: a population of nucleic acid molecules that have an extendible end, a first set of barcoded particles that each have a nucleotide sequence comprising: (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules, (ii) a unique particle identifier sequence, and (iii) a first template sequence, and a second set of barcoded particles that each have a nucleotide sequence comprising: (i) the first template sequence and (ii) a unique particle identifier sequence. In use, extension of the nucleic acid molecules using the first set of barcoded particles of as a template produces extensions products that contain the complement of a unique particle identifier sequence of a particle and the complement of the first template sequence. Methods of using the probe system to map binding events in or on a cellular sample are also provided.

Spatial mapping by serial primer extension

This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X'-A′-B′-Z′, wherein sequence A′ is complementary to a genomic fragment and sequence B′ is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.

Probe set for analyzing a DNA sample and method for using the same

Described herein is a complex comprising multiple nucleic acid molecules that are hybridized together, each comprising, from 5' to 3′, a first complementary sequence, a spacer sequence and a second complementary sequence, and either/or a 5′ end sequence that is 5′ of the first complementary sequence and terminates in a 5′ phosphate and a 3′ end sequence that is 3′ of the second complementary sequence and terminates in a 3′ hydroxyl. In this complex: the first complementary sequence of one molecule is directly or indirectly hybridized with the second complementary sequence of another molecule in the complex and the spacer sequence and the 3′ and/or 5′ end sequences are single-stranded. Methods of making and using the complex are also provided.

Rolling circle amplification product having multiple free ends

This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X'-A&#x2032;-B&#x2032;-Z&#x2032;, wherein sequence A&#x2032; is complementary to a genomic fragment and sequence B&#x2032; is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.

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Solna, Sweden

Filip Karlsson