The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array.

The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array.

Some examples described herein relate to a substrate comprising a silane functionalized surface for reversibly immobilizing a biological molecule of interest, such as oligonucleotides, polynucleotides, or protein. Methods for immobilizing the biological molecule and the use in DNA sequencing and other diagnostic applications are also disclosed.

Some examples described herein relate to a substrate comprising a silane functionalized surface for reversibly immobilizing a biological molecule of interest, such as oligonucleotides, polynucleotides, or protein. Methods for immobilizing the biological molecule and the use in DNA sequencing and other diagnostic applications are also disclosed.

The present disclosure relates to methods, kits and products for barcoding of nucleic acids. In certain embodiments, the present disclosure provides a method of producing nucleic acid for sequencing utilising clonal amplification on a solid substrate, the method comprising: (a) providing a nucleic acid sample for sequencing; (b) amplifying the nucleic acid sample using an amplifying primer comprising a degenerate nucleotide sequence and a 5′ fixed nucleotide sequence, to produce amplified nucleic acids; and (c) further amplifying the amplified nucleic acids with (i) a first primer comprising the 5′ fixed nucleotide sequence and a first adapter nucleotide sequence, and (ii) a second primer comprising the 5′ fixed nucleotide sequence and a second adapter nucleotide sequence, wherein the first adapter nucleotide sequence or the second adapter nucleotide sequence provides a sequence for subsequent priming of DNA synthesis from a nucleotide sequence attached to the solid substrate and the other adapter nucleotide sequence provides a sequence for subsequent priming of DNA synthesis from a template produced from the subsequent priming, and wherein one or more of the first primer, the second primer and the amplifying primer comprise a specific identifier sequence to identify nucleic acids amplified with the first primer, the second primer and/or the amplifying primer; thereby producing nucleic acid for sequencing utilising clonal amplification on the solid substrate.

The present disclosure relates to methods, kits and products for barcoding of nucleic acids. In certain embodiments, the present disclosure provides a method of producing nucleic acid for sequencing utilising clonal amplification on a solid substrate, the method comprising: (a) providing a nucleic acid sample for sequencing; (b) amplifying the nucleic acid sample using an amplifying primer comprising a degenerate nucleotide sequence and a 5′ fixed nucleotide sequence, to produce amplified nucleic acids; and (c) further amplifying the amplified nucleic acids with (i) a first primer comprising the 5′ fixed nucleotide sequence and a first adapter nucleotide sequence, and (ii) a second primer comprising the 5′ fixed nucleotide sequence and a second adapter nucleotide sequence, wherein the first adapter nucleotide sequence or the second adapter nucleotide sequence provides a sequence for subsequent priming of DNA synthesis from a nucleotide sequence attached to the solid substrate and the other adapter nucleotide sequence provides a sequence for subsequent priming of DNA synthesis from a template produced from the subsequent priming, and wherein one or more of the first primer, the second primer and the amplifying primer comprise a specific identifier sequence to identify nucleic acids amplified with the first primer, the second primer and/or the amplifying primer; thereby producing nucleic acid for sequencing utilising clonal amplification on the solid substrate.

Method and apparatus for nucleic acid sequencing are provided. The method includes providing a microbead disposed in one reaction well and immobilized with two capturing oligonucleotides with different sequences, immobilizing nucleic acid templates on the microbead via annealing between the templates and the capturing oligonucleotides, amplifying the immobilized nucleic acid templates and producing a population of template clones annealed with sequencing primers. The method further includes sequentially disposing different types of nucleotide trisphosphates, detecting, by ion-sensitive field-effect transistors, ion concentration change in the reaction wells in response to incorporation of one of the nucleotide trisphosphates at 3′ end of sequencing primers, when the nucleotide trisphosphates is complementary to a corresponding nucleotide in the template clones, and sequencing the template clones by repeating the sequentially disposing and the detecting. A method for producing single-stranded nucleic acid template clones on a reaction well array is also provided.

Method and apparatus for nucleic acid sequencing are provided. The method includes providing a microbead disposed in one reaction well and immobilized with two capturing oligonucleotides with different sequences, immobilizing nucleic acid templates on the microbead via annealing between the templates and the capturing oligonucleotides, amplifying the immobilized nucleic acid templates and producing a population of template clones annealed with sequencing primers. The method further includes sequentially disposing different types of nucleotide trisphosphates, detecting, by ion-sensitive field-effect transistors, ion concentration change in the reaction wells in response to incorporation of one of the nucleotide trisphosphates at 3′ end of sequencing primers, when the nucleotide trisphosphates is complementary to a corresponding nucleotide in the template clones, and sequencing the template clones by repeating the sequentially disposing and the detecting. A method for producing single-stranded nucleic acid template clones on a reaction well array is also provided.

Disclosed herein include systems, methods, compositions, and kits for 5′-based gene expression profiling. Some embodiments provide synthetic particles (e.g., beads) associated with a first plurality of oligonucleotide barcodes and a second plurality of oligonucleotide barcodes. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3′ end with the first plurality of oligonucleotide barcodes and subsequently barcoded on the 5′ end following a template switching reaction and intermolecular hybridization with the first plurality of oligonucleotide barcodes and extension. Immune repertoire profiling methods are also provided in some embodiments.

Disclosed herein include systems, methods, compositions, and kits for 5′-based gene expression profiling. Some embodiments provide synthetic particles (e.g., beads) associated with a first plurality of oligonucleotide barcodes and a second plurality of oligonucleotide barcodes. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3′ end with the first plurality of oligonucleotide barcodes and subsequently barcoded on the 5′ end following a template switching reaction and intermolecular hybridization with the first plurality of oligonucleotide barcodes and extension. Immune repertoire profiling methods are also provided in some embodiments.