The present technology relates to methods for determining whether a patient having thyroid nodules with indeterminate cytology will benefit from diagnostic surgery, e.g., lobectomy. These methods are based on screening a patient's thyroid nodules and detecting alterations in target nucleic acid sequences corresponding to a specific set of thyroid cancer-related genes. Kits for use in practicing the methods are also provided.

Provided herein are compositions and methods for the incorporation of unnatural nucleotides using mutant polymerases, such as reverse transcriptases. Further provided herein are methods of detection and sequencing of polynucleotide sequences. In some aspects, the compositions and methods are used enhance the efficiency and speed of detecting nucleotide bases. The methods and compositions described herein may further reduce time, cost, or scale of devices for next generation sequencing platforms.

The invention relates to means and methods for producing libraries of analytes, such as polynucleotides, from a plurality of samples, such as single cells. The invention uses micro-particles that include both barcoded analyte capture polynucleotides and barcoded polynucleotides having a hairpin sequence. The micro-particles are divided between compartments together with sample. During library production, the hairpin sequences dimerise to produce polynucleotides comprising two barcode sequences. The dimers provide information about how many micro-particles were co-compartmentalised and with which sample analytes. This bead hashing method allows for increased loading of micro-particles into compartments with sample leading to increased throughput, greater efficiency and reduced loss of sample from analysis.

The present disclosure provides a method for enrichment of at least one target nucleic acid in a library of nucleic acids. This present disclosure is also directed to a faster and easier method of target capture using primer extension reactions that can improve ease of use, turnaround time, and variant allele specificity by designing target enrichment primers to specifically enrich library fragments based on the relative location of the variant base(s) in the primer, the utilization of polymerases with better priming specificity, designing the variant bases in the capture primer, designing the variant bases in the release primer, and/or designing variant specific primers to the both the plus and minus strands of the target library fragment.

Provided is an array including a solid support having a surface, the surface having a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality; and a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a single species of the target nucleic acids of the library. Methods for making and using the array are also provided.

An example of a kit includes a library preparation fluid, a sample fluid, and an enrichment fluid. The library preparation fluid includes library preparation beads, where each library preparation bead includes a first solid support, and a transposome attached to the first solid support. The fluid includes a genomic deoxyribonucleic acid sequence. The enrichment fluid includes target capture beads, where each target capture bead includes a second solid support, and capture probes attached to the second solid support. Each of the capture probes includes a single stranded deoxyribonucleic acid sequence that is complementary to a targeted region of the genomic deoxyribonucleic acid in the sample fluid.

Methods of labeling or barcoding molecules within one or more portions of a plurality of cells are provided. Kits and systems for labeling or barcoding molecules within one or more portions of a plurality of cells are also provided. The methods, kits, and systems may utilize photo-controlled adapter sequences, nucleic acids tags, and/or linkers.

The invention relates to a method of preparing a nucleic acid library for sequencing comprising selecting for nucleic acid fragments greater than 5 kb in length from a fragmented nucleic acid sample using paramagnetic Solid Phase Reversible Immobilization (SPRI) beads in a binding buffer. The binding buffer comprises specified concentrations of PEG6000, NaCl and TrisHCl at pH8, and the ratio of SPRI beads in binding buffer to sample is between 0.97 and 0.91. Also provided are methods of sequencing the genome of an organism and generating novel genome assemblies.

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.