The present invention provides a computer-implemented method for detecting variant nucleic acid from a cell-free nucleic acid-containing sample. The method comprises (a) providing data representing fragment sizes of nucleic acid fragments obtained from said sample and/or representing a measure of deviation from copy number neutrality of the nucleic acid fragments obtained from said sample; b) processing the data from step a) according to a classification algorithm, wherein said classification algorithm operates to classify sample data into one of at least a first class containing the variant nucleic acid and a second class not containing the variant nucleic acid, based on a plurality of cell-free nucleic acid fragment size features and/or a deviation from copy number neutrality feature; and c) outputting the classification of the sample from step b, thereby determining whether the sample contains the variant nucleic acid or not, or a probability that the sample contains the variant nucleic acid. Related methods are also provided.

Embodiments of a method and/or system can include generating a set of quality control template (QCT) molecules; determining a set of QCT sequence read clusters based on the set of QCT molecules, such as based on variation regions of the set of QCT molecules; and based on the set of QCT sequence read clusters, determining a sequencing-related parameter, such as a contamination parameter and/or molecule count parameter, associated with the at least one of sequencing library preparation and sequencing.

Embodiments of a method and/or system can include generating a set of quality control template (QCT) molecules; determining a set of QCT sequence read clusters based on the set of QCT molecules, such as based on variation regions of the set of QCT molecules; and based on the set of QCT sequence read clusters, determining a sequencing-related parameter, such as a contamination parameter and/or molecule count parameter, associated with the at least one of sequencing library preparation and sequencing.

This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefitting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.

This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefitting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.

The technology relates in part to methods and compositions for analyzing nucleic acid. In some aspects, the technology relates to methods and compositions for generating one or more genotypes.

A method for processing genetic data, which comprise a series of sequence elements each representing a biomolecule, comprises the steps of forming sequence fragments (S2), wherein each sequence fragment comprises a section of the series of sequence elements having a fragment length of at least two sequence elements, applying a coding function to each of the sequence fragments in order to generate a multiplicity of encrypted fragment data items (S3) winch are each assigned to one of the sequence fragments, and storing the encrypted fragment data (S4), wherein the sequence fragments are formed in such a manner that the sections of the series of sequence elements overlap and each sequence element is included in at least two sequence fragments. A description is also given of a data processing device for processing genetic data and a method for querying a database containing encrypted fragment data which were generated and stored using the method for processing genetic data.

Provided are immune cell RNA sequencing methods. In some embodiments, the methods comprise producing a circularized DNA comprising a complementary DNA (cDNA) and a known heterologous sequence, wherein the cDNA is produced from an immune cell RNA. Such methods further comprise performing rolling circle amplification using the circularized DNA as template to produce a concatemer comprising repeating segments comprising the cDNA and the known heterologous sequence. Such methods further comprise sequencing the concatemer or fragments thereof. Also provided are methods comprising producing immune cell RNA sequencing reads using a R2C2 sequencing method, extracting HLA reads from the sequencing reads, and producing allele-specific HLA sequences from the extracted HLA reads. Also provided are computer-readable media, systems, compositions and kits that find use, e.g., in practicing the methods of the present disclosure.

A method and system comprising storing a set of user application programs each requiring an application specific subset of data to perform application processes and generate a respective genomic variant characterization for each of a plurality of patients with cancerous cells and receiving cancer treatment. The method including, obtaining clinical records data including cancer related information, generating genomic sequencing data for the patient's cancerous cells and normal cells, shaping at least a subset of the genomic sequencing data to generate system structured data. Storing the system structured data in a first database, selecting the application specific data from the first database, storing the application specific data in a second database for application program interfacing, receiving the respective genomic variant characterization from the user application program, and storing the genomic variant characterization from the user application program in a third database.

A method and system comprising storing a set of user application programs each requiring an application specific subset of data to perform application processes and generate a respective genomic variant characterization for each of a plurality of patients with cancerous cells and receiving cancer treatment. The method including, obtaining clinical records data including cancer related information, generating genomic sequencing data for the patient's cancerous cells and normal cells, shaping at least a subset of the genomic sequencing data to generate system structured data. Storing the system structured data in a first database, selecting the application specific data from the first database, storing the application specific data in a second database for application program interfacing, receiving the respective genomic variant characterization from the user application program, and storing the genomic variant characterization from the user application program in a third database.