The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

A collector device of environmental exposure is provided. This device may be used to collect and, after technical upgrade, monitor environmental exposure in personal and stationary settings. By coupling with advanced genomic analysis and chemical analysis technologies, the device and its accompanying methodology are capable of detecting environmental agents of diverse nature, many of which could pose health risks if going unaware of or uncontrolled. This type of information provides much needed clues to reconstruct and pinpoint the course of disease etiology at both personal and epidemic scales. By combining personal exposome and personal omics analyses, we can recapitulate with the intention to then prescribe treatment plans with unprecedented precision.

A collector device of environmental exposure is provided. This device may be used to collect and, after technical upgrade, monitor environmental exposure in personal and stationary settings. By coupling with advanced genomic analysis and chemical analysis technologies, the device and its accompanying methodology are capable of detecting environmental agents of diverse nature, many of which could pose health risks if going unaware of or uncontrolled. This type of information provides much needed clues to reconstruct and pinpoint the course of disease etiology at both personal and epidemic scales. By combining personal exposome and personal omics analyses, we can recapitulate with the intention to then prescribe treatment plans with unprecedented precision.

A method for verifying a material data chain (MDC) that is maintained by a creator is disclosed. The method includes receiving an unverified portion of the MDC from the creator including a set of consecutive material data blocks (MDBs). Each respective MDB includes respective material data, respective metadata, and a creator verification value. The method includes modifying a genomic differentiation object assigned to the verification cohort based on first genomic regulation instructions (GRI) that were used by the creator to generate the creator verification value. For each MDB in the unverified portion, the method includes determining a verifier verification value based on the MDB, a preceding MDB in the MDC, and a genomic engagement factor (GEF) determined with respect to the MDB. The GEF corresponding to an MDB is determined by extracting a sequence from the metadata of a MDB and mapping the sequence into the modified genomic differentiation object.

A method for verifying a material data chain (MDC) that is maintained by a creator is disclosed. The method includes receiving an unverified portion of the MDC from the creator including a set of consecutive material data blocks (MDBs). Each respective MDB includes respective material data, respective metadata, and a creator verification value. The method includes modifying a genomic differentiation object assigned to the verification cohort based on first genomic regulation instructions (GRI) that were used by the creator to generate the creator verification value. For each MDB in the unverified portion, the method includes determining a verifier verification value based on the MDB, a preceding MDB in the MDC, and a genomic engagement factor (GEF) determined with respect to the MDB. The GEF corresponding to an MDB is determined by extracting a sequence from the metadata of a MDB and mapping the sequence into the modified genomic differentiation object.

A device for the storage and/or the editing of digital data including at least one double stranded, replicative, composite nucleic acid molecule. The composite nucleic acid molecule includes both digital data-encoding and non-digital data-encoding nucleic acids. The non-digital data-encoding nucleic acids may allow indexing and/or the provision of metadata for the flanking digital data-encoding nucleic acid. The composite nucleic acid molecules may be pooled to constitute an array and arrays may constitute a DNA drive, which represents the physical support on which the digital data are stored.

Sequencing polynucleotides using nanopores is provided herein. A polynucleotide is disposed through a nanopore's aperture such that its 3′ end is on the nanopore's first side and its 5′ end is on the nanopore's second side. On the nanopore's first side, a duplex with the polynucleotide is formed that includes a 3′ end. The duplex is extended on the first side of the nanopore by adding a nucleotide to the 3′ end of the duplex. A first force is applied disposing the 3′ end of the duplex within the aperture, and the nanopore inhibits translocation of the 3′ end of the duplex to the second side of the nanopore. A value of an electrical property of the 3′ end of the duplex and a single-stranded portion of the polynucleotide is measured. The nucleotide at the 3′ end of the duplex is identified using the measured value.

Provided herein are novel methods, systems and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of a genetic variation, or the likelihood thereof, in a gene of interest in a subject.

Provided herein are novel methods, systems and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of a genetic variation, or the likelihood thereof, in a gene of interest in a subject.

The disclosure discloses an alignment method, device, and system. The alignment method includes: converting each read into a set of short fragments corresponding to the read to obtain a plurality of sets of short fragments; determining a corresponding position of the short fragment in a reference library to obtain a first positioning result, wherein the reference library is a hash table constructed based on a reference sequence, the reference library includes a plurality of entries, one entry of the reference library corresponds to one seed sequence, and the seed sequence is capable of matching at least one sequence on the reference sequence, a distance between two seed sequences corresponding to two adjacent entries of the reference library on the reference sequence is less than a length of the short fragment; removing a short fragment positioned on any one of the adjacent entries of the reference library in the first positioning result to obtain a second positioning result; and extending based on short fragments from the same read in the second positioning result to obtain an alignment result of the read. The alignment method can efficiently and accurately process and position sequencing data.