Systems, apparatus, and methods are provided for determining aberrations in a biological sample from an organism. Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Imbalances can be used to diagnose a patient for cancer, prognosticate a patient with cancer, or to detect the presence or monitor progress of a premalignant condition. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment).

Disclosed herein are methods for counting nucleic acid molecules (e.g., RNA molecules) of a sample by randomly truncating the nucleic acid molecules at a truncation base position within the nucleic acid molecules to produce truncated nucleic acid molecules, amplifying and sequencing the truncated nucleic acid molecules to produce sequencing reads, aligning the sequencing reads to a reference sequence to produce aligned sequencing reads, and identifying a number of nucleic acid molecules using truncation locations of aligned sequencing reads. Also disclosed herein are methods for constructing sequencing libraries that preserve truncation positions of the nucleic acid molecules. Also disclosed herein are methods for depleting or enriching a sample for one or more target sequences, using sets of blocking oligonucleotides corresponding to the one or more target sequences.

Disclosed herein are methods for counting nucleic acid molecules (e.g., RNA molecules) of a sample by randomly truncating the nucleic acid molecules at a truncation base position within the nucleic acid molecules to produce truncated nucleic acid molecules, amplifying and sequencing the truncated nucleic acid molecules to produce sequencing reads, aligning the sequencing reads to a reference sequence to produce aligned sequencing reads, and identifying a number of nucleic acid molecules using truncation locations of aligned sequencing reads. Also disclosed herein are methods for constructing sequencing libraries that preserve truncation positions of the nucleic acid molecules. Also disclosed herein are methods for depleting or enriching a sample for one or more target sequences, using sets of blocking oligonucleotides corresponding to the one or more target sequences.

Provided is a method for monitoring a change of ion strength in a sample solution by a closed-loop device that provides continuous cycling of electrochemical pH modulation between pre-defined pH values. In particular, the change of ion strength may be induced by a chemical reaction and may ultimately alter the electrical control parameters of the closed-loop device. By measuring such electrical control parameters, the degree and progress of the underlying chemical reaction may be monitored.

Provided is a method for monitoring a change of ion strength in a sample solution by a closed-loop device that provides continuous cycling of electrochemical pH modulation between pre-defined pH values. In particular, the change of ion strength may be induced by a chemical reaction and may ultimately alter the electrical control parameters of the closed-loop device. By measuring such electrical control parameters, the degree and progress of the underlying chemical reaction may be monitored.

A method is provided for determining a property of a starting sample, for example the amount of the nucleic acid (DNA) present therein.

Methods and reagents for detection and analysis of nucleic acids are provided. The methods employ proximity extension assays for detection of a target nucleic acids of interest, e.g., a target RNA. The method can additionally be used in multiplex assays with a protein proximity extension assay to detect protein.

Methods and reagents for detection and analysis of nucleic acids are provided. The methods employ proximity extension assays for detection of a target nucleic acids of interest, e.g., a target RNA. The method can additionally be used in multiplex assays with a protein proximity extension assay to detect protein.

Provided herein are fully-automated next-generation sequencing platforms and processes for detection of a target specimen (e.g., SARS-CoV-2) and for distinguishing infectious from non-infectious signals from the specimen. An analysis can provide simultaneous diagnosis and genomic surveillance of a multitude of distinct specimens in a sample information. The analysis can comprise distinguishing between infectious versus infectious specimens and provide a recommendation as to how infectious the sample can be. The information can be used to better inform the status of a subject or a location with regards to infectivity from the specimen.

Provided herein are fully-automated next-generation sequencing platforms and processes for detection of a target specimen (e.g., SARS-CoV-2) and for distinguishing infectious from non-infectious signals from the specimen. An analysis can provide simultaneous diagnosis and genomic surveillance of a multitude of distinct specimens in a sample information. The analysis can comprise distinguishing between infectious versus infectious specimens and provide a recommendation as to how infectious the sample can be. The information can be used to better inform the status of a subject or a location with regards to infectivity from the specimen.