Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Described are methods of analyzing cell free DNA based on combining analysis of cfDNA methylation with analysis of the cfDNA nucleosome footprint and/or with analysis of cfDNA copy number alteration. The diagnostic performance of these methods, in particular relating to early or earlier stage diseases or disorders, is increased compared to the diagnostic performance of the individual cfDNA analysis methods.

Described are methods of analyzing cell free DNA based on combining analysis of cfDNA methylation with analysis of the cfDNA nucleosome footprint and/or with analysis of cfDNA copy number alteration. The diagnostic performance of these methods, in particular relating to early or earlier stage diseases or disorders, is increased compared to the diagnostic performance of the individual cfDNA analysis methods.

Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).

Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).

Provided are systems and methods for detecting the presence of cancer DNA in blood and for identifying the cancer origin in a test subject. Also provided are systems and methods for monitoring likelihood of cancer recurrence in a subject previously treated for cancer, systems and methods for assessing the efficacy of a cancer treatment in a subject suffering from cancer, and systems and methods for treating cancer in a subject in need thereof. The disclosed systems and methods comprise various elements such as (a) bisulfite treating cell free DNA (cfDNA) from a liquid biopsy sample of the test subject; (b) using the bisulfite treated cfDNA to prepare a first sequencing library for (i) a plurality of specific target genomic regions and (ii) a second sequencing library for a genome from a flow through of the first sequencing library; (c) sequencing the prepared first and second sequencing libraries, thereby producing a corresponding first and second plurality of sequencing results; and (d) analyzing the corresponding first and second plurality of sequencing results; and (e) receiving output from a machine learning model.

Provided herein is technology for ovarian cancer screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of ovarian cancer and sub-types of ovarian cancer (e.g., clear cell ovarian cancer, endometrioid ovarian cancer, mucinous ovarian cancer, serous ovarian cancer).

The present invention provides a method of quantification of a target nucleic acid, using at least any two of the genes SYT10, EPHA3, PLEKHF1 and KBTBD4 as control genes. In particular, the combination of the genes SYT10, EPHA3, PLEKHF1 and KBTBD4, known as the 4Plex, is provided as a control for nucleic acid quantification. The 4Plex has particular utility as a control for nucleic acid quantification by methylation-specific droplet digital PCR.

The present invention provides methods, compositions and kits for assembling an enzyme-deoxyribonucleic acid (DNA) complex for use in preparing a double stranded DNA molecule comprising one or more loci of interest for determining the methylation status of the one or more loci of interest therein.