The present invention generally relates to microfluidics and/or epigenetic sequencing. In one set of embodiments, cells contained within a plurality of microfluidic droplets are lysed and the DNA (e.g., from nucleosomes) within the droplets are labeled, e.g., with adapters containing an identification sequence. The adapters may also contain other sequences, e.g., restriction sites, primer sites, etc., to assist with later analysis. After labeling with adapters, the DNA from the different cells may be combined and analyzed, e.g., to determine epigenetic information about the cells. For example, the DNA may be separated on the basis of certain modifications (e.g., methylation), and the DNA from the separated nucleosomes may be sequenced using techniques such as chromatin immunoprecipitation (“CUP”). In some cases, the DNA sequences may also be aligned with genomes, e.g., to determine which portions of the genome were epigenetically modified, e.g., via methylation.

The present invention generally relates to microfluidics and/or epigenetic sequencing. In one set of embodiments, cells contained within a plurality of microfluidic droplets are lysed and the DNA (e.g., from nucleosomes) within the droplets are labeled, e.g., with adapters containing an identification sequence. The adapters may also contain other sequences, e.g., restriction sites, primer sites, etc., to assist with later analysis. After labeling with adapters, the DNA from the different cells may be combined and analyzed, e.g., to determine epigenetic information about the cells. For example, the DNA may be separated on the basis of certain modifications (e.g., methylation), and the DNA from the separated nucleosomes may be sequenced using techniques such as chromatin immunoprecipitation (“CUP”). In some cases, the DNA sequences may also be aligned with genomes, e.g., to determine which portions of the genome were epigenetically modified, e.g., via methylation.

cfDNA reference material, for example, for use in verifying the accuracy and effectiveness of a diagnostic test, is generated from chromatin which may be sourced from whole cells. The chromatin may be treated with formaldehyde to form crosslinks between DNA and histones, for example, while the chromatin is contained within nuclear and/or plasma membranes. The fixed chromatin may be sheared by acoustic energy, which may also be used to lyse cell membranes within which the fixed chromatin may be contained. The sheared chromatin may be treated with an enzyme, such as micrococcal nuclease, to digest chromatin in linker regions of the DNA between nucleosomes and generate nucleosome material for use as cfDNA reference material.

cfDNA reference material, for example, for use in verifying the accuracy and effectiveness of a diagnostic test, is generated from chromatin which may be sourced from whole cells. The chromatin may be treated with formaldehyde to form crosslinks between DNA and histones, for example, while the chromatin is contained within nuclear and/or plasma membranes. The fixed chromatin may be sheared by acoustic energy, which may also be used to lyse cell membranes within which the fixed chromatin may be contained. The sheared chromatin may be treated with an enzyme, such as micrococcal nuclease, to digest chromatin in linker regions of the DNA between nucleosomes and generate nucleosome material for use as cfDNA reference material.

A method for extracting pharmacogenetic DNA from dried blood that is retained in a solid resin collection device includes one or more of the steps of combining the dried blood and at least a portion of the solid resin collection device in a first vessel, sonicating the first vessel containing the dried blood and at least a portion of the solid resin collection device, moving at least some of the contents of the first vessel including the portion of the solid resin collection device to a solid resin spin column, adding an elution buffer to the solid resin spin column, centrifuging the solid resin spin column so that at least some of the contents of the solid resin spin column are transferred to a second vessel, and processing the contents of the second vessel by conducting one of capillary electrophoresis, Next-Generation Sequencing, DNA sequencing or genotyping, and mass spectrometry-based sequencing on the contents of the second vessel.

A method for extracting pharmacogenetic DNA from dried blood that is retained in a solid resin collection device includes one or more of the steps of combining the dried blood and at least a portion of the solid resin collection device in a first vessel, sonicating the first vessel containing the dried blood and at least a portion of the solid resin collection device, moving at least some of the contents of the first vessel including the portion of the solid resin collection device to a solid resin spin column, adding an elution buffer to the solid resin spin column, centrifuging the solid resin spin column so that at least some of the contents of the solid resin spin column are transferred to a second vessel, and processing the contents of the second vessel by conducting one of capillary electrophoresis, Next-Generation Sequencing, DNA sequencing or genotyping, and mass spectrometry-based sequencing on the contents of the second vessel.

Some embodiments presented in this disclosure concern an Automated Tissue Dissection (ATD) System. An ATD system is a one stop, and potentially low-cost, system to perform dissections on a substrate from pathologist digital mark or pen mark on the substrate using non-contact and/or mechanical method to extract a Formalin-Fixed Paraffin-Embedded (FFPE) tissue sample with: (a) only the ROI or ROIs as area to be saved; and (b) remove or decompose nucleic acid content in the region of no interest (RONI) and collect all tissue sample from a standard microscope substrate into a specific container.

The invention is directed to a method for obtaining the sequence information of a target sequence from a tissue comprising at least one RNA or c-DNA strand comprising two-fold RCA.

The invention is directed to a method for obtaining the sequence information of a target sequence from a tissue comprising at least one RNA or c-DNA strand comprising two-fold RCA.

Particles are released from a particle-containing area of a first surface of a porous matrix. The particle-containing area is contacted with a liquid medium and sonic energy is applied to an opposing area on a second surface of the porous matrix, wherein the opposing area is opposite to the particle-containing area. The particles may be biological particles or non-biological particles.