Abstract: Methods and systems for sample contamination detection are disclosed. In particular, sample barcodes are utilized, wherein each sample barcode is assigned to a sample and ligated to fragments from the sample. The sample barcodes are used in conjunction with indices from sequencing libraries to accurately assign sequence reads to samples during multiplex sequencing. Molecule identifiers may also be utilized to aid in de-duping of sequence reads to precisely identify original NA fragments from a sample. Accordingly, in one or more embodiments, a sequencing method includes isolating DNA fragments in a sample, ligating the DNA fragments with unique molecule identifiers (UMIs), performing an amplification process resulting in amplicons, ligating a sample barcode onto the amplicons, and performing amplicon sequencing. The analytics system looks to whether indices are matched and whether a sample barcode matches to the pair of indices when identifying single-index or double-index hopping events.

Abstract: Methods for WBC contamination detection are disclosed. The computer-implemented methods for WBC contamination detection aim to assess whether a sample is contaminated by the WBC-shed DNA and may further determine a level of contamination. A first coverage-based approach assesses normalized coverage of sequence reads of a test sample at each genomic locus in a feature set of genomic loci. A contamination metric may be calculated based on a distance of the test sample's normalized coverage to a distribution of purified cfDNA samples. A second methylation-based approach deconvolves tissue type based on methylation features. A distribution is generated based on tissue type fractions of purified cfDNA samples from non-cancer subjects. The contamination metric is calculated based on a distance relative to the distribution of tissue type fractions. A third quantitative coverage-based approach generates distributions of coverage for cfDNA samples and for WBC samples for each genomic locus.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: a substrate having an inner surface facing a library sequencing region, and an outer surface; a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: (a) a substrate having an inner surface facing a library sequencing region, and an outer surface; (b) a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; (c) a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; (d) electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and (e) fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: (a) a substrate having an inner surface facing a library sequencing region, and an outer surface; (b) a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; (c) a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; (d) electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and (e) fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: Multi-directional microfluidic devices and methods for using the same are provided. Aspects of the invention include microfluidic devices that are configured to subject a sample to two or more directionally distinct flow fields, and include a separation medium and a binding medium, where the binding medium is in fluid communication with the separation medium. Also provided are methods of using the devices as well as systems and kits that include the devices. The devices, systems and methods find use in a variety of different applications, including diagnostic and validation assays.

Abstract: Multi-directional microfluidic devices and methods for using the same are provided. Aspects of the invention include microfluidic devices that are configured to subject a sample to two or more directionally distinct flow fields, and include a separation medium and a binding medium, where the binding medium is in fluid communication with the separation medium. Also provided are methods of using the devices as well as systems and kits that include the devices. The devices, systems and methods find use in a variety of different applications, including diagnostic and validation assays.