Abstract: This disclosure describes methods and compositions for detecting the presence of a Perilipin 1 (PLIN1) autoantibody in a biological sample obtained from a subject that has or is being treated with immune checkpoint inhibitor therapy. Also provided are methods of treating subjects with acquired lipodystrophy.

Abstract: A method of measuring malarial parasitemia includes disposing a sample including red blood cells in liquid form on a sample stage, illuminating the sample with optical radiation, capturing a plurality of images of the sample, and extracting, from the one or more of the plurality of images, a set of red blood cell images. Each red blood cell image is associated with a particular red blood cell. The method also includes for each red blood cell image in the set of red blood cell images, inputting each red blood cell image into a machine learning model and generating, using the machine learning model, a classification related to a malaria parasite lifecycle stage for each of the red blood cells. The method further includes determining the malarial parasitemia for the sample.

Abstract: This disclosure describes methods and compositions for detecting the presence of autoantibodies associated with autoimmune polyglandualar syndrome 1 (APS1) in a biological sample. In particular, detection of APS1-specific autoantibodies that specifically bind to certain APS1 associated autoantigens in such methods is described. Also provided are methods of treating subjects with APS1 or at risk of developing APS1 associated conditions. Also provided are devices and kits useful for the diagnosis and prognostic assessment of subjects having APS1 and for assessing subject risk at developing particular APS1-associated conditions.

Abstract: This disclosure describes methods and compositions for detecting the presence of a Kelch-like protein 11 autoantibody in a biological sample. Also provided are methods of treating subjects with testicular cancer or a premalignant condition and paraneoplastic encephalomyelitis.

Abstract: A method of sample analysis is provided. In some embodiments, the method comprises: (a) digesting a mixed nucleic acid sample with a plurality of reprogrammed nucleic acid-directed endonucleases that target sequences of interest to produce a digested sample, wherein at least some of the fragments in the digested sample comprise: (i) a sequence of interest and (ii) at least one ligatable end that has been generated by endonuclease cleavage; (b) enriching for fragments that contain the sequence of interest; and (c) analyzing the enriched fragments. Kits for performing the method are also provided.

Abstract: A method of sample analysis is provided. In some embodiments, the method comprises: (a) digesting a mixed nucleic acid sample with a plurality of reprogrammed nucleic acid-directed endonucleases that target sequences of interest to produce a digested sample, wherein at least some of the fragments in the digested sample comprise: (i) a sequence of interest and (ii) at least one ligatable end that has been generated by endonuclease cleavage; (b) enriching for fragments that contain the sequence of interest; and (c) analyzing the enriched fragments. Kits for performing the method are also provided.

Abstract: Spectrally encoded microbeads and methods and devices for making and using spectrally encoded microbeads are provided. The disclosed methods and devices facilitate the preparation and use of microbeads containing multiple lanthanide nanoparticles, which microbeads have uniquely identifiable spectral codes. The disclosed microbeads, and the methods and devices for making and using same, find use in multiplexing and high-throughput biomarker analysis.

Abstract: Among other things, this disclosure describes a method comprising: cleaving a plurality of target sequences in an adaptor-tagged sequencing library using population of reprogrammed nucleic acid-directed endonucleases; non-specifically amplifying the library, thereby amplifying fragments that have not been cleaved; and sequencing the amplified sample.

Abstract: Spectrally encoded microbeads and methods and devices for making and using spectrally encoded microbeads are provided. The disclosed methods and devices facilitate the preparation and use of microbeads containing multiple lanthanide nanoparticles, which microbeads have uniquely identifiable spectral codes. The disclosed microbeads, and the methods and devices for making and using same, find use in multiplexing and high-throughput biomarker analysis.