Abstract: Systems and methods for spatial analysis of analytes include placing a sample on a substrate having fiducial markers and capture spots. Then, an image of the sample is acquired and sequence reads are obtained from the capture spots. Each capture probe plurality in a set of capture probe pluralities is (i) at a different capture spot, (ii) directly or indirectly associates with analytes from the sample and (iii) has a unique spatial barcode. The sequencing reads serve to detect the analytes. Sequencing reads include a spatial barcode of the corresponding capture probe plurality. Spatial barcodes localize reads to corresponding capture spots, thereby dividing them into subsets, each subset for a respective capture spot. Fiducial markers facilitate a composite representation comprising (i) the image aligned to the capture spots and (ii) a representation of each subset of sequence reads at respective positions within the image mapping to the corresponding capture spots.

Abstract: A method determining a biological condition of a subject using a spatial distribution of haplotypes is provided in which sequence reads are obtained from a two-dimensional array of positions on a substrate upon contacting a biological sample of the subject with the two-dimensional array of positions on the substrate. Each capture probe plurality in a set of capture probe pluralities is at a different position in the two-dimensional array, associates with one or more analytes from the biological sample, and has a corresponding spatial barcode from a plurality of spatial barcodes. Each sequence read includes a spatial barcode of the corresponding capture probe plurality. The barcoded sequence reads are used to quantify each haplotype for each of a plurality of loci thereby determining the spatial distribution of the one or more haplotypes in the biological sample which, in turn, is used to characterize the biological condition of the subject.