Systems and methods for inferring cell status

A computer system having one or more processors, and memory storing one or more programs for execution by the one or more processors, the one or more programs comprising instructions for performing a method of deconvolving a first clonal population comprising a first plurality of cells of a species comprising:

• (A) obtaining a set of nucleic acid sequence reads, in electronic form, from each cell in the first plurality of cells of the first clonal population through a single cell sequencing process, thereby obtaining a first plurality of sets of nucleic acid sequence reads, wherein each respective set of nucleic acid sequence reads in the first plurality of sets of nucleic acid sequence reads is from a corresponding single cell in the first plurality of cells;
• (B) mapping the sequence reads of each respective set of sequence reads onto a corresponding bin of a plurality of bins, wherein each respective bin of the plurality of bins represents a different portion of a reference genome of the species, thereby obtaining a nucleic acid sequence read count for each respective bin of the plurality of bins for each respective cell in the first plurality of cells, wherein the plurality of bins collectively encompass at least three percent of the reference genome;
• (C) for each respective cell in the first plurality of cells, assigning the respective cell into one of a plurality of groups based upon a pattern of sequence read counts of the respective cell across the plurality of bins, wherein
• a first group in the plurality of groups represents a first mitotic stage,
• a second group in the plurality of groups represents a non-mitotic stage, and
• the assigning (C) determines whether the respective cell is to be assigned to the first group by applying a first mitotic filter to the nucleic acid read count of respective bins of the plurality of bins obtained for the respective cell, thereby deconvolving the first clonal population.

A non-transitory computer readable storage medium, wherein the non-transitory computer readable storage medium stores instructions, which when executed by a computer system, cause the computer system to perform a method of deconvolving a first clonal population comprising a first plurality of cells of a species comprising:

• (A) obtaining a set of nucleic acid sequence reads, in electronic form, from each cell in the first plurality of cells of the first clonal population through a single cell sequencing process, thereby obtaining a first plurality of sets of nucleic acid sequence reads, wherein each respective set of nucleic acid sequence reads in the first plurality of sets of nucleic acid sequence reads is from a single cell in the first plurality of cells and represents at least four percent of the genome of the corresponding cell;
• (B) mapping the sequence reads of each respective set of sequence reads onto a corresponding bin of a plurality of bins, wherein each respective bin of the plurality of bins represents a different portion of a reference genome of the species, thereby obtaining a nucleic acid sequence read count for each respective bin of the plurality of bins for each respective cell in the first plurality of cells, wherein the plurality of bins collectively encompass at least three percent of the reference genome;
• (C) for each respective cell in the first plurality of cells, assigning the respective cell into one of a plurality of groups based upon a pattern of sequence read counts of the respective cell across the plurality of bins, wherein
• a first group in the plurality of groups represents a first mitotic stage,
• a second group in the plurality of groups represents a non-mitotic stage, and
• the assigning (C) determines whether the respective cell is to be assigned to the first group by applying a first mitotic filter to the nucleic acid read count of respective bins of the plurality of bins obtained for the respective cell, thereby deconvolving the first clonal population.