Methods for analyzing genotypes

A computer-implemented method, comprising:

• a. receiving data relating to one or more phenotype identifiers of a subject;
• b. querying, with a programmed computer processor, a database using the one or more phenotype identifiers to generate data identifying a plurality of genes corresponding to the one or more phenotype identifiers, each gene of the plurality of genes assigned a weighted score with respect to a corresponding phenotype identifier of the one or more phenotype identifiers;
• c. processing, with the aid of a computer processor, the plurality of genes in (b) to yield association scores for each of the plurality of genes corresponding to the one or more phenotype identifiers, wherein each of the association scores is a composite of a plurality of weighted scores for each gene of the plurality of genes;
• d. using a programmed computer processor, ranking the plurality of genes based at least in part on the association scores to yield a ranked plurality of genes;
• e. receiving sequence reads comprising genetic variants for the subject, and intersecting the ranked plurality of genes of (d) with the genetic variants of the subject to generate a subset of the plurality of genes ranked based on their association scores;
• f. using a programmed computer processor, ranking the subset of the plurality of genes based on inheritance pattern scores, wherein the inheritance pattern scores are at least partially based on a likelihood of the subset of the plurality of genes to explain a particular inheritance pattern, a segregation pattern, or a combination thereof;
• and
• g. generating a numeric or graphical output with at least the subset of the plurality of genes ranked based on their association scores and inheritance pattern scores with the one or more phenotype identifiers, which numeric or graphical output includes the one or more phenotype identifiers.