Methods are provided of using a database that stores a plurality of reference genomes and phylogenetic information which relates the stored reference genomes to each other in a phylogenetic structure. These methods are useful in analysing the bacteria and/or bacterial lineages present in a sample and to identify a bacterium for use in therapy.

A next generation sequencing (NGS) based method includes applying, for one or more genetic loci, respective NGS data for genotype of a first subject, genotype of a second subject, and genotype of an alleged offspring of the first and second subjects to a statistical model calculating a value representing a likelihood the offspring is a true offspring of the first and second subjects. The NGS data includes genotype and sequencing read of the first tested subject; genotype and sequencing read of the second tested subject; and genotype and sequencing read of the alleged offspring. The statistical model utilizes a probability of the genotype of the first tested subject in a subject population; a probability of the genotype of the second tested subject in a subject population; and a probability of the genotype of the alleged offspring in a subject population.

Provided herein are computer implemented methods, systems and processes for determining a transmission metric or transmission path for related pathogens. Also provided herein is a non-transitory computer-readable storage medium with an executable program stored thereon, which program is configured to instruct a microprocessor to generate a transmission path for related pathogens.

Described are methods for identification of likelihood of health outcomes such as the development of a medical condition using health histories from genetically related individuals. Embodiments include: receiving a first set of genetic data associated with the human subject; comparing the first set of genetic data to a plurality of sets of genetic data from a plurality of other individuals; identifying from the comparison a family network comprising individuals genetically related to the human subject as defined by identity by descent; receiving a set of health history data for each individual and each individual in the family network; analyzing the set of health history data to generate a health outcome score for the human subject, the health outcome score being a measure of risk for the human subject to develop a pre-defined health outcome that is associated with the health outcome score; and reporting the health outcome score.

Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.

Methods and systems for generating character-based phylogeny trees from heritable data from mixture samples are provided. An example method for generating character-based phylogeny trees from heritable data for at least one mixture sample includes the step of generating a plurality of character-state trees based on the data. Each of the character-state trees comprises an arrangement of character-states associated with a particular character. The method also includes the steps of generating a pairwise compatibility graph for the character-state trees and identifying at least one maximal clique within the pairwise compatibility graph. The method additional includes the step of generating at least one phylogeny tree based on the identified at least one maximal clique.

A universal data-mining platform capable of analyzing mass spectrometry (MS) serum proteomic profiles and/or gene array data to produce biologically meaningful classification; i.e., group together biologically related specimens into clades. This platform utilizes the principles of phylogenetics, such as parsimony, to reveal susceptibility to cancer development (or other physiological or pathophysiological conditions), diagnosis and typing of cancer, identifying stages of cancer, as well as post-treatment evaluation. To place specimens into their corresponding clade(s), the invention utilizes two algorithms: a new data-mining parsing algorithm, and a publicly available phylogenetic algorithm (MIX). By outgroup comparison (i.e., using a normal set as the standard reference), the parsing algorithm identifies under and/or overexpressed gene values or in the case of sera, (i) novel or (ii) vanished MS peaks, and peaks signifying (iii) up or (iv) down regulated proteins, and scores the variations as either derived (do not exit in the outgroup set) or ancestral (exist in the outgroup set); the derived is given a score of 1, and the ancestral a score of 0these are called the polarized values. Furthermore, the shared derived characters that it identifies are potential biomarkers for cancers and other conditions and their subclasses.

Methods and kits for prenatal genetic testing and particularly for identifying and/or analyzing fetal haplotype with a high degree of confidence are provided.

The present invention generally relates to methods of generating antibodies against a species of pathogen that involve identifying the pathogen that is most genetically representative of member of pathogen species and using the identified pathogen to generate an antibody.

Methods and systems for recording and mapping lineage information and molecular events in individual cells are provided. Molecular changes, which may result from random or specific molecular events, are introduced to defined regions in cells over multiple cell cycle generations. Techniques such as fluorescent imaging are applied to track and identify the molecular changes before such information is used for lineage analysis or for identifying key processes and key players in cellular pathways.