Abstract: A method of processing an input sample, as well as related kits and compositions, is provided herein.

Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors, are provided.

Abstract: Methods and systems for determining a subject's likelihood of responding to a treatment by assessing the subject's cell-free DNA (cfDNA) sample include receiving sequence data gathered from sequencing the cfDNA sample, generating a feature matrix of values that correspond to synonymous and nonsynonymous mutations detected in the sequence data, and predicting, based on analysis of the feature matrix at a TMB prediction model, a tumor mutational burden (TMB) for a tissue of interest at the subject. The predicted TMB is evaluated to determine whether a set of criteria indicating a likely response to treatment is met. The set of criteria can include criterion(s) that are met when the predicted TMB is high, when the predicted TMB corresponds to a predicted tumoral heterogeneity indicative of homogeneous tissue, when the predicted TMB corresponds to a tumor fraction indicative of a positive responder, or any combination thereof.

Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors, are provided.

Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors, are provided.

Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors in sequence reads, and methods for identifying rare variants in a test sample, are provided.

Abstract: Embodiments include methods, compositions, and kits for creating genetic libraries useful for massively parallel genetic sequencing. Some embodiments are directed to methods of preventing the contamination of genetic libraries with material generated during the formation of other genetic libraries. In some embodiments, the methods employ adapters comprising universal priming sites. The methods can employ non-ligatable primers to generate non-ligatable amplification products so as to prevent unwanted ligation to adapters. In some embodiments, the non-ligatable primers contain uracil. Genetic material can be treated with uracil N glycosylase to prevent the unwanted ligation of uracil containing amplicons to adapters used for creating a second genetic library.