US 2026/0031186 A1 · PRE-END MOTIFS, POST-END MOTIFS, 5-EM, AND 3-EM AND COMBINATIONS FOR ANALYSIS OF CELL-FREE DNA

Abstract

This disclosure provides techniques for analyzing end motifs, e.g., nucleotides in a reference genome outside the outmost coordinates of an aligned sequenced fragment, as well as machine learning techniques that use multidimensional data structures to achieve increased accuracy in determining a property (e.g., classification of a pathology or fractional concentration of clinically-relevant DNA) of a sample or of the subject from which a sample is obtained. Various end motifs are described and used for determining such properties. Various encodings of cfDNA molecules are also described, e.g., for use with molecule-level and sample-level models. 4-end sequencing techniques are described that reduce dimer artifacts. Cleavage profiles of 3′ ends around CpG sites are also used to detect pathologies.

Claims56

Dependent claims

A method of analyzing a biological sample of a subject to determine a level of a pathology for the subject, the method comprising:

receiving sequence reads corresponding to ends of a plurality of cell-free DNA fragments in the biological sample of the subject;
for each cell-free DNA fragment of the plurality of cell-free DNA fragments:
aligning one or more sequence reads to a reference sequence;
based on the alignment, determining a 5′ end coordinate of a 5′ end of at least one strand of the cell-free DNA fragment as existed in the biological sample;
determining a pre-end motif based on the 5′ end coordinate and the reference sequence, wherein the pre-end motif is comprised of a plurality of nucleotides that occur before the 5′ end coordinate;
determining one or more amounts of a set of one or more pre-end motifs;
and
determining a classification of the level of the pathology for the subject or a fractional concentration of clinically-relevant DNA based on the one or more amounts.

5 more elements

Dependencies are inferred from the claim text.

Pre-end motifs, post-end motifs, 5-em, and 3-em and combinations for analysis of cell-free dna

Life of this patent

Pre-end motifs, post-end motifs, 5-em, and 3-em and combinations for analysis of cell-free dna

Life of this patent

Abstract

Claims56