Methods for using mosaicism in nucleic acids sampled distal to their origin

Inventors

West, John

Assignees

Personalis Inc

Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

Core Innovation

The invention provides a method for detecting a presence or recurrence of a solid tumor using mosaic variants identified from a subject by comparing whole genome sequencing reads from a tissue sample and from leukocytes. A first set of sequence reads is generated from nucleic acid molecules extracted from a tissue sample comprising benign tissue, malignant tissue, or a mixed tissue sample, and a second set of sequence reads is generated from nucleic acid molecules extracted from leukocytes from a first blood sample that is a normal sample.

Mosaic variants are identified by selecting mosaic variants present in the first set of sequence reads and not present in the second set of sequence reads. After identifying mosaic variants, the method creates a first report based on the identification of the mosaic variants and obtains one or more later blood samples from the subject at a later time point than the first tissue sample and the first blood sample.

Non-amplified nucleic acid molecules are extracted from the later blood samples using a plurality of biotin-labeled capture probes in solution, where individual instances of the capture probes hybridize to individual instances of the mosaic variants identified earlier. A sequencing assay is performed on nucleic acid molecules extracted from the later blood samples to identify the presence or absence of individual instances of the mosaic variants one or more times over the life of the subject.

A second report is provided based on the presence or absence of the individual instances of mosaic variants in the one or more blood samples, thereby detecting the presence or recurrence of the solid tumor in the subject. The method includes copy number variation, small insertions and deletions (inDels), single nucleotide polymorphisms (SNPs), multiple nucleotide polymorphisms (MNPs), or any combination.

Claims Coverage

The independent claim identified is clm-00001, which defines four inventive features for longitudinal solid tumor detection using mosaic variants identified from tissue and normal leukocytes, followed by probe-based capture and sequencing of later blood samples to generate reports for detecting presence or recurrence.

The independent claim coverage centers on identifying mosaic variants from tissue versus normal leukocytes, capturing non-amplified nucleic acids from later blood with biotin-labeled capture probes, sequencing later blood to determine presence or absence longitudinally, and generating reports to detect solid tumor presence or recurrence.

Stated Advantages

Documented Applications