DETECTING MUTATIONS FOR CANCER SCREENING AND FETAL ANALYSIS

摘要

Embodiments are related to the accurate detection of somatic mutations in the plasma (or other samples containing cell-free DNA) of cancer patients and for subjects being screened for cancer. The detection of these molecular markers would be useful for the screening, detection, monitoring, management, and prognostication of cancer patients. For example, a mutational load can be determined from the identified somatic mutations, and the mutational load can be used to screen for any or various types of cancers, where no prior knowledge about a tumor or possible cancer of the subject may be required. Embodiments can be useful for guiding the use of therapies (e.g. targeted therapy, immunotherapy, genome editing, surgery, chemotherapy, embolization therapy, anti-angiogenesis therapy) for cancers. Embodiments are also directed to identifying de novo mutations in a fetus by analyzing a maternal sample having cell-free DNA from the fetus.

主权项

1. A method for identifying somatic mutations in a human subject by analyzing a biological sample of the human subject, the biological sample including DNA fragments originating from normal cells and potentially from tumor cells or cells associated with cancer, the biological sample including cell-free DNA fragments, the method comprising:
obtaining template DNA fragments from the biological sample to be analyzed, the template DNA fragments including cell-free DNA fragments; preparing a sequencing library of analyzable DNA molecules using the template DNA fragments, the preparation of the sequencing library of analyzable DNA molecules not including a step of DNA amplification of the template DNA fragments; sequencing the sequencing library of analyzable DNA molecules to obtain a plurality of sequence reads; receiving, at a computer system, the plurality of sequence reads; aligning, by the computer system, the plurality of sequence reads to a reference human genome to determine genomic positions for the plurality of sequence reads; obtaining, by the computer system, information about a constitutional genome corresponding to the human subject; and comparing, by the computer system, the sequence reads to the constitutional genome to identify a filtered set of loci as having somatic mutations in some tissue of the human subject, wherein: at each locus of the filtered set, a number of the sequence reads having a sequence variant relative to the constitutional genome is above a cutoff value, the cutoff value being greater than one.