Grail, Inc.

Seyedmehdi Shojaee

Joerg Bredno

Onur Sakarya

Samuel S Gross

Arash Jamshidi

Oliver Claude Venn

John Beausang

M Cyrus Maher

Srinka Ghosh

Hamed Amini

Qinwen Liu

Alexander P Fields

Jan Schellenberger

Rongsu Qi

Alexander S Yip

John F Beausang

The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein includes methods of designing, making, and using the cancer assay panel for diagnosis of cancer.

Methylation markers and targeted methylation probe panel

The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein are methods of designing, making, and using the cancer assay panel for the diagnosis of cancer.

An analytics system marks duplicate fragments from an initial set of fragments from a subject. The analytics system generates a sample state vector for each fragment. Each sample state vector comprises a sample genomic location within a reference genome and a plurality of methylation states for a plurality of CpG sites in the fragment, the methylation states determined to be one of methylated, unmethylated, variant, and ambiguous. The analytics system identifies two fragments with methylation state vectors as being derived from a matching reference location, e.g., sharing a common plurality of CpG sites. The analytics system calculates a modified Hamming distance based on methylation states in the first sample state vector and methylation states in the second sample state vector. Based on the modified Hamming distance, the analytics system marks the first fragment and the second fragment as either duplicate fragments or non-duplicate fragments.

Methylation-based false positive duplicate marking reduction

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Menlo Park, CA, United States of America

Seyedmehdi Shojaee