公开(公告)号：US12024797B2

公开(公告)日：2024-07-02

申请号：US17133418

申请日：2020-12-23

申请人： GRAIL, LLC

发明人： Matthew H. Larson ,  Hyunsung John Kim ,  Nick Eattock ,  Xiao Yang

IPC分类号： C40B50/06 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6874

CPC分类号： C40B50/06 ,  C12N15/1065 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6874 ,  C12Q1/6806 ,  C12Q2525/191 ,  C12Q2533/101 ,  C12Q2535/122 ,  C12Q2565/514 ,  C12N15/1093 ,  C12Q2525/191 ,  C12Q2533/101 ,  C12Q2535/122 ,  C12Q2563/179

摘要： Aspects of the invention relate to methods for preparing and analyzing a sequencing library from a mixed cell-free DNA (cfDNA) sample, wherein the mixed sample includes double-stranded DNA (dsDNA), damaged dsDNA (e.g., nicked dsDNA), and single-stranded DNA (ssDNA) molecules. The subject methods facilitate the collection of information from dsDNA, ssDNA and damaged DNA (e.g., nicked DNA) molecules in a sample, thereby providing enhanced diagnostic information as compared to sequencing libraries that are prepared from dsDNA alone.

公开(公告)号：US20230002824A1

公开(公告)日：2023-01-05

申请号：US17901778

申请日：2022-09-01

申请人： GRAIL, LLC

发明人： Xiao Yang ,  Hyunsung John Kim ,  Wenying Pan ,  Matthew H. Larson ,  Eric Michael Scott ,  Pranav Parmjit Singh ,  Mohini Jangi Desai

IPC分类号： C12Q1/6874 ,  G16H50/20 ,  G16H50/30 ,  G16B30/00 ,  G16B5/00 ,  G16B10/00 ,  G16B20/00 ,  G16B15/00 ,  G16B25/00 ,  G16B35/00 ,  G16B40/00 ,  G16B45/00 ,  G16B50/00 ,  G16B30/20 ,  G16B30/10 ,  G16B35/10 ,  G16B35/20

摘要： Cell free nucleic acids from a test sample obtained from an individual are analyzed to identify possible fusion events. Cell free nucleic acids are sequenced and processed to generate fragments. Fragments are decomposed into kmers and the kmers are either analyzed de novo or compared to targeted nucleic acid sequences that are known to be associated with fusion gene pairs of interest. Thus, kmers that may have originated from a fusion event can be identified. These kmers are consolidated to generate gene ranges from various genes that match sequences in the fragment. A candidate fusion event can be called given the spanning of one or more gene ranges across the fragment.