公开(公告)号：US20240287504A1

公开(公告)日：2024-08-29

申请号：US18549344

申请日：2022-03-08

申请人： Illumina, Inc. ,  Illumina Cambridge Limited

发明人： Andrew Kennedy ,  Sarah Shultzaberger ,  Emma Bell ,  Oliver Miller ,  Kim Schneider ,  Esther Musgrave-Brown ,  Niall Gormley ,  Andrew Slatter ,  Feng Chen

IPC分类号： C12N15/10

CPC分类号： C12N15/1065

摘要： Genomic library preparation using Cas-gRNA RNPs, and targeted epigenetic assays, are provided herein. Some compositions include, from a first species, substantially only single-stranded polynucleotides; from a second species, substantially only double-stranded polynucleotides; and amplification primers ligated to ends of the second double-stranded polynucleotides and substantially not ligated to any ends of the first double-stranded polynucleotides. Some compositions include first and second molecules of a target polynucleotide having a sequence, the first molecule having a first end at a first subsequence, the second molecule having a first end at a second subsequence, wherein the first subsequence only partially overlaps with the second subsequence. Some examples provide a composition that includes a target polynucleotide and a first fusion protein including a Cas-gRNA RNP coupled to a transposase having an amplification adapter coupled thereto. The Cas-gRNA RNP may be hybridized to a subsequence in the target polynucleotide.

公开(公告)号：US20220290234A1

公开(公告)日：2022-09-15

申请号：US17694404

申请日：2022-03-14

申请人： ILLUMINA, INC. ,  ILLUMINA CAMBRIDGE LIMITED

发明人： Sarah Shultzaberger ,  Xiaolin Wu ,  Eric Brustad ,  Niall Gormley

IPC分类号： C12Q1/6876 ,  C12Q1/6806 ,  C07H19/16

摘要： Examples provided herein are related to detecting methylcytosine and its derivatives using S-adenosyl-L-methionine analogs (xSAMs). Compositions and methods for performing such detection are disclosed. A target polynucleotide may include cytosine (C) and methylcytosine (mC). The method may include (a) protecting the C in the target polynucleotide from deamination; and (b) after step (a), deaminating the mC in the target polynucleotide to form thymine (T). Protecting the C from deamination may include adding a protective group to the 5 position of the C, e.g., using a methyltransferase enzyme that adds the first protective group from an xSAM.

公开(公告)号：US20240191288A1

公开(公告)日：2024-06-13

申请号：US18285222

申请日：2022-03-30

申请人： Illumina, Inc.

发明人： Colin Brown ,  Sarah Shultzaberger ,  Stephen M. Gross ,  Angelica Barr ,  Samantha Snow

IPC分类号： C12Q1/6848 ,  C12Q1/48 ,  C12Q1/6855

CPC分类号： C12Q1/6848 ,  C12Q1/485 ,  C12Q1/6855

摘要： The disclosure relates to methods, compositions, and kits for the selective depletion of non-desirable fragments from amplified libraries using blocking oligonucleotides.

公开(公告)号：US20240127906A1

公开(公告)日：2024-04-18

申请号：US18484268

申请日：2023-10-10

申请人： Illumina, Inc. ,  Illumina Cambridge Limited ,  Illumina Singapore PTE. LTD.

发明人： Qi Wang ,  Suzanne Rohrback ,  Sarah Shultzaberger ,  Rebekah Karadeema ,  Leslie Beh Yee Ming ,  James Baye ,  Colin Brown

IPC分类号： G16B30/10 ,  G16B20/20

CPC分类号： G16B30/10 ,  G16B20/20

摘要： This disclosure describes methods, non-transitory computer readable media, and systems that can use a computationally efficient model to determine a corrected methylation-level value for a specific sample nucleotide sequence. For instance, the disclosed systems determine a false positive rate and a false negative rate at which a given methylation sequencing assay converts cytosine bases. Based on the determined false positive rate and false negative rate, the disclosed systems determine a corrected methylation-level value that corrects for a bias of the given methylation sequencing assay.