Patents by Inventor Peiyong Jiang
Peiyong Jiang has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11926821Abstract: The quality of cell-free DNA for analysis is improved by techniques described herein. Cell-free DNA may include DNA with defects that do not allow for analysis of those DNA with techniques such as sequencing and targeted capture enrichment. These defects may be defects within the strands of the DNA and not present at the ends of the DNA. These intrastrand defects in cell-free DNA can be repaired. The repair of the defects in cell-free DNA may then allow for these repaired cell-free DNA to be analyzed by techniques, including sequencing and targeted capture enrichment.Type: GrantFiled: October 21, 2019Date of Patent: March 12, 2024Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Cheuk Ho Tsang, Peiyong Jiang, Si Long Vong, Rossa Wai Kwun Chiu
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Patent number: 11923046Abstract: Disclosed herein are methods, systems, and apparatus for detecting microamplifications or microdeletions in the genome of a fetus. In some embodiments, the method comprises receiving sequence tags for each of a plurality of DNA fragments in a biological sample; determining genomic positions for the sequence tags; determining whether the density of DNA in each of a plurality of genomic regions is aberrantly high or low; identifying as a microamplification a set of consecutive genomic regions having aberrantly high density; and identifying as a microdeletion a set of consecutive genomic regions having aberrantly low density. The biological sample may be a blood sample obtained noninvasively from a female subject pregnant with the fetus.Type: GrantFiled: February 7, 2020Date of Patent: March 5, 2024Assignee: The Chinese University of Hong KongInventors: Yuk Ming Dennis Lo, Kwan Chee Chan, Peiyong Jiang, Cheuk Yin Jandy Yu, Rossa Wai Kwun Chiu
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Publication number: 20240043935Abstract: Measuring quantities (e.g., relative frequencies) of particular sequence motifs of cell-free DNA fragments in a biological sample can be used to analyze the biological sample. The particular sequence motifs or sequence sizes in certain genomic regions may indicate a histone modification. The sequence motifs and/or sizes can be used to measure a property of the sample (e.g., fractional concentration of a tissue type or a characteristic of the tissue type), to measure an amount of histone modifications, to determine a condition of the organism based on such measurements, and to enrich a biological sample for clinically-relevant DNA. Different tissue types can exhibit different patterns for the relative frequencies of the sequence motifs. Measures of the relative frequencies of sequence motifs of cell-free DNA can be used for analysis.Type: ApplicationFiled: July 28, 2023Publication date: February 8, 2024Inventors: Yuk-Ming Dennis Lo, Peiyong Jiang, Kwan Chee Chan, Masashi Yukawa, Lu Ji, Jinyue Bai
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Publication number: 20240018570Abstract: Systems and methods for using determination of base modification in analyzing nucleic acid molecules and acquiring data for analysis of nucleic acid molecules are described herein. Base modifications may include methylations. Methods to determine base modifications may include using features derived from sequencing. These features may include the pulse width of an optical signal from sequencing bases, the interpulse duration of bases, and the identity of the bases. Machine learning models can be trained to detect the base modifications using these features. The relative modification or methylation levels between haplotypes may indicate a disorder. Modification or methylation statuses may also be used to detect chimeric molecules.Type: ApplicationFiled: September 11, 2023Publication date: January 18, 2024Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Suk Hang Cheng, Wenlei Peng, On Yee Tse
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Publication number: 20240011105Abstract: Various embodiments are directed to detecting infection-causing microbial cell-free DNA from a biological sample based on their size profiles and/or end signatures, in which the detection of infection-causing microbial DNA can be performed without no template control (NTC) samples. Embodiments can include identifying the infection-causing pathogen-derived microbial DNA based on sizes of microbial cell-free DNA molecules. Embodiments can also include identifying from the infection-causing pathogen-derived microbial DNA based on end signatures of microbial cell-free DNA molecules. Embodiments can also include applying a machine-learning algorithm to a plurality of vectors that represent end signatures of the microbial cell-free DNA molecules, to identify the infection-causing pathogen-derived microbial DNA. By detecting the infection-causing pathogen-derived microbial DNA, a level of infection for the biological sample can be predicted.Type: ApplicationFiled: July 8, 2022Publication date: January 11, 2024Inventors: Yuk-Ming Dennis Lo, Kwan Chee Chan, Rossa Wai Kwun Chiu, Wai Kei Lam, Peiyong Jiang, Guangya Wang
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Publication number: 20230374602Abstract: Fragmentation of cell-free DNA molecules is measured and used for various purposes, including determining methylation, e.g., at a particular site of a DNA molecule, at a particular genomic site in a reference genome for a biological sample (e.g., plasma, serum, urine, saliva) of cell-free DNA of a subject, or for a particular region in the reference genome for the biological sample (also just referred to as a sample). Various types of fragmentation measurements can be used, e.g., end motifs and cleavage profiles. Another purpose is determining a fractional concentration of DNA of a particular tissue type (e.g., clinically-relevant DNA). Another purpose is determining a pathology of a subject using a biological sample including cell-free DNA. The cell-free DNA can be of the subject or of a pathogen (e.g., a virus) in the subject's sample. Sites/regions that are hypermethylated, hypomethylated, 5hmC-enriched, and 5hmC-depleted for a particular tissue type can be used.Type: ApplicationFiled: March 6, 2023Publication date: November 23, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Qing Zhou, Guannan Kang, Rong Qiao, Lu Ji
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Publication number: 20230374601Abstract: Fragmentation of cell-free DNA molecules is measured and used for various purposes, including determining methylation, e.g., at a particular site of a DNA molecule, at a particular genomic site in a reference genome for a biological sample (e.g., plasma, serum, urine, saliva) of cell-free DNA of a subject, or for a particular region in the reference genome for the biological sample (also just referred to as a sample). Various types of fragmentation measurements can be used, e.g., end motifs and cleavage profiles. Another purpose is determining a fractional concentration of DNA of a particular tissue type (e.g., clinically-relevant DNA). Another purpose is determining a pathology of a subject using a biological sample including cell-free DNA. The cell-free DNA can be of the subject or of a pathogen (e.g., a virus) in the subject's sample. Sites/regions that are hypermethylated, hypomethylated, 5hmC-enriched, and 5hmC-depleted for a particular tissue type can be used.Type: ApplicationFiled: March 6, 2023Publication date: November 23, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Qing Zhou, Guannan Kang, Rong Qiao, Lu Ji
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Publication number: 20230313314Abstract: Fragmentation of cell-free DNA molecules is measured and used for various purposes, including determining methylation, e.g., at a particular site of a DNA molecule, at a particular genomic site in a reference genome for a biological sample (e.g., plasma, serum, urine, saliva) of cell-free DNA of a subject, or for a particular region in the reference genome for the biological sample (also just referred to as a sample). Various types of fragmentation measurements can be used, e.g., end motifs and cleavage profiles. Another purpose is determining a fractional concentration of DNA of a particular tissue type (e.g., clinically-relevant DNA). Another purpose is determining a pathology of a subject using a biological sample including cell-free DNA. The cell-free DNA can be of the subject or of a pathogen (e.g., a virus) in the subject's sample. Sites/regions that are hypermethylated, hypomethylated, 5hmC-enriched, and 5hmC-depleted for a particular tissue type can be used.Type: ApplicationFiled: February 7, 2023Publication date: October 5, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Qing Zhou, Guannan Kang, Rong Qiao, Lu Ji
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Publication number: 20230279498Abstract: Methods and systems described herein include using various characteristics of cell-free DNA molecules to determine a property of a biological sample or a subject. Such characteristics can include size (e.g., where characteristic is of long cell-free DNA molecules), methylation, and end motifs. The method includes determining disease classification and/or predicting tissue of origin. In some instances, the characteristics includes determining an amount of long cell-free DNA molecules, and the disease classification can be based on the determined amount. The characteristics can also include identifying methylation pattern of a cell-free DNA molecule, then comparing the methylation pattern to a reference pattern to predict the tissue origin. In some instances, the methylation-pattern analysis includes using a trained machine-learning model.Type: ApplicationFiled: November 23, 2022Publication date: September 7, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Lok Yee Choy
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Publication number: 20230193360Abstract: Systems and methods for using determination of base modification in analyzing nucleic acid molecules and acquiring data for analysis of nucleic acid molecules are described herein. Base modifications may include methylations. Methods to determine base modifications may include using features derived from sequencing. These features may include the pulse width of an optical signal from sequencing bases, the interpulse duration of bases, and the identity of the bases. Machine learning models can be trained to detect the base modifications using these features. The relative modification or methylation levels between haplotypes may indicate a disorder. Modification or methylation statuses may also be used to detect chimeric molecules.Type: ApplicationFiled: August 19, 2022Publication date: June 22, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Suk Hang Cheng, Wenlei Peng, On Yee Tse
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Publication number: 20230197201Abstract: Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.Type: ApplicationFiled: February 15, 2023Publication date: June 22, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
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Publication number: 20230151436Abstract: Various embodiments are directed to applications (e.g., classification of biological samples) of the analysis of the count, the fragmentation patterns, and size of cell-free nucleic acids, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, such as viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).Type: ApplicationFiled: October 18, 2022Publication date: May 18, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Wai Kei Lam
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Publication number: 20230132951Abstract: Methods are provided to improve the positive predictive value for cancer detection using cell-free nucleic acid samples. Various embodiments are directed to applications (e.g., diagnostic applications) of the analysis of the fragmentation patterns and size of cell-free DNA, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, including viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).Type: ApplicationFiled: August 9, 2022Publication date: May 4, 2023Inventors: Eugeni Namsaraev, Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Kun Sun, Wai Kei Lam
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Patent number: 11615865Abstract: Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.Type: GrantFiled: September 10, 2019Date of Patent: March 28, 2023Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
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Patent number: 11605445Abstract: Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.Type: GrantFiled: September 10, 2019Date of Patent: March 14, 2023Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
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Patent number: 11591642Abstract: Methods and systems described herein involve using long cell-free DNA fragments to analyze a biological sample from a pregnant subject. The status of methylated CpG sites and single nucleotide polymorphisms (SNPs) is often used to analyze DNA fragments of a biological sample. A CpG site and a SNP are typically separated from the nearest CpG site or SNP by hundreds or thousands of base pairs. Finding two or more consecutive CpG sites or SNPs on most cell-free DNA fragments is improbable or impossible. Cell-free DNA fragments longer than 600 bp may include multiple CpG sites and/or SNPs. The presence of multiple CpG sites and/or SNPs on long cell-free DNA fragments may allow for analysis than with short cell-free DNA fragments alone. The long cell-free DNA fragments can be used to identify a tissue of origin and/or to provide information on a fetus in a pregnant female.Type: GrantFiled: May 12, 2022Date of Patent: February 28, 2023Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Suk Hang Cheng, Cheuk Yin Yu, Yee Ting Cheung, Wenlei Peng
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Publication number: 20230047963Abstract: Temporal variations in one or more characteristics measured from a cell-free DNA sample are used to estimate a gestational age of a fetus. Example characteristics include the methylation level measured from the cell-free DNA sample, size of DNA fragments measured from the cell-free DNA sample (e.g., proportion of fetal-derived DNA fragments longer than a specified size), and ending patterns of the DNA fragments align to a reference genome.Type: ApplicationFiled: October 31, 2022Publication date: February 16, 2023Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
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Patent number: 11581063Abstract: Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.Type: GrantFiled: September 10, 2019Date of Patent: February 14, 2023Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
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Publication number: 20220396838Abstract: Nuclease activity can affect the methylation level and fragmentation of cfDNA. Certain levels of nuclease activity may be correlated with certain levels of methylation in certain regions. Methylation level in certain genomic regions can be analyzed to classify nuclease activity. Methylation statuses of different genomic regions compared to methylation statuses of other genomic regions can determine a level of a condition (e.g., a disease such as cancer or disorder) in a subject. Nuclease activity can be monitored through analysis of methylation statuses of different sites. The efficacy of a treatment can also be determined using methylation levels at certain genomic regions. The number of fragments from genomic regions that are hypomethylated or hypermethylated in a reference genome can be used to provide information (e.g., fractional concentration) on the sample itself. The size distribution of extrachromosomal circular DNA can also be used to analyze a biological sample. Systems are also described.Type: ApplicationFiled: April 8, 2022Publication date: December 15, 2022Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Wing Yan Chan, Meng Ni, Diana Siao Cheng Han, Tsz Kwan Sin
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Publication number: 20220380855Abstract: Provided herein are methods and systems for identifying chimeric nucleic acid fragments, e.g., organism-pathogen chimeric nucleic acid fragments and chromosomal rearrangement chimeric nucleic acid fragments. Also provided herein are methods and systems relating to determining a pathogen integration profile or a chromosomal rearrangement in a biological sample and determining a classification of pathology based at least in part on a pathogen integration profile or a chromosomal rearrangement in a biological sample. In certain aspects of the present disclosure, cell-free nucleic acid molecules from a biological sample are analyzed.Type: ApplicationFiled: July 29, 2022Publication date: December 1, 2022Inventors: Yuk-Ming Dennis LO, Rossa Wai Kwun CHIU, Kwan Chee CHAN, Peiyong JIANG, Wai Kei LAM, Haiqiang ZHANG