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US 12,110,559 B2Granted
DNA methylation analysis to identify cell type
AssigneeInherent Biosciences, Inc.
InventorsTimothy Jenkins, Ryan Barney, Carter Norton
Life of this patent
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Abstract
Disclosed herein are methods of identifying a cell type by its genomic methylation pattern from a biological sample of a human subject. In some cases, the method can comprise identifying sperm and/or prostate cells. Also described herein are methods of identifying cell types for forensic analysis and for the treatment of a disease. The methods disclosed herein may comprise determining the DNA methylation pattern of DNA extracted from a semen sample. Also disclosed herein are methods of treating a disease or condition of a subject.
Claims17
A method for detecting a sperm cell comprising:
- a) obtaining a biological sample from a subject, wherein the biological sample comprises seminal fluid;
- b) extracting cell free DNA from the biological sample;
- c) detecting a methylation pattern of a region of the extracted cell free DNA from the biological sample with a first computer program, executed on a computer, wherein the methylation pattern comprises the presence or the absence of methylation of at least one region of the extracted cell free DNA, wherein the detecting comprises obtaining methylation data from a presence or an absence of a methylated base by a sodium bisulfite conversion, a sequencing, a differential enzymatic cleavage of DNA, an affinity capture of methylated DNA, an array, or any combination thereof;
- d) comparing the methylation pattern of the region of the extracted cell free DNA from the biological sample to a control pattern of DNA methylation with a second computer program, executed on a computer thereby determining the presence or the absence of the sperm cell in the biological sample by the methylation pattern;
- e) transferring the result of the presence or the absence of the sperm cell in the biological sample to a user interface on an electronic display via a communication network;
- and
- wherein the at least one region of the extracted cell free DNA comprises chr1:
- 182921660-182923994, chr1:
- 18807594-18809765, chr1:
- 190067323-190068181, chr1:247681102-247681932, chr1:35441734-35443497, chr1:9130738-9132197, chr1:92682167-92683822, chr10:13771107-13771466, chr10:29084707-29085500, chr10:85324700-85325063, chr11:70415188-70416310, chr11:92615215-92617119, chr12:52472758-52474048, chr13:36787282-36789909, chr16:89345548-89346492, chr16:90172237-90173535, chr17:43318045-43319383, chr17:74302589-74304620, chr17:7909776-7910041, chr19:10463037-10465258, chr19:2926081-2927446, chr19:36612371-36612912, chr19:50058328-50060307, chr2:
- 128158047-128159059, chr20:55684764-55685923, chr22:32749516-32750882, chr22:50008841-50010192, chr3:77145918-77148085, chr3:9027157-9027577, chr4:128650393-128652120, chr4:151500192-151505193, chr4:
- 189580331-189580876, chr4:
- 190731443-190732882, chr5:121186479-121188229, chr5:5057256-5057720, chr7:5540163-5541567, chr7:5645728-5648123, chr7:64330493-64331111, chr7:6524925-6525026, chr7:6865886-6867075, chr7:72741781-72743404, chr7:75023589-75024730, chr8:109143682-109144231, chr9:
- 138590204-138594308, chr9:72129977-72131656, chrX:129471948-129472963, chrX:
- 134974589-134976103, chrX:31089692-31090940, chrX:40481859-40483213, chrX:42636927-42638572 or any combination thereof.
12 more elements
A forensic analysis method of identifying a sperm cell from an article comprising:
- a) extracting cell free DNA from the article;
- b) detecting a methylation pattern of a region of the cell free DNA with a first computer program, executed on a computer, wherein the methylation pattern comprises the presence or the absence of methylation of at least one region of DNA of the cell free DNA, wherein the detecting comprises obtaining methylation data from a presence or an absence of a methylated base by a sodium bisulfite conversion, a sequencing, a differential enzymatic cleavage of DNA, an affinity capture of methylated DNA, an array, or any combination thereof;
- c) comparing the methylation pattern of the region of the extracted cell free DNA from the article to a control pattern of methylated DNA associated with a sperm cell with a second computer program, executed on a computer;
- d) determining the presence or absence of the sperm cell from the article with a third computer program, executed on a computer, wherein the methylation pattern indicates the presence or absence of the sperm cell from the article;
- e) transferring the result of the presence or the absence of the sperm cell from the article to a user interface on an electronic display via a communication network, which is a method for forensic analysis;
- and
- wherein the at least one region of the extracted cell free DNA comprises chr1:182921660-182923994, chr1:
- 18807594-18809765, chr1:
- 190067323-190068181, chr1:247681102-247681932, chr1:35441734-35443497, chr1:9130738-9132197, chr1:92682167-92683822, chr10:13771107-13771466, chr10:29084707-29085500, chr10:85324700-85325063, chr11:70415188-70416310, chr11:92615215-92617119. chr12:52472758-52474048, chr13:36787282-36789909, chr16:89345548-89346492, chr16:90172237-90173535, chr17:43318045-43319383, chr17:74302589-74304620, chr17:7909776-7910041, chr19:
- 10463037-10465258, chr19:2926081-2927446, chr19:36612371-36612912, chr19:50058328-50060307, chr2:128158047-128159059, chr20:55684764-55685923, chr22:32749516-32750882, chr22:50008841-50010192, chr3:77145918-77148085, chr3:9027157-9027577, chr4:
- 128650393-128652120, chr4:
- 151500192-151505193, chr4:189580331-189580876, chr4:190731443-190732882, chr5:121186479-121188229, chr5:5057256-5057720, chr7:5540163-5541567. chr7:5645728-5648123, chr7:64330493-64331111, chr7:6524925-6525026, chr7:6865886-6867075, chr7:72741781-72743404, chr7:75023589-75024730 chr8:
- 109143682-109144231, chr9:
- 138590204-138594308, chr9:72129977-72131656. chrX:
- 129471948-129472963, chrX:134974589-134976103, chrX:31089692-31090940, chrX:40481859-40483213, chrX:42636927-42638572 or any combination thereof.
12 more elements
Dependencies are inferred from the claim text.