The present disclosure describes a method of detecting, diagnosing, or predicting congenital heart defect (CHD). The method is a primarily minimally invasive method, as it uses a biological sample from a subject for detecting methylation changes in the nucleic acids of the subject. The method also involves the use of artificial intelligence (AI).

The present disclosure provides for and relates to the identification of novel biomarkers for diagnosis and prognosis of prostate cancer or the biochemical reoccurrence of prostate cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal prostate tissue, as set forth.

A method for the prediction, prognosis and/or diagnosis of bladder cancer or bladder cancer recurrence in a subject, the method includes: providing a test sample from the subject; measuring DNA methylation levels of at least a portion of two or more polynucleotides selected from the group consisting of HOXA9, SOX1, NPY, IRAK3, L1-MET, and ZO2 in the test sample; calculating a risk score based on the measured DNA methylation levels, comparing the calculated risk score to a cut-off value derived from a reference DNA methylation profile based on DNA methylation levels of the one or more biomarkers derived from a control group, members of which had bladder cancer; and based on the comparison calculated risk score to the cut-off value, determining at least one of: (1) whether bladder cancer has recurred; (2) whether there is likelihood that the bladder cancer will recur; and (3) whether the patient has bladder cancer.

Provided are systems and methods for detecting the presence of cancer DNA in blood and for identifying the cancer origin in a test subject. Also provided are systems and methods for monitoring likelihood of cancer recurrence in a subject previously treated for cancer, systems and methods for assessing the efficacy of a cancer treatment in a subject suffering from cancer, and systems and methods for treating cancer in a subject in need thereof. The disclosed systems and methods comprise various elements such as (a) bisulfite treating cell free DNA (cfDNA) from a liquid biopsy sample of the test subject; (b) using the bisulfite treated cfDNA to prepare a first sequencing library for (i) a plurality of specific target genomic regions and (ii) a second sequencing library for a genome from a flow through of the first sequencing library; (c) sequencing the prepared first and second sequencing libraries, thereby producing a corresponding first and second plurality of sequencing results; and (d) analyzing the corresponding first and second plurality of sequencing results; and (e) receiving output from a machine learning model.

Aspects described herein provide methods and kits for identifying at least one methylation pattern and optionally a transcription pattern in a nucleic acid from at least one exosome or circulating tumor cell in blood or other tissue sample.

The present invention relates to methods for the identification of cell culture factors for cell maintenance and cell conversion

There is described herein, a method of capturing and analyzing cell-free methylated DNA in a sample. The method involves subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA. A predetermined amount of control synthetic DNA fragments are added to the sample. The control synthetic DNA fragments each have a known nucleic acid sequence that does not align to a target genome sequence, and at least some of the control synthetic DNA fragments are methylated. The sample is denatured, and cell-free methylated DNA and the control synthetic DNA fragments are captured using a binder selective for methylated polynucleotides. The captured DNA is amplified and sequenced.

The current disclosure provides, inter alia, method of determining benign nodules from thyroid cancer in a subject that is found to have a thyroid nodule, method of treating thyroid cancer in a subject detected to have thyroid cancer by the method of the current disclosure, compositions for determining benign nodules from thyroid cancer in a subject, and kits including reagents and composition for determining benign nodules from thyroid cancer in a subject.

Provided are methods and compositions for the treatment of cancer. The methods comprise administering to an individual in need of treatment inhibitors of WHSC1 expression, function or activity in combination with PARP inhibitors or immune based therapy. In an aspect, the present disclosure provides compositions comprising one or more WHSC1 inhibitors and one or more PARP inhibitors, or one or more WHSC1 inhibitors and one or more immune checkpoint inhibitors.

Provided herein is technology for ovarian cancer screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of ovarian cancer and sub-types of ovarian cancer (e.g., clear cell ovarian cancer, endometrioid ovarian cancer, mucinous ovarian cancer, serous ovarian cancer).