There is provided a method of calculating a base methylation degree from DNA sequence analysis data, which is a calculation method for a base methylation degree, including correcting a read based on quality information of sequence analysis data in a case of using a co-methylation site, using a paired-end read, using a molecular barcode, or using a plurality of sequence analysis data. There is also provided a program for causing a computer to execute the calculation method for a base methylation degree.

Systems and methods for identifying variant alleles as somatic or germline are provided. Reference and variant alleles for a genomic position are identified. Methylation states and sequences of nucleic acid fragment sequences that map to the genomic position are obtained from a sample of a subject. Using the sequences of nucleic acid fragment sequences, each nucleic acid fragment sequence that has the reference allele is assigned to a reference subset, and each nucleic acid fragment sequence that has the variant allele is assigned to a variant subset. One or more indications of the methylation states across the nucleic acid fragment sequences in the variant subset and an indication of the number of nucleic acid fragment sequences in the reference subset versus the variant subset are applied to a trained binary classifier. An identification of the variant allele at the genomic position as somatic or germline is obtained from the classifier.

In accordance with some embodiments, the present invention comprises use of a rapid and accurate QM-MSP and cMethDNA methylation marker-based assays to quickly distinguish between cancer and benign/normal tissues in a biological sample from a subject suspected of having cancer. Methods for detecting breast, colon, and lung cancers in biological samples of suspect tissues and fluids are also provided to assist in triaging subjects suspected of having cancer for expedited biopsy and pathology review in low resource settings.

Provided herein are microfluidic devices for analyzing samples. In one aspect, the microfluidic device includes a body structure having a droplet compression chamber, a sieve structure in fluid communication with the droplet compression chamber, which sieve structure comprises an array of protrusions that extend from at least one surface of the body structure and define at least a portion of one or more fluidic circuits, and a port at least partially disposed in the body structure. Other aspects include kits, methods, systems, computer readable media, and related aspects for analyzing samples.

Aspects of the present disclosure relate to methods for modification and detection of methylated nucleotides. Embodiments are directed to detection of RNA methylation. Disclosed are methods and compositions for transcriptome-wide detection of N.sup.6-methyladenosine in mRNA. In some cases, methods for modifying a methylated nitrogenous base are described. Also disclosed are enzymes and other molecules useful for RNA methylation detection.

The present disclosure provides methods and compositions for detecting polynucleotides in a sample and for quantifying polynucleotide load in a sample. The polynucleotides can be associated with a disease, disorder, or condition. In some applications, methylated DNA is quantified, e.g., in order to determine the load of polynucleotides in a sample. The present disclosure also provides methods and compositions for determining the load of fetal polynucleotides in a biological sample, e.g., the load of fetal polynucleotides (e.g., DNA, RNA) in maternal plasma. The present disclosure provides methods and compositions for detecting cellular processes such as cellular viability, growth rates, and infection rates. This disclosure also provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some embodiments, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g., blood, plasma). The methods and materials described apply techniques for allowing detection of small, but statistically significant, differences in polynucleotide copy number.

Methods of detecting, predicting severity of, and/or predicting treatment response to respiratory virus infection in a sample obtained from a subject. The methods include assaying a methylation state of a marker in a sample obtained from a subject and identifying the subject as having respiratory virus infection, a likelihood of severe outcomes of respiratory infection, and/or a likelihood of treatment response depending on the methylation state of the marker. The markers can include bases (DMP) in differentially methylated regions (DMR) as provided herein.

Disclosed herein are methods and systems of utilizing sequencing reads for detecting and quantifying the presence of a tissue type or a disease type in cell-free DNA prepared from blood samples.

A method of processing a fecal sample from a human subject comprising removing a portion of a collected fecal sample and adding the removed portion of the sample to a buffer that prevents denaturation or degradation of blood proteins found in the sample, and detecting the presence of human blood in the removed portion of the fecal sample. The method further comprises stabilizing the remaining portion of the fecal sample.

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.