The present disclosure provides methods and systems directed to cell-free identification and/or monitoring of pregnancy-related states. A method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject may comprise assaying a cell-free biological sample derived from said subject to detect a set of biomarkers, and analyzing the set of biomarkers with an algorithm to determine the presence or susceptibility of the pregnancy-related state.

The present disclosure provides methods and systems directed to cell-free identification and/or monitoring of pregnancy-related states. A method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject may comprise assaying a cell-free biological sample derived from said subject to detect a set of biomarkers, and analyzing the set of biomarkers with an algorithm to determine the presence or susceptibility of the pregnancy-related state.

The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

A fractional concentration of fetal relevant DNA in a mixture of DNA from a biological sample is determined based on amounts of DNA fragments of a particular size or range of sizes. DNA fragments may be sequenced to obtain sequence reads, and the sequence reads may be aligned to a reference genome to determine sizes of the DNA fragments. Calibration data points (e.g., as a calibration function) indicate a correspondence between values of a parameter providing a statistical measure of a size profile and the fractional concentration of the fetal DNA. For a given sample, a value of the parameter can be determined from DNA fragments of a particular size or range of sizes in a sample. A comparison of the value to the calibration data points can provide the estimate of the fractional concentration of the fetal DNA.

A fractional concentration of fetal relevant DNA in a mixture of DNA from a biological sample is determined based on amounts of DNA fragments of a particular size or range of sizes. DNA fragments may be sequenced to obtain sequence reads, and the sequence reads may be aligned to a reference genome to determine sizes of the DNA fragments. Calibration data points (e.g., as a calibration function) indicate a correspondence between values of a parameter providing a statistical measure of a size profile and the fractional concentration of the fetal DNA. For a given sample, a value of the parameter can be determined from DNA fragments of a particular size or range of sizes in a sample. A comparison of the value to the calibration data points can provide the estimate of the fractional concentration of the fetal DNA.

A fractional concentration of tumor DNA in a plasma sample is estimated by analyzing a biological sample of an organism. One or more sequence reads obtained from a sequencing of the DNA fragment are received. The one or more sequence reads are aligned to a reference genome to obtain aligned locations for both ends of the DNA fragment. Using the aligned locations, a size of the DNA fragment is determined. For each size of a plurality of sizes, an amount of a set of the plurality of DNA fragments from the plasma sample corresponding to the size is determined. A first value of a first parameter is calculated based on the amounts of DNA fragments at multiple sizes. The first value is compared to a calibration value. A fractional concentration of tumor DNA in the plasma sample is estimated based on the comparison.

A fractional concentration of tumor DNA in a plasma sample is estimated by analyzing a biological sample of an organism. One or more sequence reads obtained from a sequencing of the DNA fragment are received. The one or more sequence reads are aligned to a reference genome to obtain aligned locations for both ends of the DNA fragment. Using the aligned locations, a size of the DNA fragment is determined. For each size of a plurality of sizes, an amount of a set of the plurality of DNA fragments from the plasma sample corresponding to the size is determined. A first value of a first parameter is calculated based on the amounts of DNA fragments at multiple sizes. The first value is compared to a calibration value. A fractional concentration of tumor DNA in the plasma sample is estimated based on the comparison.

The invention relates to a method for identifying one or more polymorphisms in nucleic acid samples, comprising: (a) performing a reproducible complexity reduction on a plurality of nucleic acid samples to provide a plurality of libraries of the nucleic acid samples comprising amplified fragments, wherein the reproducible complexity reduction comprises amplifying fragments of the nucleic acid samples using one or more primers to obtain the amplified fragments, and wherein the amplified fragments in each library comprise a unique identifier sequence to indicate origin of each library obtained by the reproducible complexity reduction; (b) combining the plurality of libraries to obtain a combined library and sequencing at least a portion of the combined library to obtain sequences; (c) aligning the sequences to obtain an alignment; and (d) identifying one or more polymorphisms in the plurality of nucleic acid samples.

The invention relates to a method for identifying one or more polymorphisms in nucleic acid samples, comprising: (a) performing a reproducible complexity reduction on a plurality of nucleic acid samples to provide a plurality of libraries of the nucleic acid samples comprising amplified fragments, wherein the reproducible complexity reduction comprises amplifying fragments of the nucleic acid samples using one or more primers to obtain the amplified fragments, and wherein the amplified fragments in each library comprise a unique identifier sequence to indicate origin of each library obtained by the reproducible complexity reduction; (b) combining the plurality of libraries to obtain a combined library and sequencing at least a portion of the combined library to obtain sequences; (c) aligning the sequences to obtain an alignment; and (d) identifying one or more polymorphisms in the plurality of nucleic acid samples.