An assay to quantify extent of methylation in a DNA sample. Kits and clinical diagnostic assays are also enabled herein, including assays to determine clinical phenotypes based on extent of methylation of a DNA target site.

An assay to quantify extent of methylation in a DNA sample. Kits and clinical diagnostic assays are also enabled herein, including assays to determine clinical phenotypes based on extent of methylation of a DNA target site.

Provided is a device including a well provided in a number of at least one, wherein a nucleic acid having at least one of a full-length nucleotide sequence and a partial nucleotide sequence of rRNA or rDNA is contained in a defined copy number in at least one well of the well, and wherein the defined copy number of the nucleic acid having at least one of a full-length nucleotide sequence and a partial nucleotide sequence of rRNA or rDNA is 1,000 or less.

Provided is a device including a well provided in a number of at least one, wherein a nucleic acid having at least one of a full-length nucleotide sequence and a partial nucleotide sequence of rRNA or rDNA is contained in a defined copy number in at least one well of the well, and wherein the defined copy number of the nucleic acid having at least one of a full-length nucleotide sequence and a partial nucleotide sequence of rRNA or rDNA is 1,000 or less.

In an example of an embodiment, a first sample set is prepared that includes a test sample prepared from a first subject sample and a reagent, and at least one control sample prepared from at least one of a positive control and a negative control, and a second sample set is prepared that includes a test sample prepared from a second subject sample and a reagent and does not contain at least one of the control samples contained in the first sample set. The nucleic acid amplification in the first sample set is measured in the first unit, the nucleic acid amplification in the second sample set is measured in the second unit, and the measurement result of each test sample contained in the first sample set and second sample set is analyzed based on the measurement result of the control sample contained in at least the first sample set.

In an example of an embodiment, a first sample set is prepared that includes a test sample prepared from a first subject sample and a reagent, and at least one control sample prepared from at least one of a positive control and a negative control, and a second sample set is prepared that includes a test sample prepared from a second subject sample and a reagent and does not contain at least one of the control samples contained in the first sample set. The nucleic acid amplification in the first sample set is measured in the first unit, the nucleic acid amplification in the second sample set is measured in the second unit, and the measurement result of each test sample contained in the first sample set and second sample set is analyzed based on the measurement result of the control sample contained in at least the first sample set.

Provided is a method including making copies of two or more populations of polynucleotides including identifier sequences, wherein the copies are attached to a substrate, hybridizing oligonucleotides to the identifier sequences, and comparing an amount of oligonucleotides hybridized to the copies of the two or more populations of polynucleotides, wherein at least one feature differs between the two or more populations of polynucleotides or between the making of the copies of the two or more populations of polynucleotides attached to the substrate.

Provided is a method including making copies of two or more populations of polynucleotides including identifier sequences, wherein the copies are attached to a substrate, hybridizing oligonucleotides to the identifier sequences, and comparing an amount of oligonucleotides hybridized to the copies of the two or more populations of polynucleotides, wherein at least one feature differs between the two or more populations of polynucleotides or between the making of the copies of the two or more populations of polynucleotides attached to the substrate.

Methods for detecting single nucleotide polymorphisms in nucleotide sequences using LAMP reactions are provided herein. Generally, two sets of LAMP primers, a wild-type primer that matches expected DNA sequences and an SNP primer that matches the expected SNP DNA are provided. One method includes providing the wild-type primer and the SNP primer in separate wells of a multi-well microfluidic array device, adding the sample nucleotide sequence into the wells seeded with the primers, and initiating LAMP reactions within the wells. The method includes observing the reaction differential between the primers and determining the status of the DNA with regard to that particular SNP. A second method includes providing the primers with tags in a mixture, adding the sample nucleotide sequence to the mixture, and initiating LAMP reactions. The method includes providing a different visual indication when the wild-type primer reacts with the sample nucleotide sequence versus when the SNP primer reacts with the sample nucleotide sequence, and determining the status of the DNA with regard to that particular SNP.

Methods for detecting single nucleotide polymorphisms in nucleotide sequences using LAMP reactions are provided herein. Generally, two sets of LAMP primers, a wild-type primer that matches expected DNA sequences and an SNP primer that matches the expected SNP DNA are provided. One method includes providing the wild-type primer and the SNP primer in separate wells of a multi-well microfluidic array device, adding the sample nucleotide sequence into the wells seeded with the primers, and initiating LAMP reactions within the wells. The method includes observing the reaction differential between the primers and determining the status of the DNA with regard to that particular SNP. A second method includes providing the primers with tags in a mixture, adding the sample nucleotide sequence to the mixture, and initiating LAMP reactions. The method includes providing a different visual indication when the wild-type primer reacts with the sample nucleotide sequence versus when the SNP primer reacts with the sample nucleotide sequence, and determining the status of the DNA with regard to that particular SNP.