Host dna as a biomarker of crohn's disease

A method for measuring abundance of DNA in stool from a human having or suspected of having Crohn's Disease (CD), said method comprising:

• a) providing a sample of stool or nucleic acid extracted from a stool sample from the human;
• b) determining the relative abundance of the human's DNA in said sample;
• and
• c) associating said abundance of the human DNA with the human providing the stool sample, or the human providing the stool sample from which the nucleic acid was extracted.

An amplification method of measuring the abundance of a target nucleic acid sequence in a sample, comprising:

• a) contacting a sample from a subject having or suspected of having Crohn's Disease (CD) comprising a target nucleic acid sequence with a set of oligonucleotide primers, each primer comprising a 5′ end and a 3′ end, wherein a first primer comprises a sequence complementary to a first region in the target nucleic acid sequence, and a second primer comprises a sequence complementary to a second region in the target nucleic acid sequence, wherein the second region is downstream of the first region;
• b) further contacting the sample with deoxynucleotide triphosphates (dNTPs), thereby forming a mixture;
• c) allowing the first and second oligonucleotide primers to anneal to the target nucleic acid sequence of a) thereby forming an oligonucleotide primer annealed target nucleic acid;
• d) exposing the oligonucleotide primer annealed target nucleic acid of step c) to a template-dependent polymerizing agent having 5′ to 3′ polymerization activity under conditions permissive for amplification, and whereby the oligonucleotide primers are extended to produce extension products;
• and
• e) detecting the extension products, thereby measuring the abundance of the target nucleic acid sequence in the sample.

A vessel having a reaction solution, the reaction solution comprising:

• a) A polymerizing agent that synthesizes or amplifies nucleic acid;
• b) a sample comprising stool or DNA extracted or isolated from stool of a subject having or suspected of having Crohn's Disease (CD);
• c) oligonucleotide primers or oligonucleotide probe designed to specifically hybridize to a target sequence of the subject's DNA;
• d) deoxynucleotide triphosphates (dNTPs);
• and
• e) buffers or other agents permissive for detection, replication or amplification of the target sequence.