Abstract: The invention relates to a method of preparing a nucleic acid library from a sample comprising high molecular weight DNA (HMW DNA), preferably genomic DNA, comprising the steps (i) contacting said DNA with a first restriction enzyme and a second restriction enzyme; (ii) contacting said DNA with a pair of oligonucleotide adapters according to any of claims 1 to 12; (iii) contacting said DNA with at least one DNA ligase; and (iv) incubating to allow digestion of the DNA by said first restriction enzyme and second restriction enzyme, annealing of said oligonucleotide adapters to the digested DNA, and ligation of the annealed oligonucleotide adapters to the digested DNA by said at least one DNA ligase. The invention also relates to oligonucleotide adapters, a kit, and uses of same.

Abstract: In some embodiments, a method for aiding prediction of the likelihood of progression from Barrett's esophagus to high grade dysplasia or esophageal adenocarcinoma in a subject, is disclosed. The method can include (a) providing an oesophagal sample from said subject (b) determining if said sample stains abnormally with Aspergillus oryzae lectin; (c) determining if there is a DNA content abnormality in said sample; and (d) determining if there is low grade dysplasia in said sample; wherein if (b) is abnormal and (c) is abnormal and low grade dysplasia is present, then an increased likelihood of progression is determined. The disclosed subject matter also relates to an apparatus, and to different uses of certain materials.

Abstract: The invention relates to a method of aiding detection of a surface abnormality in the oesophagus of a subject, wherein said surface abnormality is selected from the group consisting of low-grade dysplasia (LGD), high-grade dysplasia (HGD), asymptomatic oesophageal adenocarcinoma (OAC) and intra-mucosal cancer (IMC), the method comprising: a) providing a sample of cells from said subject, wherein said sample comprises cells collected from the surface of the subject's oesophagus; b) assaying said cells for at least two markers selected from (i) p53; (ii) c-Myc; (iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3; wherein detection of abnormal levels of at least two of said markers infers that the subject has an increased likelihood of a surface abnormality in the oesophagus. The invention also relates to certain kits, apparatus and uses.

Abstract: Some embodiments are related to a method for determining if a subject has an increased likelihood of high grade dysplasia (HGD) or esophagal adenocarcinoma (EC). An exemplary method can include providing a sample from an AFI patch of the subject's esophagus, assaying the sample for (i) aneuploidy, and (ii) abnormal p53, and (iii) abnormal Cyclin A, wherein if the sample shows the presence of at least two of (i), (ii) and (iii), then the subject is determined as having an increased likelihood of high grade dysplasia (HGD) or esophagal adenocarcinoma (EC). The invention also relates to certain methods of medical treatment.

Abstract: In some embodiments, a method for aiding prediction of the likelihood of progression from Barrett's esophagus to high grade dysplasia or esophageal adenocarcinoma in a subject, is disclosed. The method can include (a) providing an oesophagal sample from said subject (b) determining if said sample stains abnormally with Aspergillus oryzae lectin; (c) determining if there is a DNA content abnormality in said sample; and (d) determining if there is low grade dysplasia in said sample; wherein if (b) is abnormal and (c) is abnormal and low grade dysplasia is present, then an increased likelihood of progression is determined. The disclosed subject matter also relates to an apparatus, and to different uses of certain materials.

Abstract: In some embodiments, a method for aiding assessment of the likelihood of dysplasia or esophageal adenocarcinoma being present in a subject can include (a) providing an esophagal sample from said subject (b) determining the methylation status of (i) SLC22A18, (ii) PIGR, (iii) GJA12 and (iv) RIN2 in said sample wherein if 2 or more of said genes are methylated then an increased likelihood of presence of dysplasia or esophageal is determined. The invention also relates to apparatus for same.

Abstract: The present invention relates to the use of a retinoic acid antagonist in the manufacture of a medicament for the treatment or prevention of Barrett's oesophagus (Barrett's mucosa). Furthermore, the invention relates to use of a retinoic acid antagonist in the manufacture of a medicament for the treatment or prevention of ectopic development of columnar epithelium, use of such an antagonist in the conversion of columnar epithelium to squamous epithelium, in the induction or maintenance of squamous epithelium, and in the reduction of proliferation of ectopic columnar epithelium. Preferably the retinoic acid antagonist is an aldehyde dehydrogenase inhibitor such as a competitive inhibitor. Preferably the antagonist is citral.