Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences.

Over the last few years a number of restriction enzymes that cut DNA only if cytosines within their recognition sequences are methylated have been characterized and become commercially available. Cleavage with these enzymes to release DNA fragments in a methylation-dependent manner can be combined with a novel method of amplification, Helper Dependent Chain Reaction (HDCR), to selectively amplify these fragments. HDCR uses "Helper" oligonucleotides as templates for extension of the free 3' end of target fragments to incorporate tag sequences at the ends of fragments.

Evaluation of Methylation Biomarkers for Detection of Circulating Tumor DNA and Application to Colorectal Cancer.

Solid tumors shed DNA into circulation, and there is growing evidence that the detection of circulating tumor DNA (ctDNA) has broad clinical utility, including monitoring of disease, prognosis, response to chemotherapy and tracking tumor heterogeneity. The appearance of ctDNA in the circulating cell-free DNA (ccfDNA) isolated from plasma or serum is commonly detected by identifying tumor-specific features such as insertions, deletions, mutations and/or aberrant methylation. Methylation is a normal cell regulatory event, and since the majority of ccfDNA is derived from white blood cells (WBC), it is important that tumour-specific DNA methylation markers show rare to no methylation events in WBC DNA.

Little evidence for association between the TGFBR1*6A variant and colorectal cancer: a family-based association study on non-syndromic family members from Australia and Spain.

Background: Genome-wide linkage studies have identified the 9q22 chromosomal region as linked with colorectal cancer (CRC) predisposition. A candidate gene in this region is transforming growth factor β receptor 1 (TGFBR1). Investigation of TGFBR1 has focused on the common genetic variant rs11466445, a short exonic deletion of nine base pairs which results in truncation of a stretch of nine alanine residues to six alanine residues in the gene product.

A panel of genes methylated with high frequency in colorectal cancer.

Background: The development of colorectal cancer (CRC) is accompanied by extensive epigenetic changes, including frequent regional hypermethylation particularly of gene promoter regions. Specific genes, including SEPT9, VIM1 and TMEFF2 become methylated in a high fraction of cancers and diagnostic assays for detection of cancer-derived methylated DNA sequences in blood and/or fecal samples are being developed. There is considerable potential for the development of new DNA methylation biomarkers or panels to improve the sensitivity and specificity of current cancer detection tests.

Colorectal Neoplasia Differentially Expressed (CRNDE), a Novel Gene with Elevated Expression in Colorectal Adenomas and Adenocarcinomas.

An uncharacterized gene locus (Chr16:hCG_1815491), now named colorectal neoplasia differentially expressed (gene symbol CRNDE), is activated early in colorectal neoplasia. The locus is unrelated to any known protein-coding gene. Microarray analysis of 454 tissue specimens (discovery) and 68 previously untested specimens (validation) showed elevated expression of CRNDE in >90% of colorectal adenomas and adenocarcinomas.

Discovery and validation of molecular biomarkers for colorectal adenomas and cancer with application to blood testing.

Background & Aims: Colorectal cancer incidence and deaths are reduced by the detection and removal of early-stage, treatable neoplasia but we lack proven biomarkers sensitive for both cancer and pre-invasive adenomas. The aims of this study were to determine if adenomas and cancers exhibit characteristic patterns of biomarker expression and to explore whether a tissue-discovered (and validated) biomarker is differentially expressed in the plasma of patients with colorectal adenomas or cancer.

Methods: Candidate RNA biomarkers were identified by oligonucleotide microarray analysis of colorectal specimens (222 normal, 29 adenoma, 161 adenocarcinoma and 50 colitis) and validated in a previously untested cohort of 68 colorectal specimens using a custom-designed oligonucleotide microarray.

Reversing the course of forgetting.

Forgetting functions were generated for pigeons in a delayed matching-to-sample task, in which accuracy decreased with increasing retention-interval duration. In baseline training with dark retention intervals, accuracy was high overall. Illumination of the experimental chamber by a houselight during the retention interval impaired performance accuracy by increasing the rate of forgetting.

Reversing the signaled magnitude effect in delayed matching to sample: delay-specific remembering.

Pigeons performed a delayed matching-to-sample task in which large or small reinforcers for correct remembering were signaled during the retention interval. Accuracy was low when small reinforcers were signaled, and high when large reinforcers were signaled (the signaled magnitude effect). When the reinforcer-size cue was switched from small to large partway through the retention interval, accuracy accordingly changed from low to high.

Reinforcer probability, reinforcer magnitude, and the reinforcement context for remembering.

Traditional theories of delayed matching-to-sample performance do not predict that accuracy will improve when absolute levels of reinforcement are increased. This prediction emerges only when reinforcement context is considered (J. A.

A computational technique for improving estimates of discriminability and bias across multiple dimensions of choice.

Brown and White (2009) proposed measures of discriminability and bias that accommodate additional dimensions of choice--and hence, bias--in conditional discriminations such as matching-to-sample and the yes-no signal detection task. Their proposed measures increase the statistical independence of discriminability and bias estimates, thus improving their accuracy. Because Brown and White's (2009) equations partition response data more than do standard equations, however, their measures have a slightly lower ceiling.

Measuring discriminability when there are multiple sources of bias.

Performance measures such as log d and d' aim to measure stimulus discriminability independently of response bias in conditional discrimination tasks, including the yes/no signal-detection procedure. However, they assume only one dimension of bias (e.g.

Map of differential transcript expression in the normal human large intestine.

While there is considerable research related to using differential gene expression to predict disease phenotype classification, e.g., neoplastic tissue from nonneoplastic controls, there is little understanding of the range of expression in normal tissues.

Seasonal variation in pigeon body weight and delayed matching-to-sample performance.

The weights of 5 pigeons with free access to food, monitored over 3 calendar years in the laboratory, were found to fluctuate with season. All pigeons were at their heaviest in the winter and were lightest in the summer. Five different pigeons performed a standard delayed matching-to-sample task for 44 weeks from January to November.

The optimal correction for estimating extreme discriminability.

Discriminability measures such as d' and log d become infinite when performance is extremely accurate and no errors are recorded. Different arbitrary corrections can be applied to produce finite values, but how well do these values estimate true performance? To answer this question, we directly calculated the effects of a range of different corrections on the sampling distributions of d' and log d. Many arbitrary corrections produced better estimates of discriminability than did the intuitively plausible technique of rerunning problem conditions.

Remembering: the role of extraneous reinforcement.

In two experiments, pigeons' responding on an extraneous task was explicitly reinforced during delayed matching-to-sample trials. In Experiment 1, red or green sample stimuli were followed by retention intervals of 0.2, 1, 4, or 12 sec, during which pecks to a white center key were reinforced with 2.

On the effects of signaling reinforcer probability and magnitude in delayed matching to sample.

Two experiments examined whether postsample signals of reinforcer probability or magnitude affected the accuracy of delayed matching to sample in pigeons. On each trial, red or green choice responses that matched red or green stimuli seen shortly before a variable retention interval were reinforced with wheat access. In Experiment 1, the reinforcer probability was either 0.

Local proactive interference in delayed matching to sample: the role of reinforcement.

Discriminability in delayed matching to sample was lower when the samples on consecutive trials differed compared with when samples on consecutive trials were the same. This local proactive interference occurred when correct choices on the previous trial were reinforced but not when correct choices on the previous trial were not reinforced. When the choice on the previous trial was incorrect, discriminability was higher on different consecutive trials than on same trials.