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Genome Technology s Peer Review: A Weekly Forum of Recently Published Journal Articles: May 24, 2005

NEW YORK, May 24 (GenomeWeb News) - Following is a description of two recently published research papers recommended by a scientist involved in integrated biology. The recommender, Michael Tainsky, is director of the Program in Molecular Biology and Human Genetics at the Karmanos Cancer Institute at WayneStateUniversity.

 

For a complete list of recommended papers, read Genome Technology, a GenomeWeb News sister publication.


Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. Baggerly KA, Morris JS, Edmonson SR, Coombes KR, J Natl Cancer Inst. 2005 Feb 16;97(4):307-9.

 

In this report, the authors, at MD Anderson Cancer Center in Houston, write critically of the 2002 Liotta/Petricoin paper in The Lancet that presented data on a proteomic profiling approach to diagnosing early-stage ovarian cancer in serum. That publication reported good classification in one dataset using results from training on a much earlier dataset, but its authors have since reported that they did not perform the analysis as described, say Keith Baggerly and his colleagues at MD Anderson.

 

Baggerly says his group's analysis revealed that the pattern that enabled successful classification is biologically implausible and that the method, properly applied, does not classify the data accurately. The method used in previously published studies does not establish reproducibility and performs no better than chance for classifying the second dataset, in part because the second dataset is easy to classify correctly, the authors add. In conclusion, Baggerly says that the reproducibility of the proteomic profiling approach has yet to be established.

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.