Jul 2012
Are You Sure?
31/07/12 12:55 Filed in: GenomeWeb Daily Scan
Daniel MacArthur at Massachusetts General Hospital suggests that false positives are a given in genomic research, especially due to the large size of genomes and errors from high-throughput sequencing. Ann Buchanan at Penn State University also notes for these and a variety of other reasons there many sequence errors in genomics manuscripts and online databases and a higher rate of retractions. S. Pelech argues that the increased rate of retraction of scientific research results in publications in general actually reflects a wide variety of confounding factors beside greater error rates from higher throughput technologies. These include amongst others premature submission for publication due to financial and continuing employment requirements, poorer peer-review, and a proliferation of new journals eager to acquire manuscripts, which can result in outright plagiarism and even fraudulent data. Read More...
But What Does That Really Mean?
30/07/12 12:53 Filed in: GenomeWeb Daily Scan
Adam Rutherford at Nature suggested that "the present gains and future benefits of synthetic biology are too great for it to be written off with fear-mongering maxims about "playing God." Gerhard Adam in his Blog questioned what it really means to "play God", and that if we now have the power to improve our ability to cure diseases, then we have a moral responsibility to do so. S. Pelech agrees and takes issue with the very concept of "Playing God" and wonders why if people believe in divine intervention they don't also believe that scientists are guided in their actions directly by "God." Read More...
Sperm Seq
30/07/12 12:51 Filed in: GenomeWeb Daily Scan
Stephen Quake at Stanford University and his colleagues reported the first genetic comparison of 91 single sperm cells using a microfluidic chip and found that some of the cells had recombined in unexpected places. This recombination contributes to the genetic diversity between siblings, and this methodology might be used to diagnose male fertility, select eggs for in vitro fertilization, and identify mutated genes in individual cancer cells. S. Pelech points out that the ability to sequence genomes in single haploid cells provides the unique opportunity to examine the actual clustering of specific mutations on the very same protein and explore the possibilities of synergistic and antagonistic mutations. Read More...
Lab-Less Research
18/07/12 12:56 Filed in: GenomeWeb Daily Scan
Monya Baker at Nature News described how public data repositories like the NCBI's Gene Expression Omnibus (GEO) have been a boon for researchers, who are using the information they store to study genetic associations to diseases without ever having to go near a microarray. S. Pelech pointed out that while this is wonderful resource for examination of the changes in gene expression within individual studies, it is difficult to compare the data across different studies. At Kinexus, we retrieved from the GEO database the human gene expression data from over 900 different studies with over 6000 biological specimens and systematically normalized the results to permit queries of mRNA levels for 23,000 genes in the open-access website TranscriptoNET (www.transcriptonet.ca). TranscriptoNET features comprehensive information on the mRNA expression levels in about 600 types of human organs, tissues, tumours and cancer cell lines. Read More...