Sunday, May 30, 2010

Pharmacogenomics: Is miRNA the future of phenotyping?

MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine.

You can get the paper here

Posted via email from the nocx files

Monday, May 24, 2010

Extensive sequence-influenced DNA methylation polymorphism in the human genome

Hellman and Chess: Methylation is not independent of SNPs.

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GREAT improves functional interpretation of cis-regulatory regions, via @thinkgenome

'Genomic Regions Enrichment of Annotations Tool' 
Mclean et al. 
Nat Biotechnol 28:495–501 2010

The software completes an analysis showing which genes a transcription factor is likely to influence, and the relevant molecular pathways, across the genome.  It incorporates proximal and distal binding and controls for false positives using a binomial test.

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Wednesday, May 19, 2010

Anonymization of electronic medical records for validating genome-wide association studies

The "approach automatically extracts potentially linkable clinical features and modifies them in a way that they can no longer be used to link a genomic sequence to a small number of patients, while preserving the associations between genomic sequences and specific sets of clinical features corresponding to GWAS-related diseases."

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Tuesday, May 11, 2010

Genome Medicine: Locus Reference Genomic sequences: an improved basis for describing human DNA variants.

The Locus Reference Genomic (LRG) sequence format "builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-file record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants."

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Sunday, May 9, 2010

BMC Genomics: Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood

"We conclude that about 904 miRNAs are expressed in human leukocytes."

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Current Opinion Neurobiol: MicroRNA pathways in neural development and plasticity, in press

Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands

"This approach utilizes linear regression models of non-normalised hybridisation data to define methylation status. Log-transformed signal intensities of unmethylated controls on the microarray are used as a reference. The signal intensities of DNA samples digested with methylation sensitive restriction enzymes and mock digested are then transformed to the likelihood of a locus being methylated using this reference. We tested the ability of MLDA to identify loci differentially methylated as analysed by DMH between cisplatin sensitive and resistant ovarian cancer cell lines. MLDA identified 115 differentially methylated loci and 23 out of 26 of these loci have been independently validated by Methylation Specific PCR and/or bisulphite pyrosequencing."

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Cgaln: fast and space-efficient whole-genome alignment

"Cgaln takes less than 13 hours to finish an alignment between the whole genomes of human and mouse in a single run on a conventional desktop computer with a single CPU and 2 GB memory."

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Friday, May 7, 2010

NEJM Effect of Bar-Code Technology on the Safety of Medication Administration via @dirkstanley

"Observers noted 776 nontiming errors in medication administration on units that did not use the bar-code eMAR (an 11.5% error rate) versus 495 such errors on units that did use it (a 6.8% error rate)" P<0.001

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Thursday, May 6, 2010

Analysis of a polymorphic microRNA target site in the purinergic receptor P2RX7 gene

Science: A Draft Sequence of the Neandertal Genome

"a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world"

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PNAS: Epigenetic and immune function profiles associated with posttraumatic stress disorder

n=23 cases 
77 controls
"immune system functions are significantly overrepresented among the annotations associated with genes uniquely unmethylated among those with PTSD."

Could this be a result of HPA axis dysregulation?

Posted via email from the nocx files

The case for cloud computing in genome informatics

"impending collapse of the genome informatics ecosystem"

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Sunday, May 2, 2010

BMC Medical Genetics - Characterizing the founder structure of the Old Order Amish. via @BioMedCentral.

128 founders (78 females and 50 males) accounted for over 95% of the mean relative founder contribution among living Old Order Amish descendants, according to analyses with PedHunter 2.0.

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McLuhan on the objectives of new media.

"The objectives of new media have tended, fatally, to be set in terms of the parameters and frames of the older media."

-Marshall McLuhan

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@huffingtonpost: Electronic Medical Record Shift: Signs Of Harm Emerge As Doctors Move From Paper

Machines don't make things perfect. Some of the known issues with
computers in health care are discussed, including electronic ordering.

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