http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002871 QT:”
To understand the functional impact of non-coding somatic variation, we leveraged functional data generated by the ENCODE Project Consortium. We analyzed regulatory regions derived from multiple different cell types and found that melanocyte-specific regions are among the most depleted for somatic mutation accumulation.
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Archive for the 'SciLit' Category
Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes
August 25, 2012An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People
August 20, 2012Paper with the NS/S ratio: (See Fig 2C).
http://www.sciencemag.org/content/337/6090/100.abstract
Presaging what we’ll see in exomes to come….
Mutational processes molding the genomes of 21 breast cancers
August 20, 2012Here is the link to the 21 Breast Cancer genomes:
http://www.ncbi.nlm.nih.gov/pubmed/22608084
Found hotspots of mutation….
Genome sequence data have been deposited at the European Genome-Phenome Archive (http://www.ebi.ac.uk/ega/ at the EBI) with accession number EGAD00001000138. SNP6 array data have been deposited with ArrayExpress Archive (EBI, accession number E-MTAB-1087).
SIAM: M.C. Escher: More Mathematics Than Meets the Eye
August 7, 2012http://www.siam.org/news/news.php?id=474
Void in center in original is filled in by determining spatial transform and redrawing
BioTechniques – The new molecular gastronomy, or, a gustatory tour of network analysis
August 6, 2012Useful Facts about Quality Control in Exome Sequencing (Ts/Tv)
August 5, 2012http://www.biostars.org/post/show/4751/titv-ratio-confirms-snp-discovery-is-this-a-general-rule/ QT:”
The transition transversion ratio in human is observed to be around 2.1 and this can be used as a confirmation for the filtering in a snp discovery project.
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http://genome.sph.umich.edu/wiki/SNP_Call_Set_Properties
QT:”
Proportion of dbSNPs
Most of the genetic variants in any one individual have been previously observed in other individuals. Thus, it is usually a good diagnostic to investigate what fraction of variants in an individual genome have been previously described in dbSNP.
….The dbSNP database is being constantly updated so that currently (mid-2010) we’d expect >90% of the variants in an individual genome to have been previously discovered….
Transition to Transversion Ratio
…transitions (changes from A <-> G and C <-> T) are expected to occur twice as frequently as transversions (changes from A <-> C, A <-> T, G <-> C or G <-> T). Thus, another useful diagnostic is the ratio of transitions to transversions in a particular set of SNP calls. ….
Across the entire genome the ratio of transitions to transversions is typically around 2. In protein coding regions, this ratio is typically higher, often a little above 3. The higher ratio occurs because, especially when they occur in the third base of a codon, transitions are much more likely to change the encoded amino acid. “
mutation rates in cancer cells
August 5, 2012Seem to have cancer SNV calls all over the genome.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11273.html
