Paper 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….
Archive for the 'SciLit' Category
An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People
August 20, 2012Mutational 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.
”
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
NATURE GENETICS | Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma
August 5, 2012Widespread transcription at neuronal activity-regulated enhancers : Nature : Nature Publishing Group
July 29, 2012Findings on eRNAs
http://www.nature.com/nature/journal/v465/n7295/full/nature09033.html
SIAM: M.C. Escher: More Mathematics Than Meets the Eye
July 28, 2012A Whole-Cell Computational Model Predicts Phenotype from Genotype
July 21, 2012from JC :
http://www.cell.com/abstract/S0092-8674(12)00776-3
Jonathan R. Karr, Jayodita C. Sanghvi, Derek N. Macklin, Miriam V. Gutschow, Jared M. Jacobs, Benjamin Bolival, Nacyra Assad-Garcia, John I. Glass, Markus W. Covert
Cell – 20 July 2012 (Vol. 150, Issue 2, pp. 389-401)
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