QT:”One implication of this realization is that recent mutation may have a greater influence on disease susceptibility or protection than is conferred by variations that arose in distant ancestors.” http://www.ncbi.nlm.nih.gov/pubmed/21962505
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2768.html Replicative mechanisms for #CNV formation are error prone: CNVs associated with SNVs in 67 cases http://dx.doi.org/10.1038/ng.2768 MT @LeucineRichBio
Lupski paper
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2651.html
Network-based stratification of tumor mutations
Matan Hofree,
John P Shen,
Hannah Carter,
Andrew Gross
& Trey Ideker
Nature Methods(2013)doi:10.1038/nmeth.2651
QT:”
Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.
”
http://www.nature.com/nature/journal/v457/n7231/full/nature07744.html
This is a paper on increased rates of segmental duplications along the lineage to human and chimp.
This should have some implications for pseudogene numbers between organisms.
QT:”
We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years.
”
6,515 #exomes reveals the recent origin of most human protein-coding variants: ~75% #SNVs arose in last ~7.5K yrs
http://www.nature.com/nature/journal/v493/n7431/full/nature11690.html
The bread #wheat genome using… shotgun sequencing: ~5X human, from 3 diff. component genomes, many #pseudogenes
http://www.nature.com/nature/journal/v491/n7426/full/nature11650.html
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003709#pgen-1003709-g006
This paper discusses gene intolerance score — very similar to depletion of common polymorphisms. They don’t analyze non-coding regions — this is using exome data only. Blue for tolerant and red for intolerant (see Figure 1) .
http://www.ebi.ac.uk/ena/WebFeat/qualifiers/pseudogene.html
http://www.insdc.org/documents/pseudogene-qualifier-vocabulary see here as well
https://www.vectorbase.org/info/website/glossary.html
vs
http://gencodegenes.wordpress.com/toolbox
Also, on unitary pseudogene term “origin” here is the earliest use of the term findable :
http://www.talkorigins.org/faqs/molgen/
Unitary & Processed as in Gencode
Unprocessed = Duplicated
Allelic = Polymorphic
http://www.ebi.ac.uk/ena/WebFeat/qualifiers/pseudogene.html
http://www.insdc.org/documents/pseudogene-qualifier-vocabulary see here as well
https://www.vectorbase.org/info/website/glossary.html
Unitary & Processed as in Gencode
Unprocessed = Duplicated
Allelic = Polymorphic
500 whole-genome cancer sequences
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12477.html