Archive for the 'SciLit' Category

Human chimp increase in segmental duplications

September 1, 2013

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.

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

September 1, 2013

no website, github + readthedocs distribution
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants : Nature : Nature Publishing Group

August 31, 2013

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

Analysis of the bread wheat genome using whole-genome shotgun sequencing : Nature : Nature Publishing Group

August 31, 2013

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

Gene intolerance scores in a Plos Gen paper

August 26, 2013

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) .

Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.

August 21, 2013

Y sequencing by Page et al.

http://www.ncbi.nlm.nih.gov/pubmed/22367542

HeLa Cells Contaminating Other Cell Lines

August 21, 2013

Arch Pathol Lab Med. 2009 Sep;133(9):1463-7. doi: 10.1043/1543-2165-133.9.1463.

Henrietta Lacks, HeLa cells, and cell culture contamination.

Lucey BP, Nelson-Rees WA, Hutchins GM.

http://www.ncbi.nlm.nih.gov/pubmed/19722756

latest Nature paper with cancer data

August 21, 2013

500 whole-genome cancer sequences

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12477.html

Evolution of the Caenorhabditis elegans Genome

August 10, 2013

this should partially explain the high insertion rate in worm: http://mbe.oxfordjournals.org/content/26/6/1199.full

QT:”
Of the new mutations observed in MA lines, more than half were short indel mutations, with fewer deletions than insertions (Denver, Morris, Lynch, and Thomas 2004). This finding on indels contrasts with previous work with C. elegans pseudogenes in which deletions are more common than insertions (Robertson 2000; Witherspoon and Robertson 2003) but is consistent with findings in C. elegansmicrosatellite mutation data (Frisse 1999; Denver, Morris, Kewalramani, et al. 2004; Seyfert et al. 2008).

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data : Nature Methods : Nature Publishing Group

August 9, 2013

http://www.nature.com/nmeth/journal/v10/n8/full/nmeth.2557.html