Posts Tagged ‘wc’

Information-theoretic evaluation of predicted ontological annotations

Saturday, July 12th, 2014

PLOS ONE: Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

Saturday, April 19th, 2014

Burst of Young Retrogenes…in Mammals. Discusses much
retro-transposition ~40 Mya, relevant to proc. #pseudogenes

Also, ref #11 provides more detail on this.

Sex Determination Video

Saturday, April 12th, 2014

Finding the lost treasures in exome sequencing data

Sunday, April 6th, 2014

Finding lost treasures in #exome sequencing data. Mining off-target, often noncoding, reads from 1000G, TCGA, ESP, &c

Kruglyak paper on C. elegans

Thursday, January 2nd, 2014

A paper on C. elegans that’s very informative:
Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

Most notable of their findings is evidence of recent selective sweeps on chromosomes I, IV, V and (sort of) X. These sweeps have the potential to fix pseudogenes that might have been present at the time.

Whole-genome reconstruction and mutational signatures in gastric cancer – Genome Biol.

Saturday, October 12th, 2013

Genome Biol. 2012 Dec 13;13(12):R115.

Whole-genome reconstruction and mutational signatures in gastric cancer. Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Tean Teh B, Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y.

Some thoughts, much from WC:

Looks like the data is freely available via GEO ID : GSE30833

The article by Nagarajan et al. highlights the authors efforts to utilize de novo genome assembly of gastric cancer genomes to detect not only single nucleotide variants (SNV’s) and short
insertions/deletions (indels), but also larger scale genomic structural variation (SV) that could be signatures of cancer genomes. It is to be applauded that this is a whole genome analysis.

The authors present several interesting findings such as enrichment for C->A and T->A mutations in both cancer genomes, enrichment for C->A and C->T mutations in the H. pylori infected cancer genome (evidence of cytosine specific transcription mediated DNA repair due to deamination), and amplification and deletion of regions on chromosome 12 in the non-H. pylori infected genome.

Although copy number variants (CNV) could potentially be detected by exome sequencing alone, whole genome sequence enables the precise localization of such events, as well as the detection of variation in non-coding regions.

Their methodology relies on combining high-throughput short-read sequencing with longer DNA-PET (paired end tags) in order to construct higher confidence de novo assemblies with longer contiguous regions.

Human chimp increase in segmental duplications

Sunday, September 1st, 2013

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.

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.