LETTER FROM SHENZHEN
THE GENE FACTORY
A Chinese firm’s bid to crack hunger, illness, evolution—and the genetics of human intelligence.
BY MICHAEL SPECTER
JANUARY 6, 2014
http://www.newyorker.com/reporting/2014/01/06/140106fa_fact_specter
.@andrewhessel Gene Factory: Interesting food for thought on #BGI’s cognitive #genomics research & $GNOM acquisition
http://www.newyorker.com/reporting/2014/01/06/140106fa_fact_specter
A paper on C. elegans that’s very informative:
http://www.nature.com/ng/journal/v44/n3/full/ng.1050.html
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.
Young Investigator for Ekta Khurana
http://www.genomeweb.com/genomeweb-feature-eighth-annual-young-investigators
Long-span PET mapping reveals characteristic patterns of #SVs in… cancer [v norm] genomes, but no MEIs or small events
http://genome.cshlp.org/content/early/2011/04/05/gr.113555.110.abstract
The described study used long paired-end-tags (PET) to analyze and compare SVs in cancer and normal genomes. It determined the prevalence of different types of SVs in normal and cancer sample. Overall, the results are interesting and convincing on a qualitative level; however, for the reasons outlined below, more precise and quantitative delineation of the observed effects is highly desirable.
1) Small sample size of normal genomes (only 2 normal genomes)
2) Validation rate was low (< 77%) for everything except deletions, and for singletons it was even lower. .
3) Long PET is not good for finding smaller events (few kbps). Thus, this analysis missed smaller scale SVs and cancer rearrangements.
4) While there is a discussion about breakpoints and associated repeats, it is not very informative as breakpoint locations were not determined to basepair resolution.
5) No MEI were considered — particularly, no cancer MEI were considered in the analysis, while recently it was found that somatic retrotransposition occurs in cancer (Lee et al., PMID: 22745252)..
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes –
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.
Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.
Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions
L Ward & M Kellis
http://www.sciencemag.org/content/337/6102/1675.abs
In general we know that conservation across species and within humans are correlated. In this paper the authors focus on emphasize the exceptions to this trend. They show that although only ~5% of the human genome is conserved across mammals, regulatory regions in an additional 4% of the genomes are conserved amongst humans. They also show that some elements are conserved across mammals but lack functional activity from ENCODE data and also do not show purifying selection amongst humans. The authors pinpoint regulatory regions near color vision and nerve-growth genes for that show human-specific constraint. This has been criticized in various publications since there are other genes that are higher up in the authors’ list but harder to explain for lineage-specific constraint.
Mutational landscape and significance across 12 major #cancer types: Common genes mutated in different cancers
http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html
http://www.sciencedaily.com/releases/2013/10/131016132143.htm
Mutational landscape and significance across 12 major cancer types http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html
http://nar.oxfordjournals.org/content/40/D1/D930.long
HaploReg explores functional annotations, such as chromatin states in varied cell types, sequence conservation, regulatory motif
alterations and eQTLs, of linked SNPs or indels within LD block of queried SNPs. The output provides a the guide to develop hypotheses of functional impact of non-coding variants, especially GWAS SNPs. HaploReg is currently limited to known variants (e.g. 1000 Genome variants and dbSNPs) and is unable to deal with private variants.
It look as though the data are now ready for download
http://datasets.pacb.com/2013/Human10x/READS/index.html along with a brief description of the data
http://blog.pacificbiosciences.com/2013/10/data-release-long-read-shotgun.html
BioTechniques – The Myth of the Single Genome
http://www.biotechniques.com/news/The-Myth-of-the-Single-Genome/biotechniques-347272.html
The Myth of the Single #Genome: fetal Y chr left in women + smaller microchimerism in specific tissues
http://www.biotechniques.com/news/The-Myth-of-the-Single-Genome/biotechniques-347272.html MT @xberthet
linkstream2 microblog 