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Last Week's Sequencing-Related Papers of Note: Oct 4, 2011


Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation Titanium sequencing platform.
Tamaki H, Wright CL, Li X, Lin Q, et al.
PLoS One. 2011;6(9):e25263.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Renfree MB, Papenfuss AT, Deakin JE, et al.
Genome Biol. 2011 Aug 29;12(8):R81.

True single-molecule DNA sequencing of a pleistocene horse bone.
Orlando L, Ginolhac A, Raghavan M, et al.
Genome Res. 2011 Oct;21(10):1705-19.
(see our coverage of this paper, IS 8/23/2011)

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.
Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X.
Genome Res. 2011 Sep 29. [Epub ahead of print]

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.
Adli M, Bernstein BE.
Nat Protoc. 2011 Sep 29;6(10):1656-68.

A comparative analysis of exome capture.
Parla JS, Iossifov I, Grabill I, et al.
Genome Biol. 2011 Sep 29;12(9):R97.

Whole-genome sequencing data offer insights into human demography.
Pritchard JK.
Nat Genet. 2011 Sep 28;43(10):923-5.

Comprehensive comparison of three commercial human whole-exome capture platforms.
Asan NF, Xu Y, Jiang H, et al.
Genome Biol. 2011 Sep 28;12(9):R95.

Comparison of solution-based exome capture methods for next generation sequencing.
Sulonen AM, Ellonen P, Almusa H, et al.
Genome Biol. 2011 Sep 28;12(9):R94.

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Digital gene expression for non-model organisms.
Hong LZ, Li J, Schmidt-Küntzel A, Warren WC, Barsh GS.
Genome Res. 2011 Sep 29. [Epub ahead of print]

IsoLasso: A LASSO regression approach to RNA-seq based transcriptome assembly.
Li W, Feng J, Jiang T.
J Comput Biol. 2011 Sep 27. [Epub ahead of print]

Rapid genotyping of soybean cultivars using high throughput sequencing.
Varala K, Swaminathan K, Li Y, Hudson ME.
PLoS One. 2011;6(9):e24811.

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
Ranwez V, Harispe S, Delsuc F, Douzery EJ.
PLoS One. 2011;6(9):e22594.

Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.
Marine R, Polson SW, Ravel J, et al.
Appl Environ Microbiol. 2011 Sep 23. [Epub ahead of print]

Performance comparison of exome DNA sequencing technologies.
Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M.
Nat Biotechnol. 2011 Sep 25. [Epub ahead of print]
(see our coverage of this paper in last week's issue here)

A strand-specific library preparation protocol for RNA sequencing.
Borodina T, Adjaye J, Sultan M.
Methods Enzymol. 2011;500:79-98.

Local and global factors affecting RNA sequencing analysis.
Sendler E, Johnson GD, Krawetz SA.
Anal Biochem. 2011 Aug 16. [Epub ahead of print]

Base-calling for next-generation sequencing platforms.
Ledergerber C, Dessimoz C.
Brief Bioinform. 2011 Sep;12(5):489-97.

The Scan

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.

US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.