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Papers of Note: Aug 3, 2010


Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.
Wu GD, Lewis JD, Hoffmann C, Chen YY, et al.
BMC Microbiol. 2010 Jul 30;10(1):206.

Unlocking short read sequencing for metagenomics.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, et al.
PLoS One. 2010 Jul 28;5(7):e11840.

Mitochondrial DNA mutation in margins and tumors of recurrent HNSCC patients.
Dasgupta S, Koch R, Westra WH, Califano JA, et al.
Cancer Prev Res (Phila Pa). 2010 Jul 26. [Epub ahead of print]

Metagenomic sequencing for virus identification in a public health setting.
Svraka S, Rosario K, Duizer E, van der Avoort H, et al.
J Gen Virol. 2010 Jul 21. [Epub ahead of print]

Genome-scale metabolic model integrated with RNA-seq data to identify metabolic states of Clostridium thermocellum.
Gowen CM, Fong SS.
Biotechnol J. 2010 Jul;5(7):759-67.

Non PCR-amplified transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing.
Ler oux S, Feve K, Vignoles F, Bouchez O, et al.
BMC Res Notes. 2010 Jul 28;3(1):214.

Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing.
Paruzynski A, Arens A, Gabriel R, Bartholomae CC, et al.
Nat Protoc. 2010 Aug;5(8):1379-95.

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism.
Kapranov P, Ozsolak F, Kim SW, Foissac S, et al.
Nature. 2010 Jul 29;466(7306):642-6.

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.
Srivastava S, Chen L.
Nucleic Acids Res. 2010 Jul 29. [Epub ahead of print]

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.
Zagordi O, Klein R, Däumer M, Beerenwinkel N.
Nucleic Acids Res. 2010 Jul 29. [Epub ahead of print]

Reliable resequencing of the human dystrophin locus by universal long PCR and massive pyrosequencing.
Bonnal RJ, Severgnini M, Castaldi A, Bordoni R, et al.
Anal Biochem. 2010 Jul 26. [Epub ahead of print]

Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P.
Genome Biol. 2010 Jul 26;11(7):402.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.