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Papers of Note: Apr 6, 2010


Sequencing-Related Papers of Note, March 2010

Direct PCR amplification and sequencing of specimens' DNA from preservative ethanol.
Shokralla S, Singer G, Hajibabaei M.
Biotechniques. 2010 Mar;48(3):233-4.

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing.
Fontanillas P, Landry CR, Wittkopp PJ, Russ C, Gruber JD, Nusbaum C, Hartl DL.
Mol Ecol. 2010 Mar;19 Suppl 1:212-27.

The microRNA profile of prostate carcinoma obtained by deep sequencing.
Szczyrba J, Löprich E, Wach S, Jung V, Unteregger G, Barth S, Grobholz R, Wieland W, et al.
Mol Cancer Res. 2010 Mar 30. [Epub ahead of print]

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis.
Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, et al.
Nature. 2010 Mar 28. [Epub ahead of print]

Accurate prediction of genetic values for complex traits by whole genome resequencing.
Meuwissen TH, Goddard ME.
Genetics. 2010 Mar 22. [Epub ahead of print]

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process.
Leproust EM, Peck BJ, Spirin K, McCuen HB, Moore B, Namsaraev E, Caruthers MH.
Nucleic Acids Res. 2010 Mar 22. [Epub ahead of print]

Identifying single nucleotides by tunnelling current.
Tsutsui M, Taniguchi M, Yokota K, Kawai T.
Nat Nanotechnol. 2010 Mar 21. [Epub ahead of print]

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.
Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, Chen L, Tian W, et al.
Genome Res. 2010 Mar 19. [Epub ahead of print]

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Characterization of the melanoma miRNAome by deep sequencing.
Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, Whiteman DC, Parsons PG, Schmidt C, et al.
PLoS One. 2010 Mar 12;5(3):e9685.

High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak.
Lewis T, Loman NJ, Bingle L, Jumaa P, Weinstock GM, Mortiboy D, Pallen MJ.
J Hosp Infect. 2010 Mar 16. [Epub ahead of print]

Global and unbiased detection of splice junctions from RNA-seq data.
Ameur A, Wetterbom A, Feuk L, Gyllensten U.
Genome Biol. 2010 Mar 17;11(3):R34. [Epub ahead of print]

Unraveling single-stranded DNA in a solid-state nanopore.
Kowalczyk SW, Tuijtel MW, Donkers SP, Dekker C.
Nano Lett. 2010 Mar 17. [Epub ahead of print]

Calling SNPs without a reference sequence.
Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W.
BMC Bioinformatics. 2010 Mar 15;11(1):130. [Epub ahead of print]

Repeat subtraction-mediated sequence capture from a complex genome.
Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, Wu W, Swanson-Wagner R, D'Ascenzo M, et al.
Plant J. 2010 Mar 4. [Epub ahead of print]

Transcriptome genetics using second generation sequencing in a Caucasian population.
Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET.
Nature. 2010 Apr 1;464(7289):773-7.

Whole-genome resequencing reveals loci under selection during chicken domestication.
Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, Jiang L, Ingman M, et al.
Nature. 2010 Mar 25;464(7288):587-91.

DNA-functionalized solid state nanopore for biosensing.
Mussi V, Fanzio P, Repetto L, Firpo G, Scaruffi P, Stigliani S, Tonini GP, Valbusa U.
Nanotechnology. 2010 Apr 9;21(14):145102.

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Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy.
Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, et al.
N Engl J Med. 2010 Apr 1;362(13):1181-91.

Analysis of genetic inheritance in a family quartet by whole-genome sequencing.
Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, et al.
Science. 2010 Mar 10. [Epub ahead of print]

Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls.
Beck J, Urnovitz HB, Mitchell WM, Schütz E.
Mol Cancer Res. 2010 Mar;8(3):335-42.

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, et al.
Bioinformatics. 2010 Mar 5. [Epub ahead of print]

Short template amplicon and multiplex megaprimer-enabled relay (STAMMER) sequencing, a simultaneous approach to higher throughput sequence-based typing of polymorphic genes.
Roberts CH, Mayor NP, Madrigal JA, Marsh SG.
Immunogenetics. 2010 Apr;62(4):253-60.

A human gut microbial gene catalogue established by metagenomic sequencing.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, et al.
Nature. 2010 Mar 4;464(7285):59-65.

SeqSharp. A general approach for improving cycle-sequencing that facilitates a robust one-step combined amplification and sequencing method.
Sengupta DJ, Cookson BT.
J Mol Diagn. 2010 Mar 4. [Epub ahead of print]

Heteroplasmic mitochondrial DNA mutations in normal and tumour cells.
He Y, Wu J, Dressman DC, Iacobuzio-Donahue C, Markowitz SD, Velculescu VE, Diaz LA Jr, et al.
Nature. 2010 Mar 25;464(7288):610-4.

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Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing.
Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, et al.
Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254-9.

Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing.
Birzele F, Schaub J, Rust W, Clemens C, Baum P, Kaufmann H, Weith A, Schulz TW, Hildebrandt T.
Nucleic Acids Res. 2010 Mar 1. [Epub ahead of print]

Single molecule epigenetic analysis in a nanofluidic channel.
Cipriany BR, Zhao R, Murphy PJ, Levy SL, Tan CP, Craighead HG, Soloway PD.
Anal Chem. 2010 Mar 15;82(6):2480-7.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.