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Recent Sequencing-Related Papers of Note: Jul 8, 2014


Evaluation of the Ion Torrent HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing.
Børsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N.
Forensic Sci Int Genet. 2014 Jun 14. [Epub ahead of print]

Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.
Metzger J, Tonda R, Beltran S, Agueda L, et al.
BMC Genomics. 2014 Jul 4;15(1):562.

Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences.
Huang H, Knowles LL.
Syst Biol. 2014 Jul 4. [Epub ahead of print]

Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing.
Veres A, Gosis BS, Ding Q, Collins R, et al.
Cell Stem Cell. 2014 Jul 3;15(1):27-30.

Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs.
Smith C, Gore A, Yan W, Abalde-Atristain L, et al.
Cell Stem Cell. 2014 Jul 3;15(1):12-3.

Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones.
Suzuki K, Yu C, Qu J, Li M, et al.
Cell Stem Cell. 2014 Jul 3;15(1):31-6.

Exome sequencing from nanogram amounts of starting DNA: comparing three approaches.
Rykalina VN, Shadrin AA, Amstislavskiy VS, Rogaev EI, et al.
PLOS One. 2014 Jul 3;9(7):e101154.

Assessment of the impact of using a reference transcriptome in mapping short RNA-seq reads.
Zhao S.
PLOS One. 2014 Jul 3;9(7):e101374.

Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.
Choi JW, Liao X, Stothard P, Chung WH, et al.
PLOS One. 2014 Jul 3;9(7):e101127.

Genetic analysis of hair samples attributed to yeti, bigfoot and other anomalous primates.
Sykes BC, Mullis RA, Hagenmuller C, Melton TW, Sartori M.
Proc Biol Sci. 2014 Aug 22;281(1789).

Detecting DNA depurination with solid-state nanopores.
Marshall MM, Ruzicka JA, Taylor EW, Hall AR.
PLOS One. 2014 Jul 2;9(7):e101632.

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication.
Nossa CW, Havlak P, Yue JX, Lv J, et al.
Gigascience. 2014 May 14;3:9.

Microsatellite instability detection by next generation sequencing.
Salipante SJ, Scroggins SM, Hampel HL, Turner EH, Pritchard CC.
Clin Chem. 2014 Jun 30. [Epub ahead of print]

Pathway analysis with next-generation sequencing data.
Zhao J, Zhu Y, Boerwinkle E, Xiong M.
Eur J Hum Genet. 2014 Jul 2. [Epub ahead of print]

Characterization of ancient DNA supports long-term survival of Haloarchaea.
Sankaranarayanan K, Lowenstein TK, Timofeeff MN, Schubert BA, Lum JK.
Astrobiology. 2014 Jun 30. [Epub ahead of print]

Whole-genome sequence variation, population structure and demographic history of the Dutch population.
The Genome of the Netherlands Consortium, Francioli LC, Menelaou A, et al.
Nat Genet. 2014 Jun 29. [Epub ahead of print]

COSMOS: Python library for massively parallel workflows.
Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, et al.
Bioinformatics. 2014 Jun 30. [Epub ahead of print]

IVT-seq reveals extreme bias in RNA-sequencing.
Lahens NF, Kavakli IH, Zhang R, Hayer K, et al.
Genome Biol. 2014 Jun 30;15(6):R86.

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.