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In Print: Last Week's Clinical Sequencing Papers of Note: Dec 7, 2011


A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis.
Marini NJ, Hoffmann TJ, Lammer EJ, Hardin J, et al.
PLoS One. 2011;6(11):e28408.

A systematic analysis on DNA methylation and the expression of both mRNA and microRNA in bladder cancer.
Zhu J, Jiang Z, Gao F, Hu X, et al.
PLoS One. 2011;6(11):e28223.

Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma.
Guo G, Gui Y, Gao S, Tang A, et al.
Nat Genet. 2011 Dec 4. [Epub ahead of print]

Sequencing and annotated analysis of an Estonian human genome.
Lilleoja R, Sarapik A, Reimann E, Reemann P, et al.
Gene. 2011 Nov 27. [Epub ahead of print]

Finding disease variants in Mendelian disorders by using sequence data: methods and applications.
Ionita-Laza I, Makarov V, Yoon S, Raby B, et al.
Am J Hum Genet. 2011 Nov 30. [Epub ahead of print]

Accurate sampling and deep sequencing of the HIV-1 protease gene using a primer ID.
Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R.
Proc Natl Acad Sci U S A. 2011 Nov 30. [Epub ahead of print]

Genomic anatomy of Escherichia coli O157:H7 outbreaks.
Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA.
Proc Natl Acad Sci U S A. 2011 Nov 30. [Epub ahead of print]

Excess of rare variants in non-GWAS candidate genes in patients with hypertriglyceridemia.
Johansen CT, Wang J, McIntyre AD, Martins RA, et al.
Circ Cardiovasc Genet. 2011 Dec 1. [Epub ahead of print]

Comprehensive sequence analysis of nine Usher syndrome genes in the UK National Collaborative Usher Study.
Le Quesne Stabej P, Saihan Z, Rangesh N, Steele-Stallard HB, et al.
J Med Genet. 2011 Dec 1. [Epub ahead of print]

Personalized oncology through integrative high-throughput sequencing: a pilot study.
Roychowdhury S, Iyer MK, Robinson DR, Lonigro RJ, et al.
Sci Transl Med. 2011 Nov 30;3(111):111ra121.

Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies.
Pagnamenta AT, Lise S, Harrison V, Stewart H, et al.
J Hum Genet. 2011 Dec 1. [Epub ahead of print]

Detection of somatic copy number alterations in cancer using targeted exome capture sequencing.
Lonigro RJ, Grasso CS, Robinson DR, Jing X, et al.
Neoplasia. 2011 Nov;13(11):1019-25.

Targeted genomic sequencing identifies PRRT2 mutations as a cause of paroxysmal kinesigenic choreoathetosis.
Li J, Zhu X, Wang X, Sun W, et al.
J Med Genet. 2011 Nov 30. [Epub ahead of print]

Distinct p53 genomic binding patterns in normal and cancer-derived human cells.
Botcheva K, McCorkle SR, McCombie WR, Dunn JJ, Anderson CW.
Cell Cycle. 2011 Dec 15;10(24).

Specific capture and whole-genome sequencing of viruses from clinical samples.
Depledge DP, Palser AL, Watson SJ, Lai IY, et al.
PLoS One. 2011;6(11):e27805.

On the analysis of sequence data: testing for disease susceptibility loci using patterns of linkage disequilibrium.
Lipman PJ, Yip WK, Alchawa T, Ludwig KU, Mangold E, Lange C.
Genet Epidemiol. 2011 Dec;35(8):880-6.

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.