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Last Week's Sequencing-Related Papers of Note: Apr 8, 2014


Risks of double-counting in deep sequencing.
Schmitt MW, Fox EJ, Salk JJ.
Proc Natl Acad Sci U S A. 2014 Mar 20. [Epub ahead of print]

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.
Mercer TR, Clark MB, Crawford J, Brunck ME, et al.
Nat Protoc. 2014 May;9(5):989-1009.

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage.
Newman AM, Bratman SV, To J, Wynne JF, et al.
Nat Med. 2014 Apr 6. [Epub ahead of print]

Multi-perspective quality control of Illumina exome sequencing data using QC3.
Guo Y1, Zhao S2, Sheng Q3, Ye F4, Li J5, Lehmann B6, Pietenpol J7, Samuels DC8, Shyr Y9.
Genomics. 2014 Apr 2. [Epub ahead of print]

Quantification of cytosolic plasmid DNA degradation using high-throughput sequencing: implications for gene delivery.
Rattan R, Bielinska AU, Banaszak Holl MM.
J Gene Med. 2014 Apr 2. [Epub ahead of print]

De novo assembly of the quorum-sensing Pandoraea sp. strain RB-44 complete genome sequence using PacBio single-molecule real-time sequencing technology.
Ee R, Lim YL, Yin WF, Chan KG.
Genome Announc. 2014 Apr 3;2(2).

Improved hybrid genome assemblies of two strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, obtained using Illumina and 454 sequencing technologies.
Ee R, Lim YL, Yin WF, Chan KG.
Genome Announc. 2014 Apr 3;2(2).

Performance evaluation of kits for bisulfite-conversion of DNA from tissues, cell lines, FFPE tissues, aspirates, lavages, effusions, plasma, serum, and urine.
Holmes EE, Jung M, Meller S, Leisse A, et al.
PLoS One. 2014 Apr 3;9(4):e93933.

The draft genome sequence of European pear (Pyrus communis L. 'Bartlett').
Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, et al.
PLoS One. 2014 Apr 3;9(4):e92644.

PRADA: Pipeline for RNA sequencing Data Analysis.
Torres-García W, Zheng S, Sivachenko A, Vegesna R, et al.
Bioinformatics. 2014 Apr 1. [Epub ahead of print]

Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm.
Cotten M, Oude Munnink B, Canuti M, Deijs M, et al.
PLoS One. 2014 Apr 2;9(4):e93269.

Genome-wide normalized score: a novel counting algorithm to detect fetal trisomy 21 in non-invasive prenatal testing.
Yeang CH, Ma GC, Hsu HW, Lin YS, et al.
Ultrasound Obstet Gynecol. 2014 Apr 3. [Epub ahead of print]

Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.
Zhong C, Zhang S.
J Comput Biol. 2014 Apr 1. [Epub ahead of print]

Leveraging biological replicates to improve analysis in ChIP-seq experiments.
Yang Y, Fear J, Hu J, Haecker I, et al.
Comput Struct Biotechnol J. 2014 Jan 31;9:e201401002.

Choosing between RT-qPCR and RNA-seq: a back-of-the-envelope estimate towards the definition of the break-even-point.
Nonis A, De Nardi B, Nonis A.
Anal Bioanal Chem. 2014 Apr 1. [Epub ahead of print]

Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing.
Hendel A, Kildebeck EJ, Fine EJ, Clark JT, et al.
Cell Rep. 2014 Mar 26. pii: S2211-1247(14)00154-5.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.