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Last Week's Sequencing-Related Papers of Note: Apr 29, 2014


CANOES: detecting rare copy number variants from whole exome sequencing data.
Backenroth D, Homsy J, Murillo LR, Glessner J, et al.
Nucleic Acids Res. 2014 Apr 25. [Epub ahead of print]

Sequencing and annotated analysis of full genome of Holstein breed bull.
Kõks S, Reimann E, Lilleoja R, Lättekivi F, et al.
Mamm Genome. 2014 Apr 26. [Epub ahead of print]

Nucleosome acetylation sequencing to study the establishment of chromatin acetylation.
Mittal C, Blacketer MJ, Shogren-Knaak MA.
Anal Biochem. 2014 Apr 24. [Epub ahead of print]

Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland.
Wang SR, Agarwala V, Flannick J, Chiang CW, et al.
Am J Hum Genet. 2014 Apr 23. [Epub ahead of print]

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs.
van de Wiel MA, Neerincx M, Buffart TE, Sie D, Verheul HM.
BMC Bioinformatics. 2014 Apr 26;15(1):116.

Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence.
Iida N, Yamao F, Nakamura Y, Iida T.
Genes Cells. 2014 Apr 28. [Epub ahead of print]

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis.
Holstege H, Pfeiffer W, Sie D, Hulsman M, et al.
Genome Res. 2014 Apr 23. [Epub ahead of print]

The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure.
Kagale S, Koh C, Nixon J, Bollina V, et al.
Nat Commun. 2014 Apr 23;5:3706.

The genome sequence of a widespread apex predator, the Golden Eagle (Aquila chrysaetos).
Doyle JM, Katzner TE, Bloom PH, Ji Y, et al.
PLOS One. 2014 Apr 23;9(4):e95599.

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators.
Bellott DW, Hughes JF, Skaletsky H, Brown LG, et al.
Nature. 2014 Apr 24;508(7497):494-9.

Origins and functional evolution of Y chromosomes across mammals.
Cortez D, Marin R, Toledo-Flores D, Froidevaux L, et al.
Nature. 2014 Apr 24;508(7497):488-93.

Interpreting the conductance blockades of DNA translocations through solid-state nanopores.
Carlsen AT, Zahid OK, Ruzicka J, Taylor EW, Hall AR.
ACS Nano. 2014 Apr 23. [Epub ahead of print]

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, et al.
Genome Res. 2014 Apr 22. [Epub ahead of print]

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.
Berthelot C, Brunet F, Chalopin D, Juanchich A, et al.
Nat Commun. 2014 Apr 22;5:3657.

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.
Booth MJ, Marsico G, Bachman M, Beraldi D, Balasubramanian S.
Nat Chem. 2014 May;6(5):435-40.
(See our coverage of this paper here.)

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair.
Dal GM, Ergüner B, Sağıroğlu MS, Yüksel B, et al.
J Med Genet. 2014 Apr 24. [Epub ahead of print]

Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
International Glossina Genome Initiative
Science. 2014 Apr 25;344(6182):380-6.

Patterns of coding variation in the complete exomes of three Neandertals.
Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, et al.
Proc Natl Acad Sci U S A. 2014 Apr 21. [Epub ahead of print]

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.
Li J, Doyle MA, Saeed I, Wong SQ, et al.
PLOS One. 2014 Apr 21;9(4):e95217.

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
Patro R, Mount SM, Kingsford C.
Nat Biotechnol. 2014 Apr 20. [Epub ahead of print]

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.
Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, et al.
Nat Biotechnol. 2014 Apr 20. [Epub ahead of print]

Indexing a sequence for mapping reads with a single mismatch.
Crochemore M, Langiu A, Rahman MS.
Philos Trans A Math Phys Eng Sci. 2014 Apr 21;372(2016):20130167.

ExonSampler: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.
Cosart T, Beja-Pereira A, Luikart G.
Mol Ecol Resour. 2014 Apr 22. [Epub ahead of print]

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.