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In Print: Last Week's Clinical Sequencing Papers of Note: Jul 3, 2012


VAT: A computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
Habegger L, Balasubramanian S, Chen DZ, Khurana E, et al.
Bioinformatics. 2012 Jun 28. [Epub ahead of print]

Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing.
Osanto S, Qin Y, Buermans HP, Berkers J, et al.
PLoS One. 2012;7(6):e38298.

Landscape of somatic retrotransposition in human cancers.
Lee E, Iskow R, Yang L, Gokcumen O, et al.
Science. 2012 Jun 28. [Epub ahead of print]

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
McPherson AW, Wu C, Wyatt A, Shah SP, et al.
Genome Res. 2012 Jun 28. [Epub ahead of print]

Exome sequencing identifies a novel, multiple sclerosis susceptibility variant in the TYK2 gene.
Dyment DA, Cader MZ, Chao MJ, Lincoln MR, et al.
Neurology. 2012 Jun 27. [Epub ahead of print]

Exome sequencing identifies novel candidate mutations in idiopathic [scoliosis].
Moldovan F, Patten SA, Fendri K, Girard S, et al.
Stud Health Technol Inform. 2012;176:453.

PurityEst: estimating purity of human tumor samples using next-generation sequencing data.
Su X, Zhang L, Zhang J, Meric-Bernstam F, Weinstein JN.
Bioinformatics. 2012 Jun 28. [Epub ahead of print]

Non-invasive chromosomal evaluation (NICE) study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18.
Norton ME, Brar H, Weiss J, Karimi A, et al.
Am J Obstet Gynecol. 2012 Jun 1. [Epub ahead of print]

Mutations in DPAGT1 cause a limb-girdle congenital myasthenic syndrome with tubular aggregates.
Belaya K, Finlayson S, Slater CR, Cossins J, et al.
Am J Hum Genet. 2012 Jun 26. [Epub ahead of print]

Identification of somatic mutations in parathyroid tumors using whole-exome sequencing.
Cromer MK, Starker LF, Choi M, Udelsman R, et al.
J Clin Endocrinol Metab. 2012 Jun 27. [Epub ahead of print]

Exome sequencing reveals riboflavin transporter mutations as a cause of motor neuron disease.
Johnson JO, Gibbs JR, Megarbane A, Urtizberea JA, et al.
Brain. 2012 Jun 26. [Epub ahead of print]

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia.
Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, et al.
PLoS Genet. 2012 Jun;8(6):e1002781.

Rare genetic variants and treatment response: sample size and analysis issues.
Witte JS.
Stat Med. 2012 Jun 27. [Epub ahead of print]

Mitochondrial DNA heteroplasmy in diabetes and normal adults: Role of acquired and inherited mutational patterns in twins.
Avital G, Buchshtav M, Zhikov I, Tuval Feder J, et al.
Hum Mol Genet. 2012 Jun 26. [Epub ahead of print]

A high-throughput next-generation sequencing-based method for detecting the mutational fingerprint of carcinogens.
Besaratinia A, Li H, Yoon JI, Zheng A, et al.
Nucleic Acids Res. 2012 Jun 26. [Epub ahead of print]

A personal perspective on returning secondary results of clinical genome sequencing.
Dimmock D.
Genome Med. 2012 Jun 26;4(6):54.

The Scan

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.

Seagull Microbiome Altered by Microplastic Exposure

The overall diversity and the composition at gut microbiome sites appear to coincide with microplastic exposure and ingestion in two wild bird species, according to a new Nature Ecology and Evolution study.

Study Traces Bladder Cancer Risk Contributors in Organ Transplant Recipients

In eLife, genome and transcriptome sequencing reveal mutation signatures, recurrent somatic mutations, and risky virus sequences in bladder cancers occurring in transplant recipients.

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.