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In Print: Last Week's Clinical Sequencing Papers of Note: Feb 29, 2012


Comparative genomics of 2009 seasonal plague (Yersinia pestis) in New Mexico.
Gibbons HS, Krepps MD, Ouellette G, Karavis M, et al.
PLoS One. 2012;7(2):e31604.

RNA-seq reveals novel transcriptome of genes and their isoforms in human pulmonary microvascular endothelial cells treated with thrombin.
Zhang LQ, Cheranova D, Gibson M, Ding S, et al.
PLoS One. 2012;7(2):e31229.

Transcriptomic landscape of breast cancers through mRNA sequencing.
Eswaran J, Cyanam D, Mudvari P, Reddy SD, et al.
Sci Rep. 2012;2:264.

Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing.
Lysholm F, Wetterbom A, Lindau C, Darban H, et al.
PLoS One. 2012;7(2):e30875.

Virologic failures on initial boosted -PI regimen infrequently possess low-level variants with major PI resistance mutations by ultra-deep sequencing.
Lataillade M, Chiarella J, Yang R, Degrosky M, et al.
PLoS One. 2012;7(2):e30118.

Expanding the molecular basis and phenotypic spectrum of X-linked Joubert syndrome associated with OFD1 mutations.
Field M, Scheffer IE, Gill D, Wilson M, et al.
Journal of Human Genetics. 22 Feb. 2012 [Epub ahead of print]

Identification of a novel twinkle mutation in a family with infantile onset spinocerebellar ataxia by whole exome sequencing.
Dündar H, Ozgül RK, Yalnızoğlu D, Erdem S, et al.
Pediatr Neurol. 2012 Mar;46(3):172-7.

Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of 186 hemostatic/pro-inflammatory genes.
Lotta LA, Wang M, Yu J, Martinelli I, et al.
BMC Med Genomics. 2012 Feb 21;5(1):7.

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings.
Ren S, Peng Z, Mao JH, Yu Y, et al.
Cell Res. 2012 Feb 21. [Epub ahead of print]

Multiple mutations in heterogeneous miltefosine-resistant Leishmania major population as determined by whole genome sequencing.
Coelho AC, Boisvert S, Mukherjee A, Leprohon P, et al.
PLoS Negl Trop Dis. 2012 Feb;6(2):e1512.

Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic Mendelian diseases by exome sequencing.
Zhi D, Chen R.
PLoS One. 2012;7(2):e31358.

Virus identification in unknown tropical febrile illness cases using deep sequencing.
Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, et al.
PLoS Negl Trop Dis. 2012 Feb;6(2):e1485.

Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region.
Weiner B, Gomez J, Victor TC, Warren RM, et al.
PLoS One. 2012;7(2):e26038.

A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur DG, Balasubramanian S, Frankish A, Huang N, et al.
Science. 2012 Feb 17;335(6070):823-8.

International normative perspectives on the return of individual research results and incidental findings in genomic biobanks.
Zawati MH, Knoppers BM.
Genet Med. 2012 Feb 16. [Epub ahead of print]

Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project.
Biesecker LG.
Genet Med. 2012 Feb 16. [Epub ahead of print]

Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing.
Lohr JG, Stojanov P, Lawrence MS, Auclair D, et al.
Proc Natl Acad Sci U S A. 2012 Feb 17. [Epub ahead of print]

Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis.
Herdewyn S, Zhao H, Moisse M, Race V, et al.
Hum Mol Genet. 2012 Feb 17. [Epub ahead of print]

Mutations in LOXHD1, a recessive-deafness locus, cause dominant late-onset Fuchs corneal dystrophy.
Riazuddin SA, Parker DS, McGlumphy EJ, Oh EC, et al.
Am J Hum Genet. 2012 Feb 15. [Epub ahead of print]

The Scan

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.

DNA Biobank Developed for French Kidney Donors, Recipients

The KiT-GENIE biobank described in the European Journal of Human Genetics contains DNA samples, genotyping profiles, immune patterns, and clinical features for thousands of kidney donors or transplant recipients in Nantes, France.

Cardiometabolic Disease May Have Distinct Associations With Microbial Metabolites in Blood, Gut

By analyzing gut microbes in combination with related metabolites in feces and blood, researchers in Nature Communications found distinct cardiometabolic disease relationships at each site.

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.