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In Print: Last Week's Clinical Sequencing Papers of Note: Jan 18, 2012


A restricted spectrum of mutations in the SMAD4 tumor-suppressor gene underlies Myhre syndrome.
Caputo V, Cianetti L, Niceta M, Carta C, et al.
Hum Genet. 2012 Jan 13;90(1):161-9.

Mutations in SLC33A1 cause a lethal autosomal-recessive disorder with congenital cataracts, hearing loss, and low serum copper and ceruloplasmin.
Huppke P, Brendel C, Kalscheuer V, Korenke GC, et al.
Am J Hum Genet. 2012 Jan 13;90(1):61-8.

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.
Li MX, Gui HS, Kwan JS, Bao SY, Sham PC.
Nucleic Acids Res. 2012 Jan 12. [Epub ahead of print]

Next-generation sequencing for simultaneous determination of HPV load, subtype, and associated genomic copy number changes in tumors.
Conway C, Chalkley R, High A, Maclennan K, et al.
J Mol Diagn. 2012 Jan 9. [Epub ahead of print]

An integrative variant analysis suite for whole exome next-generation sequencing data.
Challis D, Yu J, Evani US, Jackson AR, et al.
BMC Bioinformatics. 2012 Jan 12;13(1):8. [Epub ahead of print]

A mild form of SLC29A3 disorder: a frameshift deletion leads to the paradoxical translation of an otherwise noncoding mRNA splice variant.
Bolze A, Abhyankar A, Grant AV, Patel B, et al.
PLoS One. 2012;7(1):e29708. Epub 2012 Jan 4.

Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus.
Peleg AY, Miyakis S, Ward DV, Earl AM, et al.
PLoS One. 2012;7(1):e28316. Epub 2012 Jan 6.

Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing.
Armenia D, Vandenbroucke I, Fabeni L, Van Marck H, et al.
J Infect Dis. 2012 Jan 11. [Epub ahead of print]

Exploiting the mutanome for tumor vaccination.
Castle JC, Kreiter S, Diekmann J, Lower M, et al.
Cancer Res. 2012 Jan 11. [Epub ahead of print]

The genetic basis of early T -cell precursor acute lymphoblastic leukaemia.
Zhang J, Ding L, Holmfeldt L, Wu G, et al.
Nature. 2012 Jan 11;481(7380):157-63.

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.
Ding L, Ley TJ, Larson DE, Miller CA, et al.
Nature. 2012 Jan 11. [Epub ahead of print]

A novel retinoblastoma therapy from genomic and epigenetic analyses.
Zhang J, Benavente CA, McEvoy J, Flores-Otero J, et al.
Nature. 2012 Jan 11. [Epub ahead of print]
(see our coverage of this paper in this issue)

Cold urticaria, immunodeficiency, and autoimmunity related to PLCG2 deletions.
Ombrello MJ, Remmers EF, Sun G, Freeman AF, et al.
N Engl J Med. 2012 Jan 11. [Epub ahead of print]

Mutations in the gene DNAJC5 cause autosomal dominant Kufs disease in a proportion of cases: study of the Parry family and 8 other families.
Velinov M, Dolzhanskaya N, Gonzalez M, Powell E, et al.
PLoS One. 2012;7(1):e29729.

Mutations in the ER-shaping protein reticulon 2 cause the axon-degenerative disorder hereditary spastic paraplegia type 12.
Montenegro G, Rebelo AP, Connell J, Allison R, et al.
J Clin Invest. 2012 Jan 9. [Epub ahead of print]

Exome sequencing reveals a novel Fanconi group defined by XRCC2 mutation.
Shamseldin HE, Elfaki M, Alkuraya FS.
J Med Genet. 2012 Jan 9. [Epub ahead of print]

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.