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In Print: Last Week's Clinical Sequencing Papers of Note: Jun 27, 2012

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Molecular effects of doxycycline treatment on pterygium as revealed by massive transcriptome sequencing.
Larráyoz IM, de Luis A, Rúa O, Velilla S, et al.
PLoS One. 2012;7(6):e39359.


Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing.
Foulongne V, Sauvage V, Hebert C, Dereure O, et al.
PLoS One. 2012;7(6):e38499.


Mitochondrial mutations and polymorphisms in psychiatric disorders.
Sequeira A, Martin MV, Rollins B, Moon EA, et al.
Front Genet. 2012;3:103.


Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.
Manske M, Miotto O, Campino S, Auburn S, et al.
Nature. 2012 Jun 13. [Epub ahead of print]


The mutational landscape of lethal castration-resistant prostate cancer.
Grasso CS, Wu YM, Robinson DR, Cao X, et al.
Nature. 2012 May 20. [Epub ahead of print]


Novel mutations target distinct subgroups of medulloblastoma.
Robinson G, Parker M, Kranenburg TA, Lu C, et al.
Nature. 2012 Jun 20. [Epub ahead of print]


Sequence analysis of mutations and translocations across breast cancer subtypes.
Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, et al.
Nature. 2012 Jun 20;486(7403):405-9.


Whole-genome analysis informs breast cancer response to aromatase inhibition.
Ellis MJ, Ding L, Shen D, Luo J, et al.
Nature. 2012 Jun 10;486(7403):353-60. (see our coverage of this paper here)


Exome sequencing is an efficient tool for genetic screening of Charcot-Marie-Tooth disease.
Choi BO, Koo SK, Park MH, Rhee H, et al.
Hum Mutat. 2012 Jun 21. [Epub ahead of print]


Complete genome sequencing and evolutionary analysis of dengue virus serotype 1 isolates from an outbreak in Kerala, South India.
Anoop M, Mathew AJ, Jayakumar B, Issac A, et al.
Virus Genes. 2012 May 22. [Epub ahead of print]


Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations.
Chatterjee R, Ramos E, Hoffman M, Vanwinkle J, et al.
Hum Genet. 2012 Jun 23. [Epub ahead of print]


De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes.
Rivière JB, Mirzaa GM, O'Roak BJ, Beddaoui M, et al.
Nat Genet. 2012 Jun 24. [Epub ahead of print]


De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly.
Lee JH, Huynh M, Silhavy JL, Kim S, et al.
Nat Genet. 2012 Jun 24. [Epub ahead of print]


Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA.
Lindhurst MJ, Parker VE, Payne F, Sapp JC, et al.
Nat Genet. 2012 Jun 24. [Epub ahead of print]


Expressed pseudogenes in the transcriptional landscape of human cancers.
Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, et al.
Cell. 2012 Jun 22;149(7):1622-34.


Diagnosis of Fanconi anemia: mutation analysis by next-generation sequencing.
Ameziane N, Sie D, Dentro S, Ariyurek Y, et al.
Anemia. 2012;2012:132856.


Serum microRNA signatures identified by Solexa sequencing predict sepsis patients' mortality: a prospective observational study.
Wang H, Zhang P, Chen W, Feng D, et al.
PLoS One. 2012;7(6):e38885.


Sequence analysis of the human virome in febrile and afebrile children.
Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA .
PLoS One. 2012;7(6):e27735.


Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.
Li E, Hamm CM, Gulati AS, Sartor RB, et al.
PLoS One. 2012;7(6):e26284.


Field monitoring of avian influenza viruses: whole genome sequencing and tracking of neuraminidase evolution using 454 pyrosequencing.
Croville G, Soubies SM, Barbieri J, Klopp C, et al.
J Clin Microbiol. 2012 Jun 20. [Epub ahead of print]


Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays.
Morgan AA, Chen R, Butte AJ.
J Am Med Inform Assoc. 2012 Jun 1;19(e1):e21-e27.


wANNOVAR: annotating genetic variants for personal genomes via the web.
Chang X, Wang K.
J Med Genet. 2012 Jun 20. [Epub ahead of print]


UBQLN2/ubiquilin 2 mutation and pathology in familial amyotrophic lateral sclerosis.
Williams KL, Warraich ST, Yang S, Solski JA, et al.
Neurobiol Aging. 2012 Jun 18. [Epub ahead of print]


Genomic diversity of 2010 Haitian cholera outbreak strains.
Hasan NA, Choi SY, Eppinger M, Clark PW, et al.
Proc Natl Acad Sci U S A. 2012 Jun 18. [Epub ahead of print]


CASK aberrations in male patients with Ohtahara syndrome and cerebellar hypoplasia.
Saitsu H, Kato M, Osaka H, Moriyama N, et al.
Epilepsia. 2012 Jun 18. [Epub ahead of print]

The Scan

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A court has reinstated Nicole Boivin as director of the Max Planck Institute for the Science of Human History, Science reports.

Research, But Implementation?

Francis Collins reflects on his years as the director of the US National Institutes of Health with NPR.

For the False Negatives

The Guardian writes that the UK Health Security Agency is considering legal action against the lab that reported thousands of false negative COVID-19 test results.

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