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In Print: Last Week's Clinical Sequencing Papers of Note: Aug 1, 2012


Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-seq data.
Huber-Keener KJ, Liu X, Wang Z, Wang Y, et al.
PLoS One. 2012;7(7):e41333.

De novo mutations in ATP1A3 cause alternating hemiplegia of childhood.
Heinzen EL, Swoboda KJ, Hitomi Y, Gurrieri F, et al.
Nat Genet. 2012 Jul 29. [Epub ahead of print]

Exome sequencing identifies NMNAT1 mutations as a cause of Leber congenital amaurosis.
Chiang PW, Wang J, Chen Y, Fu Q, et al.
Nat Genet. 2012 Jul 29. [Epub ahead of print]

Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration.
Koenekoop RK, Wang H, Majewski J, Wang X, et al.
Nat Genet. 2012 Jul 29. [Epub ahead of print]

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma.
Krauthammer M, Kong Y, Ha BH, Evans P, et al.
Nat Genet. 2012 Jul 29. [Epub ahead of print]

NMNAT1 mutations cause Leber congenital amaurosis.
Falk MJ, Zhang Q, Nakamaru-Ogiso E, Kannabiran C, et al.
Nat Genet. 2012 Jul 29. [Epub ahead of print]

Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis syndrome is caused by a POC1A mutation.
Sarig O, Nahum S, Rapaport D, Ishida-Yamamoto A, et al.
Am J Hum Genet. 2012 Jul 24. [Epub ahead of print]

Mutational processes molding the genomes of 21 breast cancers.
Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, et al.
Cell. 2012 May 25;149(5):979-93.

Abundant drug-resistant NS3 mutants detected by deep sequencing in HCV-infected patients undergoing NS3 protease inhibitor monotherapy.
Svarovskaia ES, Martin R, McHutchison JG, Miller MD, Mo H.
J Clin Microbiol. 2012 Jul 25. [Epub ahead of print]

Recurrent mutations of MYD88 and TBL1XR1 in primary central nervous system lymphomas.
Gonzalez-Aguilar A, Idbaih A, Boisselier B, Habbita N, et al.
Clin Cancer Res. 2012 Jul 26. [Epub ahead of print]

Mitochondrial phenylalanyl-tRNA synthetase mutations underlie fatal infantile Alpers encephalopathy.
Elo JM, Yadavalli SS, Euro L, Isohanni P, et al.
Hum Mol Genet. 2012 Jul 23. [Epub ahead of print]

Dissecting the genomic complexity underlying medulloblastoma.
Jones DT, Jäger N, Kool M, Zichner T, et al.
Nature. 2012 Jul 25. [Epub ahead of print]

Exploratory data from complete genomes of familial Alzheimer disease age-at-onset outliers.
Lalli MA, Garcia G, Madrigal L, Arcos-Burgos M, et al.
Hum Mutat. 2012 Jul 24. [Epub ahead of print]

Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia.
Iacobucci I, Ferrarini A, Sazzini M, Giacomelli E, et al.
Blood Cancer J. 2012 Mar;2(3):e61.

Short read sequence typing (SRST): multi-locus sequence types from short reads.
Inouye M, Conway TC, Zobel J, Holt KE.
BMC Genomics. 2012 Jul 24;13(1):338.

GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes.
Kamphans T, Krawitz PM.
Bioinformatics. 2012 Jul 23. [Epub ahead of print]

Exome sequencing overrides formal genetics: ASPM mutations in a case study of apparent X-linked microcephalic intellectual deficit.
Ariani F, Mari F, Amitrano S, Di Marco C, et al.
Clin Genet. 2012 Jul 23. [Epub ahead of print]

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.