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Recent Clinical Sequencing Papers of Note: May 28, 2014


Genomic landscape of CD34+ hematopoietic cells in myelodysplastic syndrome and gene mutation profiles as prognostic markers.
Xu L, Gu ZH, Li Y, Zhang JL, et al.
Proc Natl Acad Sci U S A. 2014 May 21. [Epub ahead of print]

Data on whole-genome-sequencing is insufficient to rule out patient-to-patient transmission as a significant source of Staphylococcus aureus acquisition in an ICU.
Mills JP, Linkin DR et al.
Clin Infect Dis. 2014 May 20. [Epub ahead of print]

Deep sequencing of HIV infected cells: insights into nascent transcription and host-directed therapy.
Peng X, Sova P, Green RR, Thomas MJ, et al.
J Virol. 2014 May 21. [Epub ahead of print]

Two novel mutations in the C-terminal region of centrosomal protein 290 (CEP290) result in classic Joubert syndrome.
Wang L, Yang Y, Song J, Mao L, et al.
J Child Neurol. 2014 May 21. [Epub ahead of print]

Expanding the phenotypic spectrum of TUBB4A-associated hypomyelinating leukoencephalopathies.
Miyatake S, Osaka H, Shiina M, Sasaki M, et al.
Neurology. 2014 May 21. [Epub ahead of print]

Whole genome sequencing for high-resolution investigation of methicillin resistant Staphylococcus aureus epidemiology and genome plasticity.
SenGupta DJ, Cummings LA, Hoogestraat DR, Butler-Wu SM, et al.
J Clin Microbiol. 2014 May 21. [Epub ahead of print]

Improving molecular diagnosis in epilepsy by a dedicated high-throughput sequencing platform.
Mina ED, Ciccone R, Brustia F, Bayindir B, et al.
Eur J Hum Genet. 2014 May 21. [Epub ahead of print]

Recessive mutations in PCBD1 cause a new type of early-onset diabetes.
Simaite D, Kofent J, Gong M, Rüschendorf F, et al.
Diabetes. 2014 May 21. [Epub ahead of print]

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing.
Hovestadt V, Jones DT, Picelli S, Wang W, et al.
Nature. 2014 May 18. [Epub ahead of print]

Whole-exome sequencing identifies rare, functional CFH variants in families with macular degeneration.
Yu Y, Triebwasser MP, Wong EK, Schramm EC, et al.
Hum Mol Genet. 2014 May 20. [Epub ahead of print]

Mitochondrial NADP(H) deficiency due to a mutation in NADK2 causes dienoyl-CoA reductase deficiency with hyperlysinemia.
Houten SM, Denis S, Te Brinke H, Jongejan A, et al.
Hum Mol Genet. 2014 May 8. [Epub ahead of print]

A novel disease-causing CD40L mutation reduces expression of CD40 ligand, but preserves CD40 binding capacity.
Günaydin NC, Chou J, Karaca NE, Aksu G, et al.
Clin Immunol. 2014 May 17. [Epub ahead of print]

CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data.
Yu Z, Liu Y, Shen Y, Wang M, Li A.
Bioinformatics. 2014 May 19. [Epub ahead of print]

Attitudes of non-African American focus group participants toward return of results from exome and whole genome sequencing.
Yu JH, Crouch J, Jamal SM, Bamshad MJ, Tabor HK.
Am J Med Genet A. 2014 May 20. [Epub ahead of print]

Clinical investigational studies for validation of a next-generation sequencing in vitro diagnostic device for cystic fibrosis testing.
Grosu DS, Hague L, Chelliserry M, Kruglyak KM, et al.
Expert Rev Mol Diagn. 2014 Jun;14(5):605-22.

Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing.
Yu SC, Chan KC, Zheng YW, Jiang P, et al.
Proc Natl Acad Sci U S A. 2014 May 19. [Epub ahead of print]

ATP1A3 mutations and genotype-phenotype correlation of alternating hemiplegia of childhood in Chinese patients.
Yang X, Gao H, Zhang J, Xu X, et al.
PLOS One. 2014 May 19;9(5):e97274.

HIV-1 Quasispecies delineation by tag linkage deep sequencing.
Wu NC, De La Cruz J, Al-Mawsawi LQ, Olson CA, et al.
PLOS One. 2014 May 19;9(5):e97505.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.