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Last Week's Clinical Sequencing Papers of Note: Feb 19, 2014

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Expansion of the spectrum of TUBB4A-related disorders: a new phenotype associated with a novel mutation in the TUBB4A gene.
Blumkin L, Halevy A, Ben-Ami-Raichman D, Dahari D, et al.
Neurogenetics. 2014 Feb 14. [Epub ahead of print]


Clinical whole-exome sequencing: are we there yet?
Atwal PS, Brennan ML, Cox R, Niaki M, et al.
Genet Med. 2014 Feb 13. [Epub ahead of print]


Cooperativity of RUNX1 and CSF3R mutations in the development of leukemia in severe congenital neutropenia: a unique pathway in myeloid leukemogenesis.
Skokowa J, Steinemann D, Katsman-Kuipers JE, Zeidler C, et al.
Blood. 2014 Feb 12. [Epub ahead of print]


Identification of a novel COL4A5 mutation in a Chinese family with X-linked Alport syndrome using exome sequencing.
Guo Y, Yuan J, Liang H, Xiao J, et al.
Mol Biol Rep. 2014 Feb 13. [Epub ahead of print]


Autosomal-recessive complicated spastic paraplegia with a novel lysosomal trafficking regulator gene mutation.
Shimazaki H, Honda J, Naoi T, Namekawa M, et al.
J Neurol Neurosurg Psychiatry. 2014 Feb 12. [Epub ahead of print]


Integration of sequence data from a consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene.
Okada Y, Diogo D, Greenberg JD, Mouassess F, et al.
PLOS One. 2014 Feb 10;9(2):e87645.


The microRNA expression signature of bladder cancer by deep sequencing: the functional significance of the miR-195/497 cluster.
Itesako T, Seki N, Yoshino H, Chiyomaru T, et al.
PLOS One. 2014 Feb 10;9(2):e84311.


Targeted NGS gene panel identifies mutations in RSPH1 causing primary ciliary dyskinesia and a common mechanism for ciliary central-pair agenesis due to radial spoke defects.
Onoufriadis A, Shoemark A, Schmidts M, Patel M, et al.
Hum Mol Genet. 2014 Feb 11. [Epub ahead of print]


ChildSeq-RNA: a next-generation sequencing-based diagnostic assay to identify known fusion transcripts in childhood sarcomas.
Qadir MA, Zhan SH, Kwok B, Bruestle J, et al.
J Mol Diagn. 2014 Feb 8. [Epub ahead of print]


Development and performance of a comprehensive targeted sequencing assay for pan-ethnic screening of carrier status.
Tanner AK, Valencia CA, Rhodenizer D, Espirages M, et al.
J Mol Diagn. 2014 Feb 8. [Epub ahead of print]


Next generation sequencing analysis of miRNAs: miR-127-3p inhibits glioblastoma proliferation and activates TGF-β signaling by targeting SKI.
Jiang H, Jin C, Liu J, Hua D, et al.
OMICS. 2014 Feb 11. [Epub ahead of print]


Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
de Castro-Miró M, Pomares E, Lorés-Motta L, Tonda R, et al.
PLOS One. 2014 Feb 7;9(2):e88410.


VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data.
Jia P, Zhao Z.
PLOS Comput Biol. 2014 Feb 6;10(2):e1003460.


TBC1D7 Mutations are associated with intellectual disability, macrocrania, patellar dislocation and celiac disease.
Alfaiz AA, Micale L, Mandriani B, Augello B, et al.
Hum Mutat. 2014 Feb 11. [Epub ahead of print]


A comparison of deep sequencing of TCRG rearrangements vs traditional capillary electrophoresis for assessment of clonality in T-cell lymphoproliferative disorders.
Schumacher JA, Duncavage EJ, Mosbruger TL, Szankasi PM, Kelley TW.
Am J Clin Pathol. 2014 Mar;141(3):348-59.


AGC1 deficiency causes infantile epilepsy, abnormal myelination, and reduced N-acetylaspartate.
Falk MJ, Li D, Gai X, McCormick E, et al.
JIMD Rep. 2014 Feb 11. [Epub ahead of print]


Solitary fibrous tumors (SFTs)/hemangiopericytomas (HPCs) with different variants of the NAB2-STAT6 gene fusion are characterized by specific histomorphology and distinct clinicopathological features.
Barthelmeß S, Geddert H, Boltze C, Moskalev EA, et al.
Am J Pathol. 2014 Feb 7. [Epub ahead of print]

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.