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In Print: Last Week's Clinical Sequencing Papers of Note: Sep 18, 2013


Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing.
Be NA, Thissen JB, Gardner SN, McLoughlin KS, et al.
PLOS One. 2013 Sep 9;8(9):e73455.

An alteration in ELMOD3, an Arl2 GTPase-activating protein, is associated with hearing impairment in humans.
Jaworek TJ, Richard EM, Ivanova AA, Giese AP, et al.
PLOS Genet. 2013 Sep;9(9):e1003774.

A comprehensive analysis of in vitro and in vivo genetic fitness of Pseudomonas aeruginosa using high-throughput sequencing of transposon libraries.
Skurnik D, Roux D, Aschard H, Cattoir V, et al.
PLOS Pathog. 2013 Sep;9(9):e1003582.

Massively-parallel sequencing assists the diagnosis and guided treatment of cancers of unknown primary.
Tothill RW, Li J, Mileshkin L, Doig K, et al.
J Pathol. 2013 Sep 4. [Epub ahead of print]

Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, et al.
Nature. 2013 Sep 15. [Epub ahead of print]

Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration.
Seddon JM, Yu Y, Miller EC, Reynolds R, et al.
Nat Genet. 2013 Sep 15. [Epub ahead of print]

A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration.
Helgason H, Sulem P, Duvvari MR, Luo H, et al.
Nat Genet. 2013 Sep 15. [Epub ahead of print]

Identification of a rare coding variant in complement 3 associated with age-related macular degeneration.
Zhan X, Larson DE, Wang C, Koboldt DC, et al.
Nat Genet. 2013 Sep 15. [Epub ahead of print]

A de novo gain-of-function mutation in SCN11A causes loss of pain perception.
Leipold E, Liebmann L, Korenke GC, Heinrich T, et al.
Nat Genet. 2013 Sep 15. [Epub ahead of print]

Unbiased next generation sequencing analysis confirms the existence of autosomal dominant Alport syndrome in a relevant fraction of cases.
Chiara F, Laura D, Rossella T, Dorella DP, et al.
Clin Genet. 2013 Sep 4. [Epub ahead of print]

A systematic approach to assessing the clinical significance of genetic variants.
Duzkale H, Shen J, McLaughlin H, Alfares A, et al.
Clin Genet. 2013 Sep 4. [Epub ahead of print]

Parental attitudes, values, and beliefs toward the return of results from exome sequencing in children.
Sapp JC, Dong D, Stark C, Ivey LE, et al.
Clin Genet. 2013 Aug 20. [Epub ahead of print]

Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia.
Jethwa A, Hüllein J, Stolz T, Blume C, et al.
Br J Haematol. 2013 Aug 27. [Epub ahead of print]

Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model.
Németh AH, Kwasniewska AC, Lise S, Parolin Schnekenberg R, et al.
Brain. 2013 Sep 11. [Epub ahead of print]

Distinguishable epidemics of multidrug-resistant Salmonella typhimurium DT104 in different hosts.
Mather AE, Reid SW, Maskell DJ, Parkhill J, et al.
Science. 2013 Sep 12. [Epub ahead of print]

Minimizing liability risks under the ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing.
Evans BJ.
Genet Med. 2013 Sep 12. [Epub ahead of print]

Clinical and biological implications of driver mutations in myelodysplastic syndromes.
Papaemmanuil E, Gerstung M, Malcovati L, Tauro S, et al.
Blood. 2013 Sep 12. [Epub ahead of print]

Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.
Chu HT, Lin H, Tsao TT, Chang CF, et al.
BMC Med Genomics. 2013 Sep 12;6(1):31. [Epub ahead of print]

The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.
Naccache SN, Greninger AL, Lee D, Coffey LL, et al.
J Virol. 2013 Sep 11. [Epub ahead of print]

High-throughput sequencing of T cell receptors reveals a homogeneous repertoire of tumor-infiltrating lymphocytes in ovarian cancer.
Emerson RO, Sherwood AM, Rieder MJ, Guenthoer J, et al.
J Pathol. 2013 Sep 11. doi: 10.1002/path.4260. [Epub ahead of print]

Exome sequencing of Bardet-Biedl syndrome patient identifies a null mutation in the BBSome subunit BBIP1 (BBS18).
Scheidecker S, Etard C, Pierce NW, Geoffroy V, et al.
J Med Genet. 2013 Sep 11. doi: 10.1136/jmedgenet-2013-101785. [Epub ahead of print]

A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation.
Boccuto L, Aoki K, Flanagan-Steet H, Chen CF, et al.
Hum Mol Genet. 2013 Sep 10. [Epub ahead of print]

The familial dementia gene revisited: a missense mutation revealed by whole exome sequencing identifies ITM2B as a candidate gene underlying a novel autosomal dominant retinal dystrophy in a large family.
Audo I, Bujakowska K, Orhan E, El Shamieh S, et al.
Hum Mol Genet. 2013 Sep 10. [Epub ahead of print]

New exome data question the pathogenicity of genetic variants previously associated with catecholaminergic polymorphic ventricular tachycardia.
Jabbari J, Jabbari R, Nielsen MW, Holst AG, et al.
Circ Cardiovasc Genet. 2013 Sep 11. [Epub ahead of print]

A homozygous mutation in a consanguineous family consolidates the role of ALDH1A3 in autosomal recessive microphthalmia.
Roos L, Fang M, Dali CI, Jensen H, et al.
Clin Genet. 2013 Sep 11. doi: 10.1111/cge.12277. [Epub ahead of print]

In-depth characterization of microRNA transcriptome in melanoma.
Kozubek J, Ma Z, Fleming E, Duggan T, et al.
PLOS One. 2013 Sep 4;8(9):e72699. doi: 10.1371/journal.pone.0072699.

Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.
Deboever C, Reid EG, Smith EN, Wang X, et al.
PLOS One. 2013 Sep 4;8(9):e73956. doi: 10.1371/journal.pone.0073956.

Molecular mechanisms of HIV-1 prophylaxis failure revealed by single genome sequencing.
Li H, Blair L, Chen Y, Learn G, et al.
J Infect Dis. 2013 Sep 9. [Epub ahead of print]

ARNT2 mutation causes hypopituitarism, post-natal microcephaly, visual and renal anomalies.
Webb EA, Almutair A, Kelberman D, Bacchelli C, et al.
Brain. 2013 Sep 10. [Epub ahead of print]

TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell-related pathology.
Dziubianau M, Hecht J, Kuchenbecker L, Sattler A, et al.
Am J Transplant. 2013 Sep 10. [Epub ahead of print]

Exome sequencing reveals novel rare variants in the ryanodine receptor and calcium channel genes in malignant hyperthermia families.
Kim JH, Jarvik GP, Browning BL, Rajagopalan R, et al.
Anesthesiology. 2013 Sep 5. [Epub ahead of print]

Comparative RNA-seq analysis reveals potential mechanisms mediating the conversion to androgen independence in an LNCaP progression cell model.
Wang Y, Wang Y, Liu Q, Xu G, et al.
Cancer Lett. 2013 Sep 3. [Epub ahead of print]

An X-linked cobalamin disorder caused by mutations in transcriptional coregulator HCFC1.
Yu HC, Sloan JL, Scharer G, Brebner A, et al.
Am J Hum Genet. 2013 Sep 5;93(3):506-14.

The dental plaque microbiome in health and disease.
Peterson SN, Snesrud E, Liu J, Ong AC, et al.
PLOS One. 2013;8(3):e58487.