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In Print: Last Week's Clinical Sequencing Papers of Note: Apr 3, 2013


Limb-girdle muscular dystrophy 1F is caused by a microdeletion in the transportin 3 gene.
Melià MJ, Kubota A, Ortolano S, Vílchez JJ, et al.
Brain. 2013 Mar 29. [Epub ahead of print]

Mutations of DEPDC5 cause autosomal dominant focal epilepsies.
Ishida S, Picard F, Rudolf G, Noé E, et al.
Nat Genet. 2013 Mar 31. [Epub ahead of print]

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome.
McDonell LM, Mirzaa GM, Alcantara D, Schwartzentruber J, et al.
Nat Genet. 2013 Mar 31. [Epub ahead of print]

Recessive mutations in DGKE cause atypical hemolytic-uremic syndrome.
Lemaire M, Frémeaux-Bacchi V, Schaefer F, Choi M, et al.
Nat Genet. 2013 Mar 31. [Epub ahead of print]

Mutations in DEPDC5 cause familial focal epilepsy with variable foci.
Dibbens LM, de Vries B, Donatello S, Heron SE, et al.
Nat Genet. 2013 Mar 31. [Epub ahead of print]

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study.
Bryant JM, Grogono DM, Greaves D, Foweraker J, et al.
Lancet. 2013 Mar 28. [Epub ahead of print]

Mutations in KCTD1 cause scalp-ear-nipple syndrome.
Marneros AG, Beck AE, Turner EH, McMillin MJ, et al.
Am J Hum Genet. 2013 Mar 26. [Epub ahead of print]

Mutations in LARS2, encoding mitochondrial leucyl-tRNA synthetase, lead to premature ovarian failure and hearing loss in Perrault syndrome.
Pierce SB, Gersak K, Michaelson-Cohen R, Walsh T, et al.
Am J Hum Genet. 2013 Mar 26. [Epub ahead of print]

Perrault syndrome is caused by recessive mutations in CLPP, encoding a mitochondrial ATP-dependent chambered protease.
Jenkinson EM, Rehman AU, Walsh T, Clayton-Smith J, et al.
Am J Hum Genet. 2013 Mar 26. [Epub ahead of print]

Quantitative and sensitive detection of GNAS mutations causing McCune-Albright syndrome with next generation sequencing.
Narumi S, Matsuo K, Ishii T, Tanahashi Y, Hasegawa T.
PLoS One. 2013;8(3):e60525.

Transcriptome sequencing of gene expression in the brain of the HIV-1 transgenic rat.
Li MD, Cao J, Wang S, Wang J, et al.
PLoS One. 2013;8(3):e59582.

Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of HCV genotype 1-infected patients.
Dietz J, Schelhorn SE, Fitting D, Mihm U, et al.
J Virol. 2013 Mar 27. [Epub ahead of print]

Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains.
Zhu J, Ofek G, Yang Y, Zhang B, et al.
Proc Natl Acad Sci U S A. 2013 Mar 27. [Epub ahead of print]

Combined linkage analysis and exome sequencing identifies novel genes for familial goiter.
Yan J, Takahashi T, Ohura T, Adachi H, et al.
J Hum Genet. 2013 Mar 28. [Epub ahead of print]

Detection of novel genetic variation in autosomal dominant retinitis pigmentosa.
Borràs E, de Sousa Dias M, Hernan I, Pascual B, et al.
Clin Genet. 2013 Mar 27. [Epub ahead of print]

Acral peeling skin syndrome resulting from a homozygous nonsense mutation in the CSTA gene encoding cystatin A.
Krunic AL, Stone KL, Simpson MA, McGrath JA.
Pediatr Dermatol. 2013 Mar 28. [Epub ahead of print]

Global H3K4me3 genome mapping reveals alterations of innate immunity signaling and overexpression of JMJD3 in human myelodysplastic syndrome CD34+ cells.
Wei Y, Chen R, Dimicoli S, Bueso-Ramos C, et al.
Leukemia. 2013 Mar 29. [Epub ahead of print]

Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing.
Hu YJ, Wang Q, Jiang YT, Ma R, et al.
Int J Oral Sci. 2013 Mar 29;5:0. [Epub ahead of print]

Investigation of radiation-induced transcriptome profile of radioresistant non-small cell lung cancer A549 cells using RNA-seq.
Yang HJ, Kim N, Seong KM, Youn H, Youn B.
PLoS One. 2013;8(3):e59319.

In vivo and in vitro oncogenic effects of HIF2A mutations in pheochromocytomas and paragangliomas.
Toledo RA, Qin Y, Srikantan S, Morales NP, et al.
Endocr Relat Cancer. 2013 Mar 26. [Epub ahead of print]

Discordant results between fetal karyotyping and non-invasive prenatal testing by maternal plasma sequencing in a case of uniparental disomy 21 due to trisomic rescue.
Pan M, Li FT, Li Y, Jiang FM, et al.
Prenat Diagn. 2013 Mar 27:1-4.

KRAS, BRAF, and TP53 deep-sequencing for colorectal carcinoma patient diagnostics.
Rechsteiner M, von Teichman A, Rüschoff JH, Fankhauser N, et al.
J Mol Diagn. 2013 Mar 23. [Epub ahead of print]

MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples.
Trifonov V, Pasqualucci L, Favera RD, Rabadan R.
BMC Syst Biol. 2013 Mar 25;7(1):25.

High-purity prostate circulating tumor cell isolation by a polymer nanofiber-embedded microchip for whole exome sequencing.
Zhao L, Lu YT, Li F, Wu K, et al.
Adv Mater. 2013 Mar 26. [Epub ahead of print]

Presence of epilepsy-associated variants in large exome databases.
Cherepanova NS, Leslie E, Ferguson PJ, Bamshad MJ, Bassuk AG.
J Neurogenet. 2013 Mar 25. [Epub ahead of print]

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.