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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

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.