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In Print: Last Week's Clinical Sequencing Papers of Note: Oct 30, 2013


Deep Sequencing and Circos Analyses of Antibody Libraries Reveal Antigen-driven Selection of Ig VH Genes during HIV-1 Infection.
Xiao M, Prabakaran P, Chen W, Kessing B, Dimitrov DS.
Exp Mol Pathol. 2013 Oct 21. [Epub ahead of print]

Whole exome sequencing identifies a novel somatic mutation in MMP8 associated with a t(1;22)-acute megakaryoblastic leukemia.
Kim Y, Schulz VP, Satake N, Gruber TA, et al.
Leukemia. 2013 Oct 25. [Epub ahead of print]

Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro.
Renzette N, Caffrey DR, Zeldovich KB, Liu P, et al.
J Virol. 2013 Oct 23. [Epub ahead of print]

Targeted next generation sequencing and non-coding RNA expression analysis of clear cell papillary renal cell carcinoma suggests distinct pathological mechanisms from other renal tumour subtypes.
Lawrie CH, Larrea E, Larrinaga G, Goicoechea I, et al.
J Pathol. 2013 Oct 23. [Epub ahead of print]

Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.
Peltekova VD, Lemire M, Qazi AM, Zaidi SH, et al.
Int J Cancer. 2013 Oct 23. [Epub ahead of print]

Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements.
Wang F, Wang H, Tuan HF, Nguyen DH, et al.
Hum Genet. 2013 Oct 24. [Epub ahead of print]

Exome Sequencing Revealed Novel Germline Mutations in Chinese Peutz-Jeghers Syndrome Patients.
Wang HH, Xie NN, Li QY, Hu YQ, et al.
Dig Dis Sci. 2013 Oct 24. [Epub ahead of print]

Whole-exome resequencing reveals recessive mutations in TRAP1 in individuals with CAKUT and VACTERL association.
Saisawat P, Kohl S, Hilger AC, Hwang DY, et al.
Kidney Int. 2013 Oct 23. [Epub ahead of print]

HLA-B*13:01 and the dapsone hypersensitivity syndrome.
Zhang FR, Liu H, Irwanto A, Fu XA, et al.
N Engl J Med. 2013 Oct 24;369(17):1620-8.

Common fusion transcripts identified in colorectal cancer cell lines by high-throughput RNA sequencing.
Nome T, Thomassen GO, Bruun J, Ahlquist T, et al.
Transl Oncol. 2013 Oct 1;6(5):546-53.

Whole exome sequencing identifies variation in CYB5A and RNF10 associated with adiposity and type 2 diabetes.
Huang K, Nair AK, Muller YL, Piaggi P, et al.
Obesity. 2013 Oct 22. [Epub ahead of print]

Exome sequencing and functional analyses suggest SIX6 is a gene involved in an altered proliferation-differentiation balance early in life and optic nerve degeneration at old age.
Iglesias AI, Springelkamp H, van der Linde H, Severijnen LA, et al.
Hum Mol Genet. 2013 Oct 22. [Epub ahead of print]

A novel mutation of DNAH5 in chronic rhinosinusitis and primary ciliary dyskinesia in a Chinese family.
Zhang J, Guan L, Wen W, Lu Y, et al.
Eur Arch Otorhinolaryngol. 2013 Oct 23. [Epub ahead of print]

Targeted cancer exome sequencing reveals recurrent mutations in myeloproliferative neoplasms.
Tenedini E, Bernardis I, Artusi V, Artuso L, et al.
Leukemia. 2013 Oct 22. [Epub ahead of print]

Deep sequencing of the T cell receptor repertoire in CD8+ T-large granular lymphocyte leukemia identifies signature landscapes.
Clemente MJ, Przychodzen B, Jerez A, Dienes BE, et al.
Blood. 2013 Oct 22. [Epub ahead of print]

Complex Patterns of Chromosome 11 Aberrations in Myeloid Malignancies Target CBL, MLL, DDB1 and LMO2.
Klampfl T, Milosevic JD, Puda A, Schönegger A, et al.
PLOS One. 2013 Oct 16;8(10):e77819.

Massively Parallel Sequencing Reveals an Accumulation of De Novo Mutations and an Activating Mutation of LPAR1 in a Patient with Metastatic Neuroblastoma.
Wei JS, Johansson P, Chen L, Song YK, et al.
PLOS One. 2013 Oct 16;8(10):e77731.

Genome-Wide Sequencing of Cellular microRNAs Identifies a Combinatorial Expression Signature Diagnostic of Sepsis.
Ma Y, Vilanova D, Atalar K, Delfour O, et al.
PLOS One. 2013 Oct 16;8(10):e75918.

Eleven candidate susceptibility genes for common familial colorectal cancer.
Gylfe AE, Katainen R, Kondelin J, Tanskanen T, et al.
PLOS Genet. 2013 Oct;9(10):e1003876.

Landscape of somatic mutations and clonal evolution in mantle cell lymphoma.
Beà S, Valdés-Mas R, Navarro A, Salaverria I, et al.
Proc Natl Acad Sci U S A. 2013 Oct 21. [Epub ahead of print]

Very early-onset lone atrial fibrillation patients have a high prevalence of rare variants in genes previously associated with atrial fibrillation.
Olesen MS, Andreasen L, Jabbari J, Refsgaard L, et al.
Heart Rhythm. 2013 Oct 18. [Epub ahead of print]

Next generation sequencing based multi-gene mutational screen for acute myeloid leukemia using miseq: applicability for diagnostics and disease monitoring.
Luthra R, Patel KP, Reddy NG, Haghshenas V, et al.
Haematologica. 2013 Oct 18. [Epub ahead of print]

STAT3 Targets Suggest Mechanisms of Aggressive Tumorigenesis in Diffuse Large B Cell Lymphoma.
Hardee JM, Ouyang Z, Zhang Y, Kundaje A, et al.
G3 . 2013 Oct 18. [Epub ahead of print]

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
Frampton GM, Fichtenholtz A, Otto GA, Wang K, et al.
Nat Biotechnol. 2013 Oct 20. [Epub ahead of print]

Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing.
Lin KT, Shann YJ, Chau GY, Hsu CN, Huang CY.
Oncogene. 2013 Oct 21. [Epub ahead of print]

Next-generation sequencing of pharmacogenes: a critical analysis focusing on schizophrenia treatment.
Drögemöller BI, Wright GE, Niehaus DJ, Emsley R, Warnich L.
Pharmacogenet Genomics. 2013 Oct 17. [Epub ahead of print]

Detection of an Atypical Teratoid Rhabdoid Brain Tumor Gene Deletion in Circulating Blood Using Next-Generation Sequencing.
Chakravadhanula M, Tembe W, Legendre C, Carpentieri D, et al.
J Child Neurol. 2013 Oct 17. [Epub ahead of print]

The genetic landscape of anaplastic astrocytoma.
Killela PJ, Pirozzi CJ, Reitman ZJ, Jones S, et al.
Oncotarget. 2013 Oct 16. [Epub ahead of print]

Detection of a novel intragenic rearrangement in the creatine transporter gene by next generation sequencing.
Yu H, van Karnebeek C, Sinclair G, Hill A, et al.
Mol Genet Metab. 2013 Oct 4. [Epub ahead of print]

Defects in the IFT-B Component IFT172 Cause Jeune and Mainzer-Saldino Syndromes in Humans.
Halbritter J, Bizet AA, Schmidts M, Porath JD, et al.
Am J Hum Genet. 2013 Oct 16. [Epub ahead of print]

No detection of the NS5B S282T mutation in treatment-naïve genotype 1 HCV/HIV-1 coinfected patients using deep sequencing.
Franco S, Casadellà M, Noguera-Julian M, Clotet B, et al.
J Clin Virol. 2013 Oct 3. [Epub ahead of print]

Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer.
Jäger N, Schlesner M, Jones DT, Raffel S, et al.
Cell. 2013 Oct 15. [Epub ahead of print]

Targeted next-generation sequencing: A novel diagnostic tool for primary immunodeficiencies.
Nijman IJ, van Montfrans JM, Hoogstraat M, Boes ML, et al.
J Allergy Clin Immunol. 2013 Oct 15. [Epub ahead of print]

Microcephaly, epilepsy, and neonatal diabetes due to compound heterozygous mutations in IER3IP1: insights into the natural history of a rare disorder.
Shalev SA, Tenenbaum-Rakover Y, Horovitz Y, Paz VP, et al.
Pediatr Diabetes. 2013 Oct 21. [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.