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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]