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In Print: Last Week's Clinical Sequencing Papers of Note: Aug 28, 2013

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Targeted exon sequencing successfully discovers rare causative genes and clarifies the molecular epidemiology of Japanese deafness patients.
Miyagawa M, Naito T, Nishio SY, Kamatani N, Usami S.
PLoS One. 2013 Aug 13;8(8):e71381.


A flexible approach for the analysis of rare variants allowing for a mixture of effects on binary or quantitative traits.
Clarke GM, Rivas MA, Morris AP.
PLoS Genet. 2013 Aug;9(8):e1003694.


Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes.
He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K.
PLoS Genet. 2013 Aug;9(8):e1003671.


Three Novel IGSF1 Mutations in Four Japanese Patients With X-Linked Congenital Central Hypothyroidism.
Nakamura A, Bak B, Silander TL, Lam J, Hotsubo T, Yorifuji T, Ishizu K, Bernard DJ, Tajima T.
J Clin Endocrinol Metab. 2013 Aug 21. [Epub ahead of print]


Targeted next-generation sequencing reveals further genetic heterogeneity in axonal Charcot-Marie-Tooth neuropathy and a mutation in HSPB1.
Ylikallio E, Johari M, Konovalova S, Moilanen JS, Kiuru-Enari S, Auranen M, Pajunen L, Tyynismaa H.
Eur J Hum Genet. 2013 Aug 21. doi: 10.1038/ejhg.2013.190. [Epub ahead of print]


Inherited mutations in the helicase RTEL1 cause telomere dysfunction and Hoyeraal-Hreidarsson syndrome.
Deng Z, Glousker G, Molczan A, Fox AJ, Lamm N, Dheekollu J, et al.
Proc Natl Acad Sci U S A. 2013 Aug 19. [Epub ahead of print]


Comprehensive mutational profiling in advanced systemic mastocytosis.
Schwaab J, Schnittger S, Sotlar K, Walz C, Fabarius A, Pfirrmann M, et al.
Blood. 2013 Aug 19. [Epub ahead of print]


Monitoring of residual disease by next-generation deep-sequencing of RUNX1 mutations can identify acute myeloid leukemia patients with resistant disease.
Kohlmann A, Nadarajah N, Alpermann T, Grossmann V, Schindela S, et al.
Leukemia. 2013 Aug 20. [Epub ahead of print]


LAMB3 Mutations Causing Autosomal-dominant Amelogenesis Imperfecta.
Kim JW, Seymen F, Lee KE, Ko J, Yildirim M, Tuna EB, Gencay K, et al.
J Dent Res. 2013 Aug 19. [Epub ahead of print]


Differential gene expression in peripheral blood T cells from patients with psoriasis, lichen planus, and atopic dermatitis.
Li X, Li J, Yang Y, Hou R, Liu R, Zhao X, Yan X, Yin G, An P, Wang Y, Zhang K.
J Am Acad Dermatol. 2013 Aug 16. pii: S0190-9622(13)00663-4. [Epub ahead of print]


A mutation in the serine protease TMPRSS4 in a novel pediatric neurodegenerative disorder.
Lahiry P, Racacho L, Wang J, Robinson J, Gloor GB, Rupar CA, Siu VM, Bulman DE, Hegele RA.
Orphanet J Rare Dis. 2013 Aug 17;8(1):126.


Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies.
Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, Desiderio S, Burns KH.
BMC Genomics. 2013 Aug 19;14(1):565.


Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions.
Shugay M, Ortiz de Mendibil I, Vizmanos JL, Novo FJ.
Bioinformatics. 2013 Aug 16. [Epub ahead of print]


Mutation in TTI2 reveals a role for Triple T complex in human brain development.
Langouët M, Saadi A, Rieunier G, Moutton S, Siquier-Pernet K, et al.
Hum Mutat. 2013 Aug 16. [Epub ahead of print]


Redefining the progeroid form of ehlers-danlos syndrome: Report of the fourth patient with B4GALT7 deficiency and review of the literature.
Guo MH, Stoler J, Lui J, Nilsson O, Bianchi DW, Hirschhorn JN, Dauber A.
Am J Med Genet A. 2013 Aug 16. [Epub ahead of print]


A Local Poisson Graphical Model for Inferring Networks From Sequencing Data.
Allen G, Liu Z.
IEEE Trans Nanobioscience. 2013 Aug 15. [Epub ahead of print]


The ACMSD gene, involved in tryptophan metabolism, is mutated in a family with cortical myoclonus, epilepsy, and parkinsonism.
Martí-Massó JF, Bergareche A, Makarov V, Ruiz-Martinez J, Gorostidi A, et al.
J Mol Med (Berl). 2013 Aug 20. [Epub ahead of print]


The extent of HCV NS3 protease variability and resistance-associated mutations assessed by next generation sequencing in HCV monoinfected and HIV/HCV coinfected patients.
Bartolini B, Giombini E, Zaccaro P, Selleri M, Rozera G, Abbate I, et al.
Virus Res. 2013 Aug 13. pii: S0168-1702(13)00264-5. [Epub ahead of print]


Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencing drug resistance assay in a routine diagnostic laboratory.
Garcia-Diaz A, Guerrero-Ramos A, McCormick AL, Macartney M, et al.
J Clin Virol. 2013 Aug 14. pii: S1386-6532(13)00284-9. [Epub ahead of print]


Whole-Genome Sequencing Uncovers the Genetic Basis of Chronic Mountain Sickness in Andean Highlanders.
Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, et al.
Am J Hum Genet. 2013 Aug 14. pii: S0002-9297(13)00331-5. [Epub ahead of print]


DrGaP: A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies.
Hua X, Xu H, Yang Y, Zhu J, Liu P, Lu Y.
Am J Hum Genet. 2013 Aug 14. pii: S0002-9297(13)00294-2. [Epub ahead of print]


Somatic Mutation of the Androgen Receptor Gene Is Not Associated with Transitional Cell Carcinoma: A "Negative" Study by Whole-exome Sequencing Analysis.
Wu S, Lv Z, Zhu J, Dong P, Zhou F, Li X, Cai Z.
Eur Urol. 2013 Aug 7. pii: S0302-2838(13)00821-X. [Epub ahead of print]


A Novel Autosomal Recessive GJA1 Missense Mutation Linked to Craniometaphyseal Dysplasia.
Hu Y, Chen IP, de Almeida S, Tiziani V, Do Amaral CM, et al.
PLoS One. 2013 Aug 12;8(8):e73576.


RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level.
Chen K, Deng S, Lu H, Zheng Y, Yang G, Kim D, Cao Q, Wu JQ.
PLoS One. 2013 Aug 9;8(8):e72567.


Re-Ranking Sequencing Variants in the Post-GWAS Era for Accurate Causal Variant Identification.
Faye LL, Machiela MJ, Kraft P, Bull SB, Sun L.
PLoS Genet. 2013 Aug;9(8):e1003609.


454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples.
Altimari A, de Biase D, De Maglio G, Gruppioni E, Capizzi E, et al.
Onco Targets Ther. 2013 Aug 5;6:1057-64.


Boston type craniosynostosis: Report of a second mutation in MSX2.
Florisson JM, Verkerk AJ, Huigh D, Hoogeboom AJ, Swagemakers S, et al.
Am J Med Genet A. 2013 Aug 15. [Epub ahead of print]


Novel truncating thyroglobulin gene mutations associated with congenital hypothyroidism.
Cangul H, Boelaert K, Dogan M, Saglam Y, Kendall M, Barrett TG, Maher ER.
Endocrine. 2013 Aug 15. [Epub ahead of print]


Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease.
Shanks ME, Downes SM, Copley RR, Lise S, Broxholme J, Hudspith KA, et al.
Eur J Hum Genet. 2013 Sep;21(9):1031.


Exome sequencing of a patient with suspected mitochondrial disease reveals a likely multigenic etiology.
Craigen WJ, Graham BH, Wong LJ, Scaglia F, Lewis RA, Bonnen PE.
BMC Med Genet. 2013 Aug 16;14(1):83. [Epub ahead of print]


The human microbiota: a new direction in the investigation of thoracic diseases.
Hui AW, Lau HW, Chan TH, Tsui SK.
J Thorac Dis. 2013 Aug;5(Suppl 2):S127-31.


Evolution and Taxonomic Classification of Alphapapillomavirus 7 Complete Genomes: HPV18, HPV39, HPV45, HPV59, HPV68 and HPV70.
Chen Z, Schiffman M, Herrero R, Desalle R, Anastos K, Segondy M, et al.
PLoS One. 2013 Aug 16;8(8):e72565.


Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment.
Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, et al.
PLoS One. 2013 Aug 19;8(8):e71806.


Genome Sequencing and Analysis of BCG Vaccine Strains.
Zhang W, Zhang Y, Zheng H, Pan Y, Liu H, Du P, Wan L, Liu J, Zhu B, Zhao G, Chen C, Wan K.
PLoS One. 2013 Aug 19;8(8):e71243.


Recessive truncating titin gene, TTN, mutations presenting as centronuclear myopathy.
Ceyhan-Birsoy O, Agrawal PB, Hidalgo C, Schmitz-Abe K, Dechene ET, et al.
Neurology. 2013 Aug 23. [Epub ahead of print]


Exome sequencing in a family with intellectual disability, early onset spasticity, and cerebellar atrophy detects a novel mutation in EXOSC3.
Zanni G, Scotton C, Passarelli C, Fang M, Barresi S, Dallapiccola B, et al.
Neurogenetics. 2013 Aug 24. [Epub ahead of print]


Molecular defects identified by whole exome sequencing in a child with Fanconi anemia.
Zheng Z, Geng J, Yao RE, Li C, Ying D, Shen Y, Ying L, Yu Y, Fu Q.
Gene. 2013 Aug 22. pii: S0378-1119(13)01061-5. [Epub ahead of print]


Significance of TP53 Mutations Determined by Next-Generation "Deep" Sequencing in Prognosis of Estrogen Receptor-Positive Breast Cancer.
Uji K, Naoi Y, Kagara N, Shimoda M, Shimomura A, Maruyama N, Shimazu K, Kim SJ, Noguchi S.
Cancer Lett. 2013 Aug 21. pii: S0304-3835(13)00603-4. [Epub ahead of print]


Molecular Diagnostic Profiling of Lung Cancer Specimens with a Semiconductor-Based Massive Parallel Sequencing Approach: Feasibility, Costs, and Performance Compared with Conventional Sequencing.
Endris V, Penzel R, Warth A, Muckenhuber A, Schirmacher P, Stenzinger A, Weichert W.
J Mol Diagn. 2013 Aug 21. pii: S1525-1578(13)00134-7. [Epub ahead of print]


Transcriptomic signatures in cartilage ageing.
Peffers MJ, Liu X, Clegg PD.
Arthritis Res Ther. 2013 Aug 23;15(4):R98.

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