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Last Week's Clinical Sequencing Papers of Note: Mar 19, 2014

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Characterization of the Merkel cell carcinoma miRNome.
Ning MS, Kim AS, Prasad N, Levy SE, et al.
J Skin Cancer. 2014;2014:289548.


Whole-exome sequencing in patients with inherited neuropathies: outcome and challenges.
Schabhüttl M, Wieland T, Senderek J, Baets J, et al.
J Neurol. 2014 Mar 15. [Epub ahead of print]


Disruption of the methyltransferase-like 23 gene METTL23 causes mild autosomal recessive intellectual disability.
Bernkopf M, Webersinke G, Tongsook C, Koyani CN, et al.
Hum Mol Genet. 2014 Mar 13. [Epub ahead of print]


Genomic view of bipolar disorder revealed by whole genome sequencing in a genetic isolate.
Georgi B, Craig D, Kember RL, Liu W, et al.
PLoS Genet. 2014 Mar 13;10(3):e1004229.


Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib.
Wagle N, Grabiner BC, Van Allen EM, Hodis E, et al.
Cancer Discov. 2014 Mar 13. [Epub ahead of print]


Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk Loci by structural variation.
Blake J, Riddell A, Theiss S, Gonzalez AP, et al.
PLoS One. 2014 Mar 13;9(3):e90894.


Social and behavioral research in genomic sequencing: approaches from the Clinical Sequencing Exploratory Research Consortium Outcomes and Measures Working Group.
Gray SW, Martins Y, Feuerman LZ, Bernhardt BA , et al.
Genet Med. 2014 Mar 13. [Epub ahead of print]


Identity-by-descent-guided mutation analysis and exome sequencing in consanguineous families reveals unusual clinical and molecular findings in retinal dystrophy.
Coppieters F, Van Schil K, Bauwens M, Verdin H, et al.
Genet Med. 2014 Mar 13. [Epub ahead of print]


Identification of a de novo heterozygous missense FLNB mutation in lethal atelosteogenesis type I by exome sequencing.
Jeon GW, Lee MN, Jung JM, Hong SY, et al.
Ann Lab Med. 2014 Mar;34(2):134-8.


GABRA1 and STXBP1: novel genetic causes of Dravet syndrome.
Carvill GL, Weckhuysen S, McMahon JM, Hartmann C, et al.
Neurology. 2014 Mar 12. [Epub ahead of print]


Investigation of key microRNAs associated with hepatocellular carcinoma using small RNA-seq data.
Lin LJ, Lin Y, Jin Y, Zheng CQ.
Mol Biol Rep. 2014 Mar 13. [Epub ahead of print]


Truncation of the E3 ubiquitin ligase component FBXO31 causes non-syndromic autosomal recessive intellectual disability in a Pakistani family.
Mir A, Sritharan K, Mittal K, Vasli N, et al.
Hum Genet. 2014 Mar 13. [Epub ahead of print]


Next-generation sequencing identifies germline MRE11A variants as markers of radiotherapy outcomes in muscle-invasive bladder cancer.
Teo MT, Dyrskjøt L, Nsengimana J, Buchwald C, et al.
Ann Oncol. 2014 Mar 12. [Epub ahead of print]


Decreased levels of BAG3 in a family with a rare variant and in idiopathic dilated cardiomyopathy.
Feldman AM, Begay RL, Knezevic T, Myers VD, et al.
J Cell Physiol. 2014 Mar 13. [Epub ahead of print]


Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy.
Voss MH, Hakimi AA, Pham CG, Brannon AR, et al.
Clin Cancer Res. 2014 Mar 12. [Epub ahead of print]


Transcriptome profiling of a multiple recurrent muscle-invasive urothelial carcinoma of the bladder by deep sequencing.
Zhang S, Liu Y, Liu Z, Zhang C, et al.
PLoS One. 2014 Mar 12;9(3):e91466.


Targeted next-generation sequencing and fine linkage disequilibrium mapping reveals association of PNPLA3 and PARVB with the severity of nonalcoholic fatty liver disease.
Kitamoto T, Kitamoto A, Yoneda M, Hyogo H, et al.
J Hum Genet. 2014 Mar 13. [Epub ahead of print]


Using a combination of whole-exome sequencing and homozygosity mapping to identify a novel mutation of SCARB2.
He M, Tang BS, Li N, Mao X, et al.
Clin Genet. 2014 Mar 13. [Epub ahead of print]


A frameshift mutation in GRXCR2 causes recessively inherited hearing loss.
Imtiaz A, Kohrman DC, Naz S.
Hum Mutat. 2014 Mar 11. [Epub ahead of print]


Quantitative assessment of mutant allele burden in solid tumors by semiconductor-based next-generation sequencing.
Portier BP, Kanagal-Shamanna R, Luthra R, Singh R, et al.
Am J Clin Pathol. 2014 Apr;141(4):559-72.


Clinical interpretation and implications of whole-genome sequencing.
Dewey FE, Grove ME, Pan C, Goldstein BA, et al.
JAMA. 2014 Mar 12;311(10):1035-45.


Massively parallel DNA sequencing facilitates diagnosis of patients with usher syndrome type 1.
Yoshimura H, Iwasaki S, Nishio SY, Kumakawa K, et al.
PLoS One. 2014 Mar 11;9(3):e90688.


Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans.
Colangeli R, Arcus VL, Cursons RT, Ruthe A, et al.
PLoS One. 2014 Mar 11;9(3):e91024.


Desmoplastic melanoma with sarcomatoid dedifferentiation.
Kiuru M, McDermott G, Berger M, Halpern AC, Busam KJ.
Am J Surg Pathol. 2014 Mar 10. [Epub ahead of print]


Whole exome sequencing in Thai patients with retinitis pigmentosa reveals novel mutations in six genes.
Jinda W, Taylor TD, Suzuki Y, Thongnoppakhun W, et al.
Invest Ophthalmol Vis Sci. 2014 Mar 11. [Epub ahead of print]


Molecular profiling of premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis.
Ooi AT, Gower AC, Zhang KX, Vick JL, et al.
Cancer Prev Res (Phila). 2014 Mar 11. [Epub ahead of print]


Refining the structure and content of clinical genomic reports.
Dorschner MO, Amendola LM, Shirts BH, Kiedrowski L, et al.
Am J Med Genet C Semin Med Genet. 2014 Mar 10. [Epub ahead of print]


Deep sequencing identifies IDH1 R132S mutation in adult medulloblastoma.
Snuderl M, Triscott J, Northcott PA, Shih HA, et al.
J Clin Oncol. 2014 Mar 10. [Epub ahead of print]


Minimal residual disease monitoring in t(8;21) acute myeloid leukemia based on RUNX1-RUNX1T1 fusion quantification on genomic DNA.
Duployez N, Nibourel O, Marceau-Renaut A, Willekens C, et al.
Am J Hematol. 2014 Feb 25. [Epub ahead of print]


Targeted and genomewide NGS data disqualify mutations in MYO1A, the "DFNA48 Gene", as a cause of deafness.
Eisenberger T, Di Donato N, Baig SM, Neuhaus C, et al.
Hum Mutat. 2014 Feb 25. [Epub ahead of print]


Detection of fetal sex chromosome aneuploidy by massively parallel sequencing of maternal plasma DNA: initial experience in a Chinese hospital.
Yao H, Jiang F, Hu H, Gao Y, et al.
Ultrasound Obstet Gynecol. 2014 Mar 10. [Epub ahead of print]


Expanding the clinical and mutational spectrum of Kaufman oculocerebrofacial syndrome with biallelic UBE3B mutations.
Basel-Vanagaite L, Yilmaz R, Tang S, Reuter MS, et al.
Hum Genet. 2014 Mar 11. [Epub ahead of print]


Detection and analysis of human papillomavirus (HPV) DNA in breast cancer patients by an effective method of HPV capture.
Wang T, Zeng X, Li W, Zhu H, et al.
PLoS One. 2014 Mar 10;9(3):e90343.


Whole-exome sequencing reveals GPIHBP1 mutations in a case of infantile colitis with severe hypertriglyceridemia.
Gonzaga-Jauregui C, Mir S, Penney S, Jhangiani S, et al.
J Pediatr Gastroenterol Nutr. 2014 Mar 6. [Epub ahead of print]


Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability.
Tatton-Brown K, Seal S, Ruark E, Harmer J, et al.
Nat Genet. 2014 Mar 9. [Epub ahead of print]


Identification of the transforming STRN-ALK fusion as a potential therapeutic target in the aggressive forms of thyroid cancer.
Kelly LM, Barila G, Liu P, Evdokimova VN, et al.
Proc Natl Acad Sci U S A. 2014 Feb 3. [Epub ahead of print]


Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos.
Fiorentino F, Biricik A, Bono S, Spizzichino L, et al.
Fertil Steril. 2014 Mar 6. [Epub ahead of print]


Functional heterogeneity of genetically defined subclones in acute myeloid leukemia.
Klco JM, Spencer DH, Miller CA, Griffith M, et al.
Cancer Cell. 2014 Mar 4. pii: S1535-6108(14)00054-3.


RANBP2-ALK fusion combined with monosomy 7 in acute myelomonocytic leukemia.
Lim JH, Jang S, Park CJ, Cho YU, et al.
Cancer Genet. 2014 Jan 21. [Epub ahead of print]


Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes.
Liyanapathirana V, Ang I, Tsang D, Fung K, et al.
BMC Microbiol. 2014 Mar 10;14(1):60.


Deep sequencing analysis of variants resistant to the NS5A inhibitor daclatasvir in patients with genotype 1b hepatitis C virus infection.
Miura M, Maekawa S, Sato M, Komatsu N, et al.
Hepatol Res. 2014 Feb 25. [Epub ahead of print]


A robust approach for blind detection of balanced chromosomal rearrangements with whole-genome low-coverage sequencing.
Dong Z, Jiang L, Yang C, Hu H, et al.
Hum Mutat. 2014 Mar 7. [Epub ahead of print]


Exome sequencing of filaggrin and related genes in African-American children with atopic dermatitis.
Margolis DJ, Gupta J, Apter AJ, Hoffstad O, et al.
J Invest Dermatol. 2014 Mar 7. [Epub ahead of print]


Comprehensive molecular diagnosis of Bardet-Biedl syndrome by high-throughput targeted exome sequencing.
Xing DJ, Zhang HX, Huang N, Wu KC, et al.
PLoS One. 2014 Mar 7;9(3):e90599.


Concordance of genomic alterations between primary and recurrent breast cancer.
Meric-Bernstam F, Frampton GM, Ferrer-Lozano J, Yelensky R, et al.
Mol Cancer Ther. 2014 Mar 7. [Epub ahead of print]


Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma.
New MI, Tong YK, Yuen T, Jiang P, et al.
J Clin Endocrinol Metab. 2014 Feb 28 [Epub ahead of print]

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