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Last Week's Clinical Sequencing Papers of Note: Mar 26, 2014


Genomic counseling in the newborn period: experiences and views of genetic counselors.
Nardini MD, Matthews AL, McCandless SE, Baumanis L, Goldenberg AJ.
J Genet Couns. 2014 Mar 23. [Epub ahead of print]

Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type.
Witkowski L, Carrot-Zhang J, Albrecht S, Fahiminiya S, et al.
Nat Genet. 2014 Mar 23. [Epub ahead of print]

Noninvasive prenatal screening for fetal trisomies 21, 18, 13 and the common sex chromosome aneuploidies from maternal blood using massively parallel genomic sequencing of DNA.
Porreco RP, Garite TJ, Maurel K, Marusiak B, et al.
Am J Obstet Gynecol. 2014 Mar 19. [Epub ahead of print]

Hereditary hearing loss: a 96 gene targeted sequencing protocol reveals novel alleles in a series of Italian and Qatari patients.
Vozzi D, Morgan A, Vuckovic D, D'Eustacchio A , et al.
Gene. 2014 Mar 19. [Epub ahead of print]

Mutations in QARS, encoding glutaminyl-tRNA synthetase, cause progressive microcephaly, cerebral-cerebellar atrophy, and intractable seizures.
Zhang X, Ling J, Barcia G, Jing L , et al.
Am J Hum Genet. 2014 Mar 18. [Epub ahead of print]

Whole DNA methylome profiling in lung cancer cells before and after epithelial-to-mesenchymal transition.
Liu F, Zhou Y, Zhou D, Kan M, et al.
Diagn Pathol. 2014 Mar 20;9(1):66.

Somatic activating ARAF mutations in Langerhans cell histiocytosis.
Nelson DS, Quispel W, Badalian-Very G, van Halteren AG, et al. Blood. 2014 Mar 20. [Epub ahead of print]

Autosomal recessive cone-rod dystrophy associated with compound heterozygous mutations in the EYS gene.
Katagiri S, Akahori M, Hayashi T, Yoshitake K, et al.
Doc Ophthalmol. 2014 Mar 21. [Epub ahead of print]

Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway.
Enns GM, Shashi V, Bainbridge M, Gambello MJ, et al.
Genet Med. 2014 Mar 20. [Epub ahead of print]

Homozygous mutation of MTPAP causes cellular radiosensitivity and persistent DNA double-strand breaks.
Martin NT, Nakamura K, Paila U, Woo J, et al.
Cell Death Dis. 2014 Mar 20;5:e1130.

Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.
Wu J, Li Y, Jiang R.
PLOS Genet. 2014 Mar 20;10(3):e1004237.

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.
Kool M, Jones DT, Jäger N, Northcott PA, et al.
Cancer Cell. 2014 Mar 17;25(3):393-405.

De novo SCN2A splice site mutation in a boy with Autism spectrum disorder.
Tavassoli T, Kolevzon A, Wang AT, Curchack-Lichtin J, Halpern D , Schwartz L, Soffes S,
BMC Med Genet. 2014 Mar 20;15(1):35.

Deriving group A Streptococcus typing information from short-read whole genome sequencing data.
Athey TB, Teatero S, Li A, Marchand-Austin A, et al.
J Clin Microbiol. 2014 Mar 19. [Epub ahead of print]

Detection of chromosomal aneuploidy in human pre-implantation embryos by next generation sequencing.
Wang L, Wang X, Zhang J, Song Z, et al.
Biol Reprod. 2014 Mar 19. [Epub ahead of print]

MMP13 mutations are the cause of recessive metaphyseal dysplasia, Spahr type.
Bonafé L, Liang J, Gorna MW, Zhang Q, et al.
Am J Med Genet A. 2014 Mar 19. [Epub ahead of print]

Unexpected exome sequencing result: De novo TRPS1 mutation in an infant with infantile scoliosis, mild developmental delay, and history of consanguinity.
Casci I, Accousti W, Lacassie Y.
Am J Med Genet A. 2014 Mar 19. [Epub ahead of print]

NTRK1 fusion in glioblastoma multiforme.
Kim J, Lee Y, Cho HJ, Lee YE, et al.
PLOS One. 2014 Mar 19;9(3):e91940.

Congenital lethal motor neuron disease with a novel defect in ribosome biogenesis.
Butterfield RJ, Stevenson TJ, Xing L, Newcomb TM, et al.
Neurology. 2014 Mar 19. [Epub ahead of print]

Prognostic value of deep sequencing method for minimal residual disease detection in multiple myeloma.
Martinez-Lopez J, Lahuerta JJ, Pepin F, González M, et al.
Blood. 2014 Mar 19. [Epub ahead of print]

The global landscape of intron retentions in lung adenocarcinoma.
Zhang Q, Li H, Jin H, Tan H, et al.
BMC Med Genomics. 2014 Mar 20;7(1):15.

The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine.
Vassy JL, Lautenbach DM, McLaughlin HM, Kong SW, et al.
Trials. 2014 Mar 20;15(1):85.

Sources of individual variability: miRNAs that predispose to neuropathic pain identified using genome-wide sequencing.
Bali KK, Hackenberg M, Lubin A, Kuner R, Devor M.
Mol Pain. 2014 Mar 19;10(1):22.

Autosomal dominant polycystic kidney disease caused by somatic and germline mosaicism.
Tan AY, Blumenfeld J, Michaeel A, Donahue S, et al.
Clin Genet. 2014 Mar 18. [Epub ahead of print]

Differential microRNA expression by Solexa sequencing in the sera of ovarian cancer patients.
Ji T1, Zheng ZG, Wang FM, Xu LJ, et al.
Asian Pac J Cancer Prev. 2014;15(4):1739-1743.

TBX1 mutation identified by exome sequencing in a Japanese family with 22q11.2 deletion syndrome-like craniofacial features and hypocalcemia.
Ogata T, Niihori T, Tanaka N, Kawai M, et al.
PLOS One. 2014 Mar 17;9(3):e91598.

Somatic mosaicism in a Cornelia de Lange syndrome patient with NIPBL mutation identified by different next generation sequencing approaches.
Baquero-Montoya C1, Gil-Rodríguez MC, Braunholz D, Teresa-Rodrigo ME, Obieglo C,
Clin Genet. 2014 Jan 26. [Epub ahead of print]

Mosaic KCNJ2 mutation in Andersen-Tawil syndrome: targeted deep sequencing is useful for the detection of mosaicism.
Hasegawa K, Ohno S, Kimura H, Itoh H, et al.
Clin Genet. 2014 Feb 7. [Epub ahead of print]

Integrated next generation sequencing and Avatar mouse models for personalized cancer treatment.
Garralda E, Paz K, López-Casas PP, Jones S, et al.
Clin Cancer Res. 2014 Mar 14. [Epub ahead of print]

Discovery of somatic mutations in the progression of chronic myeloid leukemia by whole-exome sequencing.
Huang Y, Zheng J, Hu JD, Wu YA, et al.
Genet Mol Res. 2014 Feb 19;13(1):945-53.

Whole-genome sequencing of an aggressive BRAF wild-type papillary thyroid cancer identified EML4-ALK translocation as a therapeutic target.
Demeure MJ, Aziz M, Rosenberg R, Gurley SD, et al.
World J Surg. 2014 Mar 15. [Epub ahead of print]

PyClone: statistical inference of clonal population structure in cancer.
Roth A, Khattra J, Yap D, Wan A, et al.
Nat Methods. 2014 Mar 16. [Epub ahead of print]

Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma.
Meerzaman DM, Yan C, Chen QR, Edmonson MN, et al.
Cancer Genomics Proteomics. 2014 Jan-Feb;11(1):1-12.

Recurrent PTPRB and PLCG1 mutations in angiosarcoma.
Behjati S, Tarpey PS, Sheldon H, Martincorena I, et al.
Nat Genet. 2014 Mar 16. [Epub ahead of print]

Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients.
Walker BA, Wardell CP, Brioli A, Boyle E, et al.
Blood Cancer J. 2014 Mar 14;4:e191.

Exome sequencing analysis identifies compound heterozygous mutation in ABCA4 in a Chinese family with Stargardt disease.
Zhou Y, Tao S, Chen H, Huang L, et al.
PLOS One. 2014 Mar 14;9(3):e91962.

Whole-exome sequence analysis of ataxia telangiectasia-like phenotype.
Hasegawa S, Imai K, Yoshida K, Okuno Y, et al.
J Neurol Sci. 2014 Mar 4. [Epub ahead of print]

Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing.
McFadden DG, Papagiannakopoulos T, Taylor-Weiner A, Stewart C, et al.
Cell. 2014 Mar 13;156(6):1298-311.

Deep sequencing reveals myeloma cells in peripheral blood in majority of multiple myeloma patients.
Vij R, Mazumder A, Klinger M, O'Dea D, et al.
Clin Lymphoma Myeloma Leuk. 2014 Apr;14(2):131-139.e1.

Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma.
Jeck WR, Parker J, Carson CC, Shields JM, et al.
Pigment Cell Melanoma Res. 2014 Mar 15. [Epub ahead of print]

Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines.
Sen SK, Barb JJ, Cherukuri PF, Accame DS, et al.
BMC Genomics. 2014 Mar 14;15(1):198.

Whole exome analysis identifies dominant COL4A1 mutations in patients with complex ocular phenotypes involving microphthalmia.
Deml B, Reis LM, Maheshwari M, Griffis C, et al.
Clin Genet. 2014 Mar 14. [Epub ahead of print]