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Recent Clinical Sequencing Papers of Note: Jun 25, 2014


Whole genome and exome sequencing of monozygotic twins with trisomy 21, discordant for a congenital heart defect and epilepsy.
Chaiyasap P, Kulawonganunchai S, Srichomthong C, Tongsima S, et al.
PLOS One. 2014 Jun 20;9(6):e100191.

The "Grep" command but not FusionMap, FusionFinder or ChimeraScan captures the CIC-DUX4 fusion gene from whole transcriptome sequencing data on a small round cell tumor with t(4;19)(q35;q13) .
Panagopoulos I, Gorunova L, Bjerkehagen B, Heim S.
PLOS One. 2014 Jun 20;9(6):e99439.

NGS nominated CELA1, HSPG2, and KCNK5 as candidate genes for predisposition to Balkan endemic nephropathy.
Toncheva D, Mihailova-Hristova M, Vazharova R, Staneva R, et al.
Biomed Res Int. 2014;2014:920723.

Whole-exome sequencing improves mutation detection in a diagnostic epidermolysis bullosa laboratory.
Takeichi T, Liu L, Fong K, Ozoemena L, et al.
Br J Dermatol. 2014 Jun 19. [Epub ahead of print]

Nicotine and oxidative stress induced exomic variations are concordant and overrepresented in cancer-associated genes.
Bavarva JH, Tae H, McIver L, Garner HR.
Oncotarget. 2014 May 28. [Epub ahead of print]

Targeted next-generation sequencing on Hirschsprung disease: a pilot study exploits DNA pooling.
Gui H, Bao JY, Tang CS, So MT, et al.
Ann Hum Genet. 2014 Jun 20. [Epub ahead of print]

Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy.
Nicole S, Chaouch A, Torbergsen T, Bauché S, et al.
Brain. 2014 Jun 20. [Epub ahead of print]

Novel recurrently mutated genes and a prognostic mutation signature in colorectal cancer.
Yu J, Wu WK, Li X, He J, et al.
Gut. 2014 Jun 20. [Epub ahead of print]

The mutational landscape of Hodgkin lymphoma cell lines determined by whole exome sequencing.
Liu Y, Razak FR, Terpstra M, Chan FC, et al.
Leukemia. 2014 Jun 20. [Epub ahead of print]

Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin.
Alakus H, Babicky ML, Ghosh P, Yost S, et al.
Genome Med. 2014 May 29;6(5):43.

Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection.
De Vlaminck I, Valantine HA, Snyder TM, Strehl C, et al.
Sci Transl Med. 2014 Jun 18;6(241):241ra77.

Emergence of resistant variants detected by ultra-deep sequencing after asunaprevir and daclatasvir combination therapy in patients infected with hepatitis C virus genotype 1.
Kosaka K, Imamura M, Hayes CN, Abe H, et al.
J Viral Hepat. 2014 Jun 19. [Epub ahead of print]

Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer.
Shanmugam V, Ramanathan RK, Lavender NA, Sinari S, et al.
BMC Med Genomics. 2014 Jun 18;7(1):36.

ALK fusion and its association with other driver gene mutations in Finnish non-small cell lung cancer patients.
Tuononen K, Kero M, Mäki-Nevala S, Sarhadi VK, et al.
Genes Chromosomes Cancer. 2014 Jun 19. [Epub ahead of print]

Novel PRKD gene rearrangements and variant fusions in cribriform adenocarcinoma of salivary gland origin.
Weinreb I, Zhang L, Tirunagari LM, Sung YS, et al.
Genes Chromosomes Cancer. 2014 Jun 18. [Epub ahead of print]

Clinical activity of FOLFIRI plus cetuximab according to extended gene mutation status by next generation sequencing: findings from the CAPRI-GOIM trial.
Ciardiello F, Normanno N, Maiello E, Martinelli E, et al.
Ann Oncol. 2014 Jun 18. [Epub ahead of print]

Loss-of-function mutations in APOC3, triglycerides, and coronary disease.
The TG and HDL Working Group of the Exome Sequencing Project, National Heart, Lung, and Blood Institute.
N Engl J Med. 2014 Jun 18. [Epub ahead of print]

Germline mutation of RPS20, encoding a ribosomal protein, causes predisposition to hereditary nonpolyposis colorectal carcinoma without DNA mismatch repair deficiency.
Nieminen TT, O'Donohue MF, Wu Y, Lohi H, et al.
Gastroenterology. 2014 Jun 15. [Epub ahead of print]

Whole exome sequencing identifies a novel splice-site mutation in ADAMTS17 in an Indian family with Weill-Marchesani syndrome.
Shah MH, Bhat V, Shetty JS, Kumar A.
Mol Vis. 2014 Jun 12;20:790-6.

Mutation analysis of pre-mRNA splicing genes in Chinese families with retinitis pigmentosa.
Pan X, Chen X, Liu X, Gao X, et al.
Mol Vis. 2014 Jun 2;20:770-9.

Novel mutations in PXDN cause microphthalmia and anterior segment dysgenesis.
Choi A, Lao R, Ling-Fung Tang P, Wan E, et al.
Eur J Hum Genet. 2014 Jun 18. [Epub ahead of print]

Germline PTPN11 and somatic PIK3CA variant in a boy with megalencephaly-capillary malformation syndrome (MCAP) — pure coincidence?
Döcker D, Schubach M, Menzel M, Spaich C, et al.
Eur J Hum Genet. 2014 Jun 18. [Epub ahead of print]

Heterozygous germline mutations in A2ML1 are associated with a disorder clinically related to Noonan syndrome.
Vissers LE, Bonetti M, Paardekooper Overman J, Nillesen WM, et al.
Eur J Hum Genet. 2014 Jun 18. [Epub ahead of print]

Rapid molecular genetic diagnosis of hypertrophic cardiomyopathy by semiconductor sequencing.
Li Z, Huang J, Zhao J, Chen C, et al.
J Transl Med. 2014 Jun 17;12(1):173.

Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing.
Xu Y, Guan L, Shen T, Zhang J, et al.
Hum Genet. 2014 Jun 18. [Epub ahead of print]

Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors.
Kim HK, Park WC, Lee KM, Hwang HL, et al.
PLOS One. 2014 Jun 17;9(6):e100089.

Exome sequencing identifies DLG1 as a novel gene for potential susceptibility to Crohn's disease in a Chinese family study.
Xu S, Zhou F, Tao J, Song L, et al.
PLOS One. 2014 Jun 17;9(6):e99807.

Synthetic lethality in ATM-deficient RAD50-mutant tumors underlie outlier response to cancer therapy.
Al-Ahmadie H, Iyer G, Hohl M, Asthana S, et al.
Cancer Discov. 2014 Jun 16. [Epub ahead of print]

Severe manifestations of hand-foot-genital syndrome associated with a novel HOXA13 mutation.
Imagawa E, Kayserili H, Nishimura G, Nakashima M, et al.
Am J Med Genet A. 2014 Jun 16. [Epub ahead of print]

A mitochondrial origin for frontotemporal dementia and amyotrophic lateral sclerosis through CHCHD10 involvement.
Bannwarth S, Ait-El-Mkadem S, Chaussenot A, Genin EC, et al.
Brain. 2014 Jun 16. [Epub ahead of print]

A novel splice site mutation in DFNA5 causes late-onset progressive non-syndromic hearing loss in a Chinese family.
Chai Y, Chen D, Wang X, Wu H, Yang T.
Int J Pediatr Otorhinolaryngol. 2014 May 21. [Epub ahead of print]

Neurofibromin deficiency-associated transcriptional dysregulation suggests a novel therapy for tibial pseudoarthrosis in NF1.
Paria N, Cho TJ, Choi IH, Kamiya N, et al.
J Bone Miner Res. 2014 Jun 16. [Epub ahead of print]

'Druggable' alterations detected by Ion Torrent in metastatic colorectal cancer patients.
Fang W, Radovich M, Zheng Y, Fu CY, et al.
Oncol Lett. 2014 Jun;7(6):1761-1766.

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
Hajirasouliha I, Mahmoody A, Raphael BJ.
Bioinformatics. 2014 Jun 15;30(12):i78-i86.

PGM3 mutations cause a congenital disorder of glycosylation with severe immunodeficiency and skeletal dysplasia.
Stray-Pedersen A, Backe PH, Sorte HS, Mørkrid L, et al.
Am J Hum Genet. 2014 Jun 11. [Epub ahead of print]

Identification of novel therapeutic targets in the PI3K/AKT/mTOR pathway in hepatocellular carcinoma using targeted next generation sequencing.
Janku F, Kaseb AO, Tsimberidou AM, Wolff RA, Kurzrock R.
Oncotarget. 2014 May 30;5(10):3012-22.

De novo CCND2 mutations leading to stabilization of cyclin D2 cause megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome.
Mirzaa GM, Parry DA, Fry AE, Giamanco KA, et al.
Nat Genet. 2014 May;46(5):510-5.

Recurrent activating ACVR1 mutations in diffuse intrinsic pontine glioma.
Taylor KR, Mackay A, Truffaux N, Butterfield YS, et al.
Nat Genet. 2014 May;46(5):457-61.

Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling.
Rice GI, del Toro Duany Y, Jenkinson EM, Forte GM, et al.
Nat Genet. 2014 May;46(5):503-9.

Recurrent SMARCA4 mutations in small cell carcinoma of the ovary.
Jelinic P, Mueller JJ, Olvera N, Dao F, et al.
Nat Genet. 2014 May;46(5):424-6.

Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.
Ramos P, Karnezis AN, Craig DW, Sekulic A, et al.
Nat Genet. 2014 May;46(5):427-9.