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Last Week's Clinical Sequencing Papers of Note: Apr 9, 2014


Whole-genome sequencing and the clinician: a tale of two cities.
Foley AR, Pitceathly RD, He J, Kim J, et al.
J Neurol Neurosurg Psychiatry. 2014 Apr 4. [Epub ahead of print]

Mutations in the enzyme glutathione peroxidase 4 cause Sedaghatian-type spondylometaphyseal dysplasia.
Smith AC, Mears AJ, Bunker R, Ahmed A, et al.
J Med Genet. 2014 Apr 4. [Epub ahead of print]

Whole-exome sequencing reveals LRP5 mutations and canonical Wnt signaling associated with hepatic cystogenesis.
Cnossen WR, Te Morsche RH, Hoischen A, Gilissen C, et al.
Proc Natl Acad Sci U S A. 2014 Mar 24. [Epub ahead of print]

Cancer beyond organ and tissue specificity: next-generation-sequencing gene mutation data reveal complex genetic similarities across major cancers.
Heim D, Budczies J, Stenzinger A, Treue D, et al.
Int J Cancer. 2014 Apr 7. [Epub ahead of print]

First trimester diagnosis of Meckel-Gruber syndrome by fetal ultrasound, with molecular identification of CC2D2A mutations by next-generation sequencing.
Jones D, Fiozzo F, Waters B, McKnight D, Brown S.
Ultrasound Obstet Gynecol. 2014 Apr 4. [Epub ahead of print]

PIGA mutations cause early-onset epileptic encephalopathies and distinctive features.
Kato M, Saitsu H, Murakami Y, Kikuchi K, et al.
Neurology. 2014 Apr 4. [Epub ahead of print]

Mutation spectrum of six genes in Chinese phenylketonuria patients obtained through next-generation sequencing.
Gu Y, Lu K, Yang G, Cen Z, et al.
PLOS One. 2014 Apr 4;9(4):e94100.

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage.
Newman AM, Bratman SV, To J, Wynne JF, et al.
Nat Med. 2014 Apr 6. [Epub ahead of print]

Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations.
Buczkowicz P, Hoeman C, Rakopoulos P, Pajovic S, et al.
Nat Genet. 2014 Apr 6. [Epub ahead of print]

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma.
the St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project, Wu G, Diaz AK, Paugh BS, Rankin SL, et al.
Nat Genet. 2014 Apr 6. [Epub ahead of print]

Recurrent somatic mutations in ACVR1 in pediatric midline high-grade astrocytoma.
Fontebasso AM, Papillon-Cavanagh S, Schwartzentruber J, Nikbakht H, et al.
Nat Genet. 2014 Apr 6. [Epub ahead of print]

Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data.
Cimino PJ, Zhao G, Wang D, Sehn JK, et al.
Exp Mol Pathol. 2014 Apr 1. [Epub ahead of print]

Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma.
Chen X, Bahrami A, Pappo A, Easton J, et al.
Cell Rep. 2014 Apr 2. [Epub ahead of print]

Rare variants in NR2F2 cause congenital heart defects in humans.
Al Turki S, Manickaraj AK, Mercer CL, Gerety SS, et al.
Am J Hum Genet. 2014 Apr 3;94(4):574-85.

Whole exome sequencing reveals TOPBP1 as a novel gene in idiopathic pulmonary arterial hypertension.
de Jesus Perez VA, Yuan K, Lyuksyutova MA, Dewey F, et al.
Am J Respir Crit Care Med. 2014 Apr 4. [Epub ahead of print]

Mild recessive mutations in six Fraser syndrome-related genes cause isolated congenital anomalies of the kidney and urinary tract.
Kohl S, Hwang DY, Dworschak GC, Hilger AC, et al.
J Am Soc Nephrol. 2014 Apr 3. [Epub ahead of print]

Autosomal recessive spastic tetraplegia caused by AP4M1 and AP4B1 gene mutation: Expansion of the facial and neuroimaging features.
Tüysüz B, Bilguvar K, Koçer N, Yalçınkaya C, et al.
Am J Med Genet A. 2014 Apr 3. [Epub ahead of print]

A novel EBP c.224T>A mutation supports the existence of a male-specific disorder independent of CDPX2.
Barboza-Cerda MC, Wong LJ, Martínez-de-Villarreal LE, Zhang VW, Déctor MA.
Am J Med Genet A. 2014 Apr 3. [Epub ahead of print]

Gain-of-function ADCY5 mutations in familial dyskinesia with facial myokymia.
Chen YZ, Friedman JR, Chen DH, Chan GC, et al.
Pham Ann Neurol. 2014 Feb 15. [Epub ahead of print]

A novel homozygous ERCC5 truncating mutation in a family with prenatal arthrogryposis-Further evidence of genotype-phenotype correlation.
Drury S, Boustred C, Tekman M, Stanescu H, et al.
Am J Med Genet A. 2014 Apr 3. [Epub ahead of print]

Activating hotspot L205R mutation in PRKACA and adrenal Cushing's syndrome.
Cao Y, He M, Gao Z, Peng Y, et al.
Science. 2014 Apr 3. [Epub ahead of print]

CTNNB1 mutational analysis of solid-pseudopapillary neoplasms of the pancreas using endoscopic ultrasound-guided fine-needle aspiration and next-generation deep sequencing.
Kubota Y, Kawakami H, Natsuizaka M, Kawakubo K, et al.
J Gastroenterol. 2014 Apr 4. [Epub ahead of print]

Deep sequencing to identify the causes of viral encephalitis.
Chan BK, Wilson T, Fischer KF, Kriesel JD.
PLOS One. 2014 Apr 3;9(4):e93993.

Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing.
Yu C, Yu J, Yao X, Wu WK, et al.
Cell Res. 2014 Apr 4. [Epub ahead of print]

Lessons from whole-exome sequencing in MODYX families.
Dusatkova P, Fang M, Pruhova S, Gjesing AP, et al.
Diabetes Res Clin Pract. 2014 Mar 19. [Epub ahead of print]

Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels.
Sassi A, Lazaroski S, Wu G, Haslam SM, et al.
J Allergy Clin Immunol. 2014 Apr 1. [Epub ahead of print]

Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011-2013.
Schmid D, Allerberger F, Huhulescu S, Pietzka A, et al.
Clin Microbiol Infect. 2014 Apr 3. [Epub ahead of print]

Exome sequencing extends the phenotypic spectrum for ABHD12 mutations: from syndromic to nonsyndromic retinal degeneration.
Nishiguchi KM, Avila-Fernandez A, van Huet RA, Corton M, et al.
Ophthalmology. 2014 Mar 31. [Epub ahead of print]

De novo EEF1A2 mutations in patients with characteristic facial features, intellectual disability and, autistic behaviors and epilepsy.
Nakajima J, Okamoto N, Tohyama J, Kato M, et al.
Clin Genet. 2014 Apr 3. [Epub ahead of print]

Multigene profiling to identify alternative treatment options for glioblastoma: a pilot study.
Tabone T, Abuhusain HJ, Nowak AK; Australian Genomics and Clinical Outcome of Glioma (AGOG) Network, et al.
J Clin Pathol. 2014 Apr 2. [Epub ahead of print]

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.
Li Y, Xie X.
Bioinformatics. 2014 Apr 2. [Epub ahead of print]

Rare germline mutations identified by targeted next-generation sequencing of susceptibility genes in pheochromocytoma and paraganglioma.
Welander J, Andreasson A, Juhlin CC, Wiseman RW, et al.
J Clin Endocrinol Metab. 2014 Apr 2 [Epub ahead of print]

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder.
Davies MN, Krause L, Bell JT, Gao F, et al.
Genome Biol. 2014 Apr 2;15(4):R56.

Exome sequencing identifies MUTYH mutations in a family with colorectal cancer and an atypical phenotype.
Seguí N, Navarro M, Pineda M, Köger N, et al.
Gut. 2014 Apr 1. [Epub ahead of print]

Epithelial inflammation resulting from an inherited loss-of-function mutation in EGFR.
Campbell P, Morton P, Takeichi T, Salam A, et al.
J Invest Dermatol. 2014 Apr 1. [Epub ahead of print]

Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene panel.
Brett M, McPherson J, Zang ZJ, Lai A, et al.
PLOS One. 2014 Apr 1;9(4):e93409.

Novel TBL1XR1, EPHA7 and SLFN12 mutations in a Sezary syndrome patient discovered by whole exome sequencing.
Andersson E, Eldfors S, Edgren H, Ellonen P, et al.
Exp Dermatol. 2014 Apr 1. [Epub ahead of print]

A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes.
Hansen MF, Neckmann U, Lavik LA, Vold T, et al.
Mol Genet Genomic Med. 2014 Mar;2(2):186-200.

Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet-Biedl family.
González-Del Pozo M, Méndez-Vidal C, Santoyo-Lopez J, Vela-Boza A, et al.
Mol Genet Genomic Med. 2014 Mar;2(2):124-33.

A novel transcript, VNN1-AB, as a biomarker for colorectal cancer.
Løvf M, Nome T, Bruun J, Eknaes M, et al.
Int J Cancer. 2014 Mar 19. [Epub ahead of print]

Evaluation of a new high-throughput next-generation sequencing method based on a custom AmpliSeq™ library and Ion Torrent PGM sequencing for the rapid detection of genetic variations in long QT syndrome.
Millat G, Chanavat V, Rousson R.
Mol Diagn Ther. 2014 Apr 1. [Epub ahead of print]

Genomic and molecular characterization of esophageal squamous cell carcinoma.
Lin DC, Hao JJ, Nagata Y, Xu L, et al.
Nat Genet. 2014 Mar 30. [Epub ahead of print]

POT1 loss-of-function variants predispose to familial melanoma.
Robles-Espinoza CD, Harland M, Ramsay AJ, Aoude LG, et al.
Nat Genet. 2014 Mar 30. [Epub ahead of print]

Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma.
Shi J, Yang XR, Ballew B, Rotunno M, et al.
Nat Genet. 2014 Mar 30. [Epub ahead of print]

Mutations in the Matrin 3 gene cause familial amyotrophic lateral sclerosis.
Johnson JO, Pioro EP, Boehringer A, Chia R, et al.
Nat Neurosci. 2014 Mar 30. [Epub ahead of print]