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Last Week's Clinical Sequencing Papers of Note: Feb 11, 2014

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Phenotypic expansion of DGKE-associated diseases.
Westland R, Bodria M, Carrea A, Lata S, et al.
J Am Soc Nephrol. 2014 Feb 7. [Epub ahead of print]


Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling.
Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, et al.
J Immunol. 2014 Feb 7. [Epub ahead of print]


Distinguishing hypertrophic cardiomyopathy-associated mutations from background genetic noise.
Kapplinger JD, Landstrom AP, Bos JM, Salisbury BA, et al.
J Cardiovasc Transl Res. 2014 Feb 8. [Epub ahead of print]


Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge.
Kassahn KS, Scott HS, Caramins MC.
Hum Mutat. 2014 Feb 7. [Epub ahead of print]


Integrated analysis of cancer-related pathways affected by genetic and epigenetic alterations in gastric cancer.
Yoda Y, Takeshima H, Niwa T, Kim JG, et al.
Gastric Cancer. 2014 Feb 9. [Epub ahead of print]


Dense genomic sampling identifies highways of pneumococcal recombination.
Chewapreecha C, Harris SR, Croucher NJ, Turner C, et al.
Nat Genet. 2014 Feb 9. [Epub ahead of print]


Identification of functional cooperative mutations of SETD2 in human acute leukemia.
Zhu X, He F, Zeng H, Ling S, et al.
Nat Genet. 2014 Feb 9. [Epub ahead of print]


5'RNA-seq identifies Fhl1 as a genetic modifier in cardiomyopathy.
Christodoulou DC, Wakimoto H, Onoue K, Eminaga S, et al.
J Clin Invest. 2014 Feb 10. [Epub ahead of print]


Molecular characterization of gallbladder cancer using somatic mutation profiling.
Javle M, Rashid A, Churi C, Kar S, et al.
Hum Pathol. 2013 Nov 12. [Epub ahead of print]


Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol.
Lange LA, Hu Y, Zhang H, Xue C, et al.
Am J Hum Genet. 2014 Feb 6;94(2):233-45.


Panel-based testing for inherited colorectal cancer: a descriptive study of clinical testing performed by a U.S. laboratory.
Cragun D, Radford C, Dolinsky J, Caldwell M, et al.
Clin Genet. 2014 Feb 9. [Epub ahead of print]


Evaluation of whole genome sequencing for outbreak detection of Salmonella enteric.
Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM.
PLOS One. 2014 Feb 4;9(2):e87991.


Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.
Egan JB, Barrett MT, Champion MD, Middha S, et al.
PLOS One. 2014 Feb 5;9(2):e87113.


From days to hours: reporting clinically actionable variants from whole genome sequencing.
Middha S, Baheti S, Hart SN, Kocher JP.
PLOS One. 2014 Feb 5;9(2):e86803.


Tissue-specific RNA-seq in human evoked inflammation identifies blood and adipose lincRNA signatures of cardiometabolic diseases.
Liu Y, Ferguson JF, Xue C, Ballantyne RL, et al.
Arterioscler Thromb Vasc Biol. 2014 Feb 6. [Epub ahead of print]


Mutations in WDR19 encoding the intraflagellar transport component IFT144 cause a broad spectrum of ciliopathies.
Fehrenbach H, Decker C, Eisenberger T, Frank V, et al.
Pediatr Nephrol. 2014 Feb 7. [Epub ahead of print]


Next generation sequencing improves the accuracy of KRAS mutation analysis in endoscopic ultrasound fine needle aspiration pancreatic lesions.
de Biase D, Visani M, Baccarini P, Polifemo AM, et al.
PLOS One. 2014 Feb 4;9(2):e87651.


Whole genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition.
Turajlic S, Furney SJ, Stamp G, Rana S, et al.
Ann Oncol. 2014 Feb 6. [Epub ahead of print]


Multilayer-omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome.
Arai E, Sakamoto H, Ichikawa H, Totsuka H, et al.
Int J Cancer. 2014 Feb 6. [Epub ahead of print]


Clinical characteristics of ovarian cancer classified by BRCA1, BRCA2, and RAD51C status.
Cunningham JM, Cicek MS, Larson NB, Davila J, et al.
Sci Rep. 2014 Feb 7;4:4026.


The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing.
Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, et al.
Genet Med. 2014 Feb 6. [Epub ahead of print]


Atypical Alstrom syndrome with novel ALMS1 mutations precluded by current diagnostic criteria.
Casey J, McGettigan P, Brosnahan D, Curtis E, et al.
Eur J Med Genet. 2014 Feb 3. [Epub ahead of print]


LipidSeq: a next-generation clinical resequencing panel for monogenic dyslipidemias.
Johansen CT, Dube JB, Loyzer MN, Macdonald A, et al.
J Lipid Res. 2014 Feb 6. [Epub ahead of print]


Activating mutations in PTPN3 promote cholangiocarcinoma cell proliferation and migration and are associated with tumor recurrence in patients.
Gao Q, Zhao YJ, Wang XY, Guo WJ, et al.
Gastroenterology. 2014 Feb 3. [Epub ahead of print]


X chromosome exome sequencing reveals a novel ALG13 mutation in a nonsyndromic intellectual disability family with multiple affected male siblings.
Bissar-Tadmouri N, Donahue WL, Al-Gazali L, Nelson SF, et al.
Am J Med Genet A. 2014 Jan;164A(1):164-9.


Whole exome sequencing is an efficient, sensitive and specific method of mutation detection in osteogenesis imperfecta and Marfan syndrome.
McInerney-Leo AM, Marshall MS, Gardiner B, Coucke PJ, et al.
Bonekey Rep. 2013 Dec 4;2:456.


Exome sequencing identifies de novo gain of function missense mutation in KCND2 in identical twins with autism and seizures that slows potassium channel inactivation.
Lee H, Lin MC, Kornblum HI, Papazian DM, Nelson SF.
Hum Mol Genet. 2014 Feb 5. [Epub ahead of print]


Ubiquitin ligase defect by DCAF8 mutation causes HMSN2 with giant axons.
Klein CJ, Wu Y, Vogel P, Goebel HH, et al.
Neurology. 2014 Feb 5. [Epub ahead of print]


Multiple phenotypes in phosphoglucomutase 1 deficiency.
Tegtmeyer LC, Rust S, van Scherpenzeel M, Ng BG, et al.
N Engl J Med. 2014 Feb 6;370(6):533-42.


Exome sequencing identifies NFS1 deficiency in a novel Fe-S cluster disease, infantile mitochondrial complex II/III deficiency.
Farhan SM, Wang J, Robinson JF, Lahiry P, et al.
Mol Genet Genomic Med. 2014 Jan;2(1):73-80.


Identification and validation of loss of function variants in clinical contexts.
Lescai F, Marasco E, Bacchelli C, Stanier P, et al.
Mol Genet Genomic Med. 2014 Jan;2(1):58-63.


Experience of targeted Usher exome sequencing as a clinical test.
Besnard T, García-García G, Baux D, Vaché C, et al.
Mol Genet Genomic Med. 2014 Jan;2(1):30-43.


Next-generation DNA sequencing of HEXA: a step in the right direction for carrier screening.
Hoffman JD, Greger V, Strovel ET, Blitzer MG, et al.
Mol Genet Genomic Med. 2013 Nov;1(4):260-8.


Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases.
Spinelli R, Pirola A, Redaelli S, Sharma N, et al.
Mol Genet Genomic Med. 2013 Nov;1(4):246-59.


Mutations in the interleukin receptor IL11RA cause autosomal recessive Crouzon-like craniosynostosis.
Keupp K, Li Y, Vargel I, Hoischen A, et al.
Mol Genet Genomic Med. 2013 Nov;1(4):223-37.


Genome-wide linkage, exome sequencing and functional analyses identify ABCB6 as the pathogenic gene of dyschromatosis universalis hereditaria.
Liu H, Li Y, Hung KK, Wang N, et al.
PLOS One. 2014 Feb 3;9(2):e87250.


Megalencephaly syndromes: exome pipeline strategies for detecting low-level mosaic mutations.
Tapper WJ, Foulds N, Cross NC, Aranaz P, et al.
PLOS One. 2014 Jan 31;9(1):e86940.


PLCG1 mutations in cutaneous T-cell lymphomas.
Vaqué JP, Gómez-López G, Monsálvez V, Varela I, et al.
Blood. 2014 Feb 4. [Epub ahead of print]


Placental mosaicism for trisomy 13: a challenge in providing the cell-free fetal DNA testing.
Liu XY, Zhang HG, Wang RX, Chen S, et al.
J Assist Reprod Genet. 2014 Feb 5. [Epub ahead of print]


Exome sequencing reveals a heterozygous DLX5 mutation in a Chinese family with autosomal-dominant split-hand/foot malformation.
Wang X, Xin Q, Li L, Li J, et al.
Eur J Hum Genet. 2014 Feb 5. [Epub ahead of print]


Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease.
Poole A, Urbanek C, Eng C, Schageman J, et al.
J Allergy Clin Immunol. 2014 Feb 1. [Epub ahead of print]


Tracing the development of acute myeloid leukemia in CBL syndrome.
Becker H, Yoshida K, Blagitko-Dorfs N, Claus R, et al.
Blood. 2014 Feb 3. [Epub ahead of print]


Accurate fetal chromosome dosage determination by shotgun sequencing of maternal plasma DNA without PCR amplification during library preparation.
Jin S, Lim YC, Ng DP, Law HY, et al.
Clin Chem. 2014 Feb 3. [Epub ahead of print]


On the reproducibility of TCGA ovarian cancer microRNA profiles.
Wan YW, Mach CM, Allen GI, Anderson ML, Liu Z.
PLOS One. 2014 Jan 29;9(1):e87782.


Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery.
Chandrananda D, Thorne NP, Ganesamoorthy D, Bruno DL, et al.
PLOS One. 2014 Jan 29;9(1):e86993.


The personal human oral microbiome obscures the effects of treatment on periodontal disease.
Schwarzberg K, Le R, Bharti B, Lindsay S, et al.
PLOS One. 2014 Jan 29;9(1):e86708.


Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer.
Teles Alves I, Hartjes T, McClellan E, Hiltemann S, et al.
Oncogene. 2014 Feb 3. [Epub ahead of print]


Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing.
Gerlinger M, Horswell S, Larkin J, Rowan AJ, et al.
Nat Genet. 2014 Feb 2. [Epub ahead of print]


Exome sequencing identified new mutations in a Marfan syndrome family.
Li G, Yu J, Wang K, Wang B, et al.
Diagn Pathol. 2014 Jan 31;9(1):25.

The Scan

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people over 65 or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.