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Last Week's Clinical Sequencing Papers of Note: Jan 29, 2014


Polyreactive monoclonal autoantibodies in multiple sclerosis: functional selection from phage display library and characterization by deep sequencing analysis.
Lomakin YA, Zakharova MY, Belogurov AA, Bykova NA, et al.
Acta Naturae. 2013 Oct;5(4):94-104.

KSHV 2.0: A comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features.
Arias C, Weisburd B, Stern-Ginossar N, Mercier A, et al.
PLoS Pathog. 2014 Jan;10(1):e1003847.

High resolution non-invasive detection of a fetal microdeletion using the GCREM algorithm.
Chu T, Yeniterzi S, Rajkovic A, Hogge WA, et al.
Prenat Diagn. 2014 Jan 22. [Epub ahead of print]

Comprehensive microRNA profiling of prostate cancer cells after ionizing radiation treatment.
Leung CM, Li SC, Chen TW, Ho MR, et al.
Oncol Rep. 2014 Jan 21. [Epub ahead of print]

SPAG7 is a candidate gene for the periodic fever, aphthous stomatitis, pharyngitis and adenopathy (PFAPA) syndrome.
Bens S, Zichner T, Stütz AM, Caliebe A, et al.
Genes Immun. 2014 Jan 23. [Epub ahead of print]

A new TRPV3 missense mutation in a patient with Olmsted syndrome and erythromelalgia.
Duchatelet S, Pruvost S, de Veer S, Fraitag S, et al.
JAMA Dermatol. 2014 Jan 22. [Epub ahead of print]

Diagnostic utility of targeted next-generation sequencing in problematic cases.
Sehn JK, Hagemann IS, Pfeifer JD, Cottrell CE, Lockwood CM.
Am J Surg Pathol. 2014 Jan 21. [Epub ahead of print]

MePIC, Metagenomic Pathogen Identification for Clinical Specimens.
Takeuchi F, Sekizuka T, Yamashita A, Ogasawara Y, et al.
J Infect Dis. 2014;67(1):62-5.

Diagnosis of Noonan syndrome and related disorders using target next generation sequencing.
Lepri FR, Scavelli R, Digilio MC, Gnazzo M, et al.
BMC Med Genet. 2014 Jan 23;15(1):14.

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships.
McHardy IH, Goudarzi M, Tong M, Ruegger PM, et al.
Microbiome. 2013 Jun 5;1(1):17.

Identification of somatic alterations in stage I lung adenocarcinomas by next-generation sequencing.
Zhao Y, Yang J, Chen Z, Gao Z, Zhou, et al.
Genes Chromosomes Cancer. 2014 Jan 22. [Epub ahead of print]

Lynch syndrome patients' views of and preferences for return of results following whole exome sequencing.
Hitch K, Joseph G, Guiltinan J, Kianmahd J, et al.
J Genet Couns. 2014 Jan 22. [Epub ahead of print]

Somatic deletions implicated in functional diversity of brain cells of individuals with schizophrenia and unaffected controls.
Kim J, Shin JY, Kim JI, Seo JS, et al.
Sci Rep. 2014 Jan 22;4:3807.

Mitochondrial DNA variant discovery in normal-tension glaucoma patients by next-generation sequencing.
Jeoung JW, Seong MW, Park SS, Kim DM, et al.
Invest Ophthalmol Vis Sci. 2014 Jan 21. [Epub ahead of print]

Rare and private variations in neural crest, apoptosis and sarcomere genes define the polygenic background of isolated tetralogy of fallot.
Grunert M, Dorn C, Schueler M, Dunkel I, et al.
Hum Mol Genet. 2014 Jan 23. [Epub ahead of print]

Next generation sequencing of chromosomal rearrangements in patients with split-hand/split-foot malformation provides evidence for DYNC1I1 exonic enhancers of DLX5/6 expression in humans.
Lango Allen H, Caswell R, Xie W, Xu X, et al.
J Med Genet. 2014 Jan 23. [Epub ahead of print]

Sensory neuropathy with bone destruction due to a mutation in the membrane-shaping atlastin GTPase 3.
Kornak U, Mademan I, Schinke M, Voigt M, et al.
Brain. 2014 Jan 22. [Epub ahead of print]

A novel WTX mutation in a female patient with osteopathia striata with cranial sclerosis and hepatoblastoma.
Fujita A, Ochi N, Fujimaki H, Muramatsu H, et al.
Am J Med Genet A. 2014 Jan 23. [Epub ahead of print]

An individual with blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) and additional features expands the phenotype associated with mutations in KAT6B.
Yu HC, Geiger EA, Medne L, Zackai EH, Shaikh TH.
Am J Med Genet A. 2014 Jan 23. [Epub ahead of print]

Laboratory policies on reporting secondary findings in clinical whole exome sequencing: Initial uptake of the ACMG's recommendations.
Hufnagel SB, Antommaria AH.
Am J Med Genet A. 2014 Jan 23. [Epub ahead of print]

The NATA/RCPA accreditation of next generation sequencing - the story so far.
Griffin A.
Pathology. 2014 Feb;46 Suppl 1:S25.

Identification of reference genes for qRT-PCR in human lung squamous-cell carcinoma by RNA-seq.
Zhan C, Zhang Y, Ma J, Wang L, et al.
Acta Biochim Biophys Sin. 2014 Jan 23. [Epub ahead of print]

The supposed tumor suppressor gene WWOX is mutated in an early lethal microcephaly syndrome with epilepsy, growth retardation and retinal degeneration.
Abdel-Salam G, Thoenes M, Afifi HH, Körber F, et al.
Orphanet J Rare Dis. 2014 Jan 23;9(1):12. [Epub ahead of print]

Noninvasive fetal sex determination by maternal plasma sequencing and application in X-linked disorder counseling.
Pan X, Zhang C, Li X, Chen S, et al.
J Matern Fetal Neonatal Med. 2014 Jan 20. [Epub ahead of print]

Whole exome sequencing detects homozygosity for ABCA4 p.Arg602Trp missense mutation in a pediatric patient with rapidly progressive retinal dystrophy.
Ortube MC, Strom SP, Nelson SF, Nusinowitz S, et al.
BMC Med Genet. 2014 Jan 20;15(1):11.

Subclonal variant calling with multiple samples and prior knowledge.
Gerstung M, Papaemmanuil E, Campbell PJ.
Bioinformatics. 2014 Jan 16. [Epub ahead of print]

Transcriptome analysis of psoriasis in a large case-control sample: Rna-seq provides insights into disease mechanisms.
Li B, Tsoi LC, Swindell WR, Gudjonsson JE, et al.
J Invest Dermatol. 2014 Jan 17. [Epub ahead of print]

Exome analysis based molecular autopsy in cases of sudden unexplained death in the young.
Bagnall RD, K JD, Duflou J, Semsarian C.
Heart Rhythm. 2014 Jan 16. pii: S1547-5271(14)00040-X.

Mate pair sequencing of oropharyngeal squamous cell carcinomas reveals that HPV integration occurs much less frequently than in cervical cancer.
Gao G, Johnson SH, Kasperbauer JL, Eckloff BW, et al.
J Clin Virol. 2013 Dec 28. pii: S1386-6532(13)00537-4.

Missense variant in TREML2 protects against Alzheimer's disease.
Benitez BA, Jin SC, Guerreiro R, Graham R, et al.
Neurobiol Aging. 2013 Dec 21. pii: S0197-4580(13)00649-0.

Integrin alpha 8 recessive mutations are responsible for bilateral renal agenesis in humans.
Humbert C, Silbermann F, Morar B, Parisot M, et al.
Am J Hum Genet. 2014 Jan 14. pii: S0002-9297(13)00614-9.