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In Print: Last Week's Clinical Sequencing Papers of Note: Jun 26, 2013


Whole genome sequencing identifies recurrent mutations in hepatocellular carcinoma.
Kan Z, Zheng H, Liu X, Li S, et al.
Genome Res. 2013 Jun 20. [Epub ahead of print]

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
Green RC, Berg JS, Grody WW, Kalia SS, et al.
Genet Med. 2013 Jun 20. [Epub ahead of print]

Identification of functional variants from whole-exome sequencing, combined with neuroimaging genetics.
Nho K, Corneveaux JJ, Kim S, Lin H, et al.
Mol Psychiatry. 2013 Jul;18(7):739.

Exome analysis reveals a Japanese family with spinocerebellar ataxia, autosomal recessive 1.
Ichikawa Y, Ishiura H, Mitsui J, Takahashi Y, et al.
J Neurol Sci. 2013 Jun 17. [Epub ahead of print]

Novel SACS mutations identified by whole exome sequencing in a Norwegian family with autosomal recessive spastic ataxia of Charlevoix-Saguenay.
Tzoulis C, Johansson S, Haukanes BI, Boman H, et al.
PLoS One. 2013 Jun 13;8(6):e66145.

Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics.
Mook OR, Haagmans MA, Soucy JF, van de Meerakker JB, et al.
J Med Genet. 2013 Jun 19. [Epub ahead of print]

Reflecting on earlier experiences with unsolicited findings: Points to consider for next generation sequencing and informed consent in diagnostics.
Rigter T, Henneman L, Kristoffersson U, Hall A, et al.
Hum Mutat. 2013 Jun 19. [Epub ahead of print]

In-depth characterization of the microRNA transcriptome in normal thyroid and papillary thyroid carcinoma.
Swierniak M, Wojcicka A, Czetwertynska M, Stachlewska E, et al.
J Clin Endocrinol Metab. 2013 Jun 19. [Epub ahead of print]

A sensitive and accurate protein domain classification tool (SALT) for short reads.
Zhang Y, Sun Y, Cole JR.
Bioinformatics. 2013 Jun 19. [Epub ahead of print]

SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies.
Chung RH, Shih CC.
BMC Bioinformatics. 2013 Jun 20;14(1):199.

Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma.
Crona J, Verdugo AD, Granberg D, Welin S, et al.
Endocr Connect. 2013 May 28;2(2):104-11.

Deep sequencing of the transcriptome reveals inflammatory features of porcine visceral adipose tissue.
Wang T, Jiang A, Guo Y, Tan Y, et al.
Int J Biol Sci. 2013 Jun 9;9(6):550-6.

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.
Bashashati A, Ha G, Tone A, Ding J, et al.
J Pathol. 2013 Jun 18. [Epub ahead of print]

Whole exome sequencing of adenoid cystic carcinoma.
Stephens PJ, Davies HR, Mitani Y, Van Loo P, et al.
J Clin Invest. 2013 Jun 17. [Epub ahead of print]

Distinct microRNAs expression profile in primary biliary cirrhosis and evaluation of miR 505-3p and miR197-3p as novel biomarkers.
Ninomiya M, Kondo Y, Funayama R, Nagashima T, et al.
PLoS One. 2013 Jun 12;8(6):e66086.

Exome sequencing of 47 Chinese families with cone-rod dystrophy: mutations in 25 known causative genes.
Huang L, Zhang Q, Li S, Guan L, et al.
PLoS One. 2013 Jun 11;8(6):e65546.

Best practice guidelines for the use of next generation sequencing (NGS) applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories.
Weiss MM, Van der Zwaag B, Jongbloed JD, Vogel MJ, et al.
Hum Mutat. 2013 Jun 17. [Epub ahead of print]

HOXA2 haploinsufficiency in dominant bilateral microtia and hearing loss.
Brown KK, Viana LM, Helwig CC, Artunduaga MA, et al.
Hum Mutat. 2013 Jun 17. [Epub ahead of print]

A capture-sequencing strategy identifies IRF8, EBF1 and APRIL as novel IGH fusion partners in B-cell lymphoma.
Bouamar H, Abbas S, Lin AP, Wang L, et al.
Blood. 2013 Jun 17. [Epub ahead of print]

Familial rhabdoid tumour "avant la lettre" - from pathology review to exome sequencing and back again.
Witkowski L, Lalonde E, Zhang J, Albrecht S, et al.
J Pathol. 2013 Jun 14. [Epub ahead of print]

A comprehensive assay for CFTR mutational analysis using next-generation sequencing.
Abou Tayoun AN, Tunkey CD, Pugh TJ, Ross T, et al.
Clin Chem. 2013 Jun 17. [Epub ahead of print]

Next-generation sequencing analysis of gene regulation in the rat model of retinopathy of prematurity.
Griffith RM, Li H, Zhang N, Favazza TL, et al.
Doc Ophthalmol. 2013 Jun 18. [Epub ahead of print]

Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers.
Huang RL, Gu F, Kirma NB, Ruan J, et al.
Epigenetics. 2013 May 10;8(6).

Mutational landscape of basal cell carcinomas by whole exome sequencing.
Jayaraman SS, Rayhan DJ, Hazany S, Kolodney MS.
J Invest Dermatol. 2013 Jun 17. [Epub ahead of print]

Whole exome sequence analysis of serous borderline tumors of the ovary.
Boyd J, Luo B, Peri S, Wirchansky B, et al.
Gynecol Oncol. 2013 Jun 14. [Epub ahead of print]

Exome sequencing identification of a GJB1 missense mutation in a kindred with X-linked spinocerebellar ataxia (SCA-X1).
Caramins M, Colebatch JG, Bainbridge MN, Scherer SS, et al.
Hum Mol Genet. 2013 Jun 16. [Epub ahead of print]

Two homozygous nonsense mutations of GNPTAB gene in two Chinese families with mucolipidosis II alpha/beta using targeted next-generation sequencing.
Yang Y, Wu J, Liu H, Chen X, et al.
Genomics. 2013 Jun 14. [Epub ahead of print]

Analysis of hepatitis B virus genotyping and drug resistance gene mutations based on massively parallel sequencing.
Han Y, Zhang Y, Mei Y, Wang Y, et al.
J Virol Methods. 2013 Jun 14. [Epub ahead of print]

Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients.
Das S, Roychowdhury T, Kumar P, Kumar A, et al.
BMC Genomics. 2013 Jun 17;14(1):404.

Large scale pooled next-generation sequencing of 1077 genes to identify genetic causes of short stature.
Wang SR, Carmichael H, Andrew SF, Miller TC, et al.
J Clin Endocrinol Metab. 2013 Jun 14. [Epub ahead of print]

Improved genetic testing for monogenic diabetes using targeted next-generation sequencing.
Ellard S, Lango Allen H, De Franco E, Flanagan SE, et al.
Diabetologia. 2013 Jun 15. [Epub ahead of print]

Genetic analysis through OtoSeq of Pakistani families segregating prelingual hearing loss.
Shahzad M, Sivakumaran TA, Qaiser TA, Schultz JM, et al.
Otolaryngol Head Neck Surg. 2013 Jun 14. [Epub ahead of print]

Whole-genome sequence-based analysis of high-density lipoprotein cholesterol.
the Cohorts for Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium, Morrison AC, Voorman A, et al.
Nat Genet. 2013 Jun 16. [Epub ahead of print]

Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Lawrence MS, Stojanov P, Polak P, Kryukov GV, et al.
Nature. 2013 Jun 16. [Epub ahead of print]

Mutations in KARS, encoding lysyl-tRNA synthetase, cause autosomal-recessive nonsyndromic hearing impairment DFNB89.
Santos-Cortez RL, Lee K, Azeem Z, Antonellis PJ, et al.
Am J Hum Genet. 2013 Jun 12. [Epub ahead of print]

Mutations in GDP-mannose pyrophosphorylase B cause congenital and limb-girdle muscular dystrophies associated with hypoglycosylation of α-dystroglycan.
Carss KJ, Stevens E, Foley AR, Cirak S, et al.
Am J Hum Genet. 2013 Jun 11. [Epub ahead of print]

Genetic etiology study of the non-syndromic deafness in Chinese Hans by targeted next-generation sequencing.
Yang T, Wei X, Chai Y, Li L, Wu H.
Orphanet J Rare Dis. 2013 Jun 14;8(1):85.