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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.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.