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In Print: Last Week's Clinical Sequencing Papers of Note: Apr 18, 2012


Distinct microRNA subcellular size and expression patterns in human cancer cells.
Chen B, Zhang B, Luo H, Yuan J, et al.
Int J Cell Biol. 2012;2012:672462.

Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in head and neck adenoid cystic carcinoma.
Persson M, Andrén Y, Moskaluk CA, Frierson HF Jr, et al.
Genes Chromosomes Cancer. 2012 Apr 16. [Epub ahead of print]

PON-P: Integrated predictor for pathogenicity of missense variants.
Olatubosun A, Väliaho J, Härkönen J, Thusberg J, Vihinen M.
Hum Mutat. 2012 Apr 13. [Epub ahead of print]

Mainzer-Saldino syndrome is a ciliopathy caused by IFT140 mutations.
Perrault I, Saunier S, Hanein S, Filhol E, et al.
Am J Hum Genet. 2012 Apr 12. [Epub ahead of print]

Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins.
Lindberg J, Klevebring D, Liu W, Neiman M, et al.
Eur Urol. 2012 Mar 31. [Epub ahead of print]

Non-invasive prenatal diagnosis of fetal aneuploidies using massively parallel sequencing-by-ligation and evidence that cell-free fetal DNA in the maternal plasma originates from cytotrophoblastic cells.
Faas BH, de Ligt J, Janssen I, Eggink AJ, et al.
Expert Opin Biol Ther. 2012 Apr 16. [Epub ahead of print]

Reorganization of the host epigenome by a viral oncogene.
Ferrari R, Su T, Li B, Bonora G, et al.
Genome Res. 2012 Apr 12. [Epub ahead of print]

Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability.
Kou Y, Betancur C, Xu H, Buxbaum JD, Ma'ayan A.
Am J Med Genet C Semin Med Genet. 2012 Apr 12. [Epub ahead of print]

Molecular diagnosis in mitochondrial complex I deficiency using exome sequencing.
Haack TB, Haberberger B, Frisch EM, Wieland T, et al.
J Med Genet. 2012 Apr;49(4):277-83.

Recessive mutations in MCM4/PRKDC cause a novel syndrome involving a primary immunodeficiency and a disorder of DNA repair.
Casey JP, Nobbs M, McGettigan P, Lynch S, Ennis S.
J Med Genet. 2012 Apr;49(4):242-5.

Genomic analysis of mitochondrial diseases in a consanguineous population reveals novel candidate disease genes.
Shamseldin HE, Alshammari M, Al-Sheddi T, Salih MA, et al.
J Med Genet. 2012 Apr;49(4):234-41.

Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains.
Pritchard L, Holden NJ, Bielaszewska M, Karch H, Toth IK.
PLoS One. 2012;7(4):e34498.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
Shah SP, Roth A, Goya R, Oloumi A, et al.
Nature. 2012 Apr 4. [Epub ahead of print]

Patterns and rates of exonic de novo mutations in autism spectrum disorders.
Neale BM, Kou Y, Liu L, Ma'ayan A, et al.
Nature. 2012 Apr 4. [Epub ahead of print]

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.
O'Roak BJ, Vives L, Girirajan S, Karakoc E, et al.
Nature. 2012 Apr 4. [Epub ahead of print]

De novo mutations revealed by whole-exome sequencing are strongly associated with autism.
Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, et al.
Nature. 2012 Apr 4. [Epub ahead of print]

Next-generation sequencing for mitochondrial diseases reveals wide diagnostic spectrum.
Vasta V, Merritt JL 2nd, Saneto RP, Hahn SH.
Pediatr Int. 2012 Apr 12. [Epub ahead of print]

Phylogenetic incongruence in E. coli O104: understanding the evolutionary relationships of emerging pathogens in the face of homologous recombination.
Hao W, Allen VG, Jamieson FB, Low DE, Alexander DC.
PLoS One. 2012;7(4):e33971.

Phenotypic diversity in type 1 Gaucher disease: discovering the genetic basis of Gaucher disease/hematological malignancy phenotype by individual genome analysis.
Lo SM, Choi M, Liu J, Jain D, et al.
Blood. 2012 Apr 4. [Epub ahead of print]

Gene identification in the congenital disorders of glycosylation type I by whole-exome sequencing.
Timal S, Hoischen A, Lehle L, Adamowicz M, et al.
Hum Mol Genet. 2012 Apr 5. [Epub ahead of print]

Estimating the order of mutations during tumorigenesis from tumor genome sequencing data.
Youn A, Simon R.
Bioinformatics. 2012 Apr 6. [Epub ahead of print]

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens.
Yost SE, Smith EN, Schwab RB, Bao L, et al.
Nucleic Acids Res. 2012 Apr 6. [Epub ahead of print]

Leukoencephalopathy with thalamus and brainstem involvement and high lactate 'LTBL' caused by EARS2 mutations.
Steenweg ME, Ghezzi D, Haack T, Abbink TE, et al.
Brain. 2012 Apr 4. [Epub ahead of print]

A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies.
Gronbaek K, Muller-Tidow C, Perini G, Lehmann S, et al.
Haematologica. 2012 Apr 4. [Epub ahead of print]

The impact of genomics on public health practice: the case for change.
Zimmern RL, Khoury MJ.
Public Health Genomics. 2012;15(3-4):118-24.

Next generation sequencing fails to identify human virus sequences in cutaneous squamous cell carcinoma.
Ganzenmueller T, Yakushko Y, Kluba J, Henke-Gendo C, et al.
Int J Cancer. 2012 Apr 5. [Epub ahead of print]

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.