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In Print: Last Week's Clinical Sequencing Papers of Note: Oct 10, 2012


Next-generation sequencing reveals DGUOK mutations in adult patients with mitochondrial DNA multiple deletions.
Ronchi D, Garone C, Bordoni A, Gutierrez Rios P, et al.
Brain. 2012 Oct 4. [Epub ahead of print]

Two novel CCDC88C mutations confirm the role of DAPLE in autosomal recessive congenital hydrocephalus.
Drielsma A, Jalas C, Simonis N, Désir J, et al.
J Med Genet. 2012 Oct 5. [Epub ahead of print]

De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia.
Xu B, Ionita-Laza I, Roos JL, Boone B, et al.
Nat Genet. 2012 Oct 3. [Epub ahead of print]

Whole-exome capture and sequencing identifies HEATR2 mutation as a cause of primary ciliary dyskinesia.
Horani A, Druley TE, Zariwala MA, Patel AC, et al.
Am J Hum Genet. 2012 Oct 5;91(4):685-93.

Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes.
Morán I, Akerman I, van de Bunt M, Xie R, et al.
Cell Metab. 2012 Oct 3;16(4):435-48.

CSF1R mutations identified in three families with autosomal dominantly inherited leukoencephalopathy.
Mitsui J, Matsukawa T, Ishiura H, Higasa K, et al.
Am J Med Genet B Neuropsychiatr Genet. 2012 Oct 4. [Epub ahead of print]

Lifting the lid on unborn lethal Mendelian phenotypes through exome sequencing.
Shamseldin HE, Swaid A, Alkuraya FS.
Genet Med. 2012 Oct 4. [Epub ahead of print]

Identification of cross-reactive IgG antibodies from an acute HIV-1-infected patient using phage display and high-throughput sequencing technologies.
Chen W, Prabakaran P, Zhu Z, Feng Y, et al.
Exp Mol Pathol. 2012 Oct 1. [Epub ahead of print]

Non-invasive prenatal screening of fetal Down syndrome by maternal plasma DNA sequencing in twin pregnancies.
Lau TK, Jiang F, Chan MK, Zhang H, et al.
J Matern Fetal Neonatal Med. 2012 Oct 4. [Epub ahead of print]

Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units.
Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, et al.
Sci Transl Med. 2012 Oct 3;4(154):154ra135. (See our coverage of this paper here.)

Gene expression profiles in paired gingival biopsies from periodontitis-affected and healthy tissues revealed by massively parallel sequencing.
Davanian H, Stranneheim H, Båge T, Lagervall M, et al.
PLoS One. 2012;7(9):e46440.

A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients.
Kagan RM, Johnson EP, Siaw M, Biswas P, et al.
PLoS One. 2012;7(9):e46334.

The diagnostic utility of exome sequencing in Joubert syndrome and related disorders.
Tsurusaki Y, Kobayashi Y, Hisano M, Ito S, et al.
J Hum Genet. 2012 Oct 4. [Epub ahead of print]

Diagnostic exome sequencing in persons with severe intellectual disability.
de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, et al.
N Engl J Med. 2012 Oct 3. [Epub ahead of print] (See our coverage of this paper here.)

Molecular analysis of the breast cancer genes BRCA1 and BRCA2 using amplicon-based massive parallel pyrosequencing.
Michils G, Hollants S, Dehaspe L, Van Houdt J, et al.
J Mol Diagn. 2012 Sep 25. [Epub ahead of print]

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events.
Liu J, Lee W, Jiang Z, Chen Z, et al.
Genome Res. 2012 Oct 2. [Epub ahead of print]

Whole exome sequencing reveals uncommon mutations in the recently identified Fanconi anemia gene SLX4/FANCP.
Schuster B, Knies K, Stoepker C, Velleuer E, et al.
Hum Mutat. 2012 Oct 3. [Epub ahead of print]

Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters.
Graessler J, Qin Y, Zhong H, Zhang J, et al.
Pharmacogenomics J. 2012 Oct 2. [Epub ahead of print]

High-throughput sequencing identifies an NFIA/CBFA2T3 fusion gene in acute erythroid leukemia with t(1;16)(p31;q24).
Micci F, Thorsen J, Panagopoulos I, Nyquist KB, et al.
Leukemia. 2012 Sep 11. [Epub ahead of print]

Exome sequencing identifies rare deleterious mutations in DNA repair genes FANCC and BLM as potential breast cancer susceptibility alleles.
Thompson ER, Doyle MA, Ryland GL, Rowley SM, et al.
PLoS Genet. 2012 Sep;8(9):e1002894.

Deep sequencing of antiviral T-cell responses to HCMV and EBV in humans reveals a stable repertoire that is maintained for many years.
Klarenbeek PL, Remmerswaal EB, Ten Berge IJ, Doorenspleet ME, et al.
PLoS Pathog. 2012 Sep;8(9):e1002889.

Confidence-based somatic mutation evaluation and prioritization.
Löwer M, Renard BY, de Graaf J, Wagner M, et al.
PLoS Comput Biol. 2012 Sep;8(9):e1002714.

Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer.
Liang H, Cheung LW, Li J, Ju Z, et al.
Genome Res. 2012 Oct 1. [Epub ahead of print]

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.