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In Print: Last Week's Clinical Sequencing Papers of Note: Jan 8, 2014


Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia.
Yu L, Bennett JT, Wynn J, Carvill GL, et al.
J Med Genet. 2014 Jan 2. [Epub ahead of print]

Analysis of coding variants identified from exome sequencing resources for association with diabetic and non-diabetic nephropathy in African Americans.
Cooke Bailey JN, Palmer ND, Ng MC, Bonomo JA, et al.
Hum Genet. 2014 Jan 3. [Epub ahead of print]

A novel test for testing the optimally weighted combination of rare and common variants based on data of parents and affected children.
Sha Q, Zhang S.
Genet Epidemiol. 2013 Dec 30. [Epub ahead of print]

Regularized rare variant enrichment analysis for case-control exome sequencing data.
Larson NB, Schaid DJ.
Genet Epidemiol. 2013 Dec 30. [Epub ahead of print]

Exome sequencing reveals frequent inactivating mutations in ARID1A,ARID1B,ARID2, and ARID4A in microsatellite unstable colorectal cancer.
Cajuso T, Hänninen UA, Kondelin J, Gylfe AE, et al.
Int J Cancer. 2013 Dec 31. [Epub ahead of print]

Epigenetics meets genetics in acute myeloid leukemia: clinical impact of a novel seven-gene score.
Marcucci G, Yan P, Maharry K, Frankhouser D, et al.
J Clin Oncol. 2013 Dec 30. [Epub ahead of print]

Next-generation sequencing of lung cancer EGFR exons 18-21 allows effective molecular diagnosis of small routine samples (cytology and biopsy).
de Biase D, Visani M, Malapelle U, Simonato Fet al.
PLOS One 2013 Dec 23;8(12):e83607.

Exome sequencing identifies early gastric carcinoma as an early stage of advanced gastric cancer.
Kang G, Hwang WC, Do IG, Wang K, et al.
PLOS One. 2013 Dec 23;8(12):e82770.

Predictive efficacy of low burden EGFR mutation detected by next-generation sequencing on response to EGFR tyrosine kinase inhibitors in non-small-cell lung carcinoma.
Kim HS, Sung JS, Yang SJ, Kwon NJ, et al.
PLOS One 2013 Dec 20;8(12):e81975.

A homozygous mutation in the TUB gene associated with retinal dystrophy and obesity.
Borman AD, Pearce LR, Mackay DS, Nagel-Wolfrum K, et al.
Hum Mutat. 2013 Nov 12. [Epub ahead of print]

Diamund: direct comparison of genomes to detect mutations.
Salzberg SL, Pertea M, Fahrner JA, Sobreira N.
Hum Mutat. 2013 Dec 25. [Epub ahead of print]

Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing.
Tan AY, Michaeel A, Liu G, Elemento O, et al.
J Mol Diagn. 2013 Dec 26. pii: S1525-1578(13)00250-X.

Validation for clinical use of, and initial clinical experience with, a novel approach to population-based carrier screening using high-throughput, next-generation DNA sequencing.
Hallam S, Nelson H, Greger V, Perreault-Micale C, et al.
J Mol Diagn. 2013 Dec 26. pii: S1525-1578(13)00251-1.

Multiplex genetic cancer testing identifies pathogenic mutations in TP53 and CDH1 in a patient with bilateral breast and endometrial adenocarcinoma.
Heitzer E, Lax S, Lafer I, Müller SM, et al.
BMC Med Genet. 2013 Dec 29;14(1):129.

Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study.
Sanderson SC, Linderman MD, Kasarskis A, Bashir A, et al.
Genome Med. 2013 Dec 30;5(12):113.

Differentiation of primary and metastatic tumours in synchronous multifocal colonic and bronchopulmonary adenocarcinoma by targeted next generation sequencing.
Kunze K, Frank M, Bodner J, Reichert M, et al.
Histopathology. 2013 Dec 26. [Epub ahead of print]

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.