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In Print: Last Week's Clinical Sequencing Papers of Note: May 23, 2012


Gene expression profiling of liver cancer stem cells by RNA-sequencing.
Ho DW, Yang ZF, Yi K, Lam CT, et al.
PLoS One. 2012;7(5):e37159.

Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs.
Kandpal RP, Rajasimha HK, Brooks MJ, Nellissery J, et al.
Mol Vis. 2012;18:1123-1146.

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people.
Nelson MR, Wegmann D, Ehm MG, Kessner D, et al.
Science. 2012 May 17. [Epub ahead of print]

Evolution and functional impact of rare coding variation from deep sequencing of human exomes.
Tennessen JA, Bigham AW, O'Connor TD, Fu W, et al.
Science. 2012 May 17. [Epub ahead of print]

Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing.
Wu J, Shen E, Shi D, Sun Z, Cai T .
Genet Med. 2012 May 17. [Epub ahead of print]

Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient.
Heyn H, Vidal E, Sayols S, Sanchez-Mut JV, et al.
Epigenetics. 2012 Jun 1;7(6).

High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia.
Wu D, Sherwood A, Fromm JR, Winter SS, et al.
Sci Transl Med. 2012 May 16;4(134):134ra63.

Somatic STAT3 mutations in large granular lymphocytic leukemia.
Koskela HL, Eldfors S, Ellonen P, van Adrichem AJ, et al.
N Engl J Med. 2012 May 17;366(20):1905-13.

Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy.
Kwok H, Tong AH, Lin CH, Lok S, et al.
PLoS One. 2012;7(5):e36939.

High-throughput, high-fidelity HLA genotyping with deep sequencing.
Wang C, Krishnakumar S, Wilhelmy J, Babrzadeh F, et al.
Proc Natl Acad Sci U S A. 2012 May 15. [Epub ahead of print]

Deep sequencing unearths NumtS under LHON-associated false heteroplasmic mitochondrial DNA variants.
Petruzzella V, Carrozzo R, Calabrese C, Dell'aglio R, et al.
Hum Mol Genet. 2012 May 15. [Epub ahead of print]

A mutation in KIF7 is responsible for the autosomal recessive syndrome of macrocephaly, multiple epiphyseal dysplasia and distinctive facial appearance.
Ali BR, Silhavy JL, Akawi NA, Gleeson JG, Al-Gazali L
Orphanet J Rare Dis. 2012 May 15;7(1):27.

Incidental medical information in whole-exome sequencing.
Solomon BD, Hadley DW, Pineda-Alvarez DE, et al.
Pediatrics. 2012 May 14. [Epub ahead of print]

DNA sequencing of maternal plasma to identify Down syndrome and other trisomies in multiple gestations.
Canick JA, Kloza EM, Lambert-Messerlian GM, Haddow JE, et al.
Prenat Diagn. 2012 May 14:1-5.

High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.
Wagle N, Berger MF, Davis MJ, Blumenstiel B, et al.
Cancer Discov. 2012 Jan;2(1):82-93.

Molecular ontogeny of donor-derived follicular lymphomas occurring after hematopoietic cell transplantation.
Weigert O, Kopp N, Lane AA, Yoda A, et al.
Cancer Discov. 2012 Jan;2(1):47-55.

ATM mutations in patients with hereditary pancreatic cancer.
Roberts NJ, Jiao Y, Yu J, Kopelovich L, et al.
Cancer Discov. 2012 Jan;2(1):41-46.

Novel rare variants in congenital cardiac arrhythmia genes are frequent in drug-induced torsades de pointes.
Ramirez AH, Shaffer CM, Delaney JT, Sexton DP, et al.
Pharmacogenomics J. 2012 May 15. [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.