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In Print: Last Week's Clinical Sequencing Papers of Note: Oct 17, 2012


Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing.
Chan KC, Jiang P, Zheng YW, Liao GJ, et al.
Clin Chem. 2012 Oct 11. [Epub ahead of print]

A homozygous missense mutation in HERC2 associated with global developmental delay and autism spectrum disorder.
Puffenberger EG, Jinks RN, Wang H, Xin B, et al.
Hum Mutat. 2012 Oct 15. [Epub ahead of print]

Genotype calling and haplotyping in parent-offspring trios.
Chen W, Li B, Zeng Z, Sanna S, et al.
Genome Res. 2012 Oct 11. [Epub ahead of print]

A common single-nucleotide variant in T is strongly associated with chordoma.
Pillay N, Plagnol V, Tarpey PS, Lobo SB, et al.
Nat Genet. 2012 Oct 14. [Epub ahead of print]

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.
Kulis M, Heath S, Bibikova M, Queirós AC, et al.
Nat Genet. 2012 Oct 14. [Epub ahead of print]

Bacterial flora of dental periradicular lesions analyzed by the 454-pyrosequencing technology.
Saber MH, Schwarzberg K, Alonaizan FA, Kelley ST, et al.
J Endod. 2012 Nov;38(11):1484-8. Epub 2012 Aug 9.

Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome.
Handley SA, Thackray LB, Zhao G, Presti R, et al.
Cell. 2012 Oct 12;151(2):253-66.

Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.
Maughan H, Wang PW, Diaz Caballero J, Fung P, et al.
PLoS One. 2012;7(10):e45791.

A likelihood-based framework for variant calling and de novo mutation detection in families.
Li B, Chen W, Zhan X, Busonero F, et al.
PLoS Genet. 2012 Oct;8(10):e1002944.

Use of targeted exome sequencing as a diagnostic tool for familial hypercholesterolaemia.
Futema M, Plagnol V, Whittall RA, Neil HA et al.
J Med Genet. 2012 Oct;49(10):644-649.

Study of autosomal recessive osteogenesis imperfecta in Arabia reveals a novel locus defined by TMEM38B mutation.
Shaheen R, Alazami AM, Alshammari MJ, Faqeih E, et al.
J Med Genet. 2012 Oct;49(10):630-5.

A balanced translocation truncates neurotrimin in a family with intracranial and thoracic aortic aneurysm.
Luukkonen TM, Pöyhönen M, Palotie A, Ellonen P, et al.
J Med Genet. 2012 Oct;49(10):621-9.

Phylogenetic analysis of non-O157 Shiga toxin-producing Escherichia coli by whole genome sequencing.
Ju W, Cao G, Rump L, Strain E, et al.
J Clin Microbiol. 2012 Oct 10. [Epub ahead of print]

Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing.
Lee GQ, Swenson LC, Poon AF, Martin JN, et al.
PLoS One. 2012;7(9):e46181.

qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles.
Song S, Nones K, Miller D, Harliwong I, et al.
PLoS One. 2012;7(9):e45835.

Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease.
Ricanek P, Lothe SM, Frye SA, Rydning A, et al.
Clin Exp Gastroenterol. 2012;5:173-186.

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival.
Engstrom PG, Tommei D, Stricker SH, Ender C, et al.
Genome Med. 2012 Oct 9;4(10):76.

Approaches to informed consent for hypothesis-testing and hypothesis-generating clinical genomics research.
Facio F, Sapp J, Linn A, Biesecker L.
BMC Med Genomics. 2012 Oct 10;5(1):45.

Whole-exome sequencing of a pedigree segregating asthma.
Dewan AT, Egan KB, Hellenbrand K, Sorrentino K, et al.
BMC Med Genet. 2012 Oct 9;13(1):95.

Next-generation sequencing and de novo assembly, genome organization, and comparative genomic analyses of the genomes of two Helicobacter pylori isolates from duodenal ulcer patients in India.
Kumar N, Mukhopadhyay AK, Patra R, De R, et al.
J Bacteriol. 2012 Nov;194(21):5963-4.

Identification of a novel mutation in the CDHR1 gene in a family with recessive retinal degeneration.
Duncan JL, Roorda A, Navani M, Vishweswaraiah S, et al.
Arch Ophthalmol. 2012 Oct 1;130(10):1301-8.

Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn's but not in ulcerative colitis.
Hansen R, Russell RK, Reiff C, Louis P, et al.
Am J Gastroenterol. 2012 Oct 9. [Epub ahead of print]

Using exome sequencing to reveal mutations in TREM2 presenting as a frontotemporal dementia-like syndrome without bone involvement.
Guerreiro RJ, Lohmann E, Brás JM, Gibbs JR, et al.
Arch Neurol. 2012 Oct 8:1-7. [Epub ahead of print]

Exome sequencing: an efficient diagnostic tool for complex neurodegenerative disorders.
Hammer MB, Eleuch-Fayache G, Gibbs JR, Arepalli SK, et al.
Eur J Neurol. 2012 Oct 9. [Epub ahead of print]

Olorin: Combining gene flow with exome sequencing in large family studies of complex disease.
Morris JA, Barrett JC.
Bioinformatics. 2012 Oct 10. [Epub ahead of print]

"Location, Location, Location": A spatial approach for rare-variant analysis and an application to a study on nonsyndromic cleft lip with or without cleft palate.
Fier H, Won S, Prokopenko D, Alchawa T, et al.
Bioinformatics. 2012 Oct 8. [Epub ahead of print]

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.