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In Print: Clinical Sequencing Papers of Note of the Last Two Weeks: Nov 30, 2011


Identification of a novel DLX5 mutation in a family with autosomal recessive split hand and foot malformation.
Shamseldin HE, Faden MA, Alashram W, Alkuraya FS.
J Med Genet. 2011 Nov 25. [Epub ahead of print]

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains.
Berman BP, Weisenberger DJ, Aman JF, Hinoue T, et al.
Nat Genet. 2011 Nov 27. [Epub ahead of print]

Rapid genetic diagnosis of heritable platelet function disorders using next generation sequencing: proof-of-principle with Hermansky-Pudlak syndrome.
Jones ML, Murden SL, Bem D, Mundell SJ, et al.
J Thromb Haemost. 2011 Nov 24. [Epub ahead of print]

Genetic defect in CYP24A1, the vitamin D 24-hydroxylase gene, in a patient with severe infantile hypercalcemia.
Dauber A, Nguyen TT, Sochett E, Cole DE, et al.
J Clin Endocrinol Metab. 2011 Nov 23. [Epub ahead of print]

Multilocus sequence typing of Salmonella strains by high-throughput sequencing of selectively amplified target genes.
Singh P, Foley SL, Nayak R, Kwon YM.
J Microbiol Methods. 2011 Nov 11. [Epub ahead of print]

Whole genome sequencing of penicillin resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease.
Fani F, Leprohon P, Legare D, Ouellette M.
Genome Biol. 2011 Nov 22;12(11):R115.

Whole-exome sequencing of pediatric acute lymphoblastic leukemia.
Lilljebjörn H, Rissler M, Lassen C, Heldrup J, et al.
Leukemia. 2011 Nov 18. [Epub ahead of print]

Aberrant expression of serum miRNAs in schizophrenia.
Shi W, Du J, Qi Y, Liang G, et al.
J Psychiatr Res. 2011 Nov 15. [Epub ahead of print]

Clinical impact of the use of 16S rRNA sequencing method for the identification of 'difficult-to-identify' bacteria in immunocompromised hosts.
Bharadwaj R, Swaminathan S, Salimnia H, Fairfax M, et al.
Transpl Infect Dis. 2011 Oct 28. [Epub ahead of print]

Application of high-throughput sequencing to measure the performance of commonly used selective cultivation methods for the foodborne pathogen Campylobacter.
Oakley BB, Morales CA, Line JE, Seal BS, Hiett KL.
FEMS Microbiol Ecol. 2011 Oct 11. [Epub ahead of print]

Study provides insight into HIV-neutralizing antibody evolution via deep-sequencing and structural analysis.
[no authors available]
Expert Rev Vaccines. 2011 Oct;10(10):1369.

Deep sequencing of MYC DNA-binding sites in Burkitt lymphoma.
Seitz V, Butzhammer P, Hirsch B, Hecht J, et al.
PLoS One. 2011;6(11):e26837.

Low-grade serous carcinomas of the ovary contain very few point mutations.
Jones S, Wang TL, Kurman RJ, Nakayama K, et al.
J Pathol. 2011 Nov 21. [Epub ahead of print]

Mutations in MEGF10, a regulator of satellite cell myogenesis, cause early onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD).
Logan CV, Lucke B, Pottinger C, Abdelhamed ZA, et al.
Nat Genet. 2011 Nov 20. [Epub ahead of print]

Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia.
Chen WJ, Lin Y, Xiong ZQ, Wei W, et al.
Nat Genet. 2011 Nov 20. [Epub ahead of print]

Recessive mutations in ELOVL4 cause ichthyosis, intellectual disability, and spastic quadriplegia.
Aldahmesh MA, Mohamed JY, Alkuraya HS, Verma IC, et al.
Am J Hum Genet. 2011 Nov 16. [Epub ahead of print]

Calling amplified haplotypes in next generation tumor sequence data.
Dewal N, Hu Y, Freedman ML, Laframboise T, Pe'er I.
Genome Res. 2011 Nov 16. [Epub ahead of print]

TREAT: A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
Asmann YW, Middha S, Hossain A, Baheti S, et al.
Bioinformatics. 2011 Nov 15. [Epub ahead of print]

Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection.
Peng X, Gralinski L, Ferris MT, Frieman MB, et al.
MBio. 2011 Nov 15;2(6). pii: e00198-11.

Feature based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
Ding J, Bashashati A, Roth A, Oloumi A, et al.
Bioinformatics. 2011 Nov 13. [Epub ahead of print]

Integration of regulatory networks by NKX3.1 promotes androgen-dependent prostate cancer survival.
Tan PY, Chang CW, Chng KR, Wansa KD, et al.
Mol Cell Biol. 2011 Nov 14. [Epub ahead of print]

Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue.
Fanelli M, Amatori S, Barozzi I, Minucci S.
Nat Protoc. 2011 Nov 10;6(12):1905-19.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.