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Clinical Sequencing Papers of Note: Jul 27, 2011


Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy.
Galmiche L, Serre V, Beinat M, Assouline Z, Lebre AS, Chretien D, Nietschke P, Benes V, Boddaert N, Sidi D, Brunelle F, Rio M, et al.
Hum Mutat. 2011 Jul 22. [Epub ahead of print]

To share or not to share: A randomized trial of consent for data sharing in genome research.
McGuire AL, Oliver JM, Slashinski MJ, et al.
Genet Med. 2011 Jul 22. [Epub ahead of print]

Combined malonic and methylmalonic aciduria: exome sequencing reveals mutations in the ACSF3 gene in patients with a non-classic phenotype.
Alfares A, Nunez LD, Al-Thihli K, et al.
J Med Genet. 2011 Jul 23. [Epub ahead of print]

Mutations in ANKRD11 cause KBG syndrome, characterized by intellectual disability, skeletal malformations, and macrodontia.
Sirmaci A, Spiliopoulos M, Brancati F, et al.
Am J Hum Genet. 2011 Jul 20. [Epub ahead of print]

Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine.
Holbrook JD, Parker JS, Gallagher KT, et al.
J Transl Med. 2011 Jul 25;9(1):119.

Ranking insertion, deletion and nonsense mutations based on their effect on genetic information.
Zia A, Moses AM.
BMC Bioinformatics. 2011 Jul 22;12(1):299.

Qualitative thematic analysis of consent forms used in cancer genome sequencing.
Allen C, Foulkes WD.
BMC Med Ethics. 2011 Jul 19;12(1):14.

Exome sequencing identifies SMAD3 mutations as a cause of familial thoracic aortic aneurysm and dissection with intracranial and other arterial aneurysms.
Regalado ES, Guo DC, Villamizar C, et al.
Circ Res. 2011 Jul 21. [Epub ahead of print]

Comparison of statistical tests for disease association with rare variants.
Basu S, Pan W.
Genet Epidemiol. 2011 Jul 18. [Epub ahead of print]

Personalized genomic medicine: Lessons from the exome.
Solomon BD, Pineda-Alvarez DE, Hadley DW, et al.
Mol Genet Metab. 2011 Jul 5. [Epub ahead of print]

Digital karyotyping reveals probable target genes at 7q21.3 locus in hepatocellular carcinoma.
Dong H, Zhang H, Liang J, et al.
BMC Med Genomics. 2011 Jul 19;4(1):60.

Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis.
Zaragosi LE, Wdziekonski B, Le Brigand K, et al.
Genome Biol. 2011 Jul 18;12(7):R64.

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Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer.
Martens-Uzunova ES, Jalava SE, Dits NF, et al.
Oncogene. 2011 Jul 18. [Epub ahead of print]

Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome.
Kahr WH, Hinckley J, Li L, et al.
Nat Genet. 2011 Jul 17. [Epub ahead of print]

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome.
Albers CA, Cvejic A, Favier R, et al.
Nat Genet. 2011 Jul 17. [Epub ahead of print]

Exome sequencing identifies GATA-2 mutation as the cause of dendritic cell, monocyte, B and NK lymphoid deficiency.
Dickinson RE, Griffin H, Bigley V, et al.
Blood. 2011 Jul 15. [Epub ahead of print]

Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations.
Thompson JF, Reifenberger JG, Giladi E, et al.
Genome Res. 2011 Jul 15. [Epub ahead of print]

Mutations in the alpha 1,2-mannosidase gene, MAN1B1, cause autosomal-recessive intellectual disability.
Rafiq MA, Kuss AW, Puettmann L, et al.
Am J Hum Genet. 2011 Jul 15;89(1):176-82.

A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease.
Zimprich A, Benet-Pagès A, Struhal W, et al.
Am J Hum Genet. 2011 Jul 15;89(1):168-75.

VPS35 mutations in Parkinson disease.
Vilariño-Güell C, Wider C, Ross OA, et al.
Am J Hum Genet. 2011 Jul 15;89(1):162-7.

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants.
Capriotti E, Altman RB.
Genomics. 2011 Jul 7. [Epub ahead of print]

MYO1E mutations and childhood familial focal segmental glomerulosclerosis.
Mele C, Iatropoulos P, Donadelli R, et al.
N Engl J Med. 2011 Jul 14. [Epub ahead of print]

Lampe1: An ENU-germline mutation causing spontaneous hepatosteatosis identified through targeted exon-enrichment and next-generation sequencing.
Sheridan R, Lampe K, Shanmukhappa SK, et al.
PLoS One. 2011;6(7):e21979.

Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing.
Chen EZ, Chiu RW, Sun H, et al.
PLoS One. 2011;6(7):e21791. [See CSN's coverage here]

Somatic mutations of the mitochondrial genome in human breast cancers.
Tseng LM, Yin PH, Yang CW, et al.
Genes Chromosomes Cancer. 2011 Jul 11. [Epub ahead of print]

Analysis of the resistome of a multidrug-resistant NDM-1-producing Escherichia coli by high-throughput genome sequencing.
Poirel L, Bonnin RA, Nordmann P.
Antimicrob Agents Chemother. 2011 Jul 11. [Epub ahead of print]

Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles.
Kumar V, Sun P, Vamathevan J, et al.
Antimicrob Agents Chemother. 2011 Jul 11. [Epub ahead of print]

Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer.
Barber LJ, Rosa Rosa JM, Kozarewa I, et al.
PLoS One. 2011;6(7):e21639.

Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of Hepitype evolution in tumors.
Herrmann A, Haake A, Ammerpohl O, et al.
PLoS One. 2011;6(7):e21332.

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.