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Papers of Note: Mar 8, 2011


Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis.
Isidor B, Lindenbaum P, Pichon O, Bézieau S, et al.
Nat Genet. 2011 Mar 6. [Epub ahead of print]

A rare variant in MYH6 is associated with high risk of sick sinus syndrome.
Holm H, Gudbjartsson DF, Sulem P, Masson G, et al.
Nat Genet. 2011 Mar 6. [Epub ahead of print]

Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss.
Simpson MA, Irving MD, Asilmaz E, Gray MJ, et al.
Nat Genet. 2011 Mar 6. [Epub ahead of print]

Whole genome sequencing of Staphylococcus aureus strain RN4220, a key laboratory strain used in virulence research, identifies mutations that affect not only virulence factors but also the fitness of the strain.
Nair D, Memmi G, Hernandez D, Bard J, et al.
J Bacteriol. 2011 Mar 4. [Epub ahead of print]

Noninvasive prenatal diagnosis of a case of Down syndrome due to Robertsonian translocation by massively parallel sequencing of maternal plasma DNA.
Lun FM, Jin YY, Sun H, Leung TY, et al.
Clin Chem. 2011 Mar 4. [Epub ahead of print]

Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability.
Hamdan FF, Gauthier J, Araki Y, Lin DT, et al.
Am J Hum Genet. 2011 Mar 2. [Epub ahead of print]

Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing.
Legendre M, Santini S, Rico A, Abergel C, Claverie JM.
Virol J. 2011 Mar 4;8(1):99.

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.
Yamashita R, Sathira NP, Kanai A, Tanimoto K, et al.
Genome Res. 2011 Mar 3. [Epub ahead of print]

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UMARS: Un-MAppable Reads Solution.
Li SC, Chan WC, Lai CH, Tsai KW, et al.
BMC Bioinformatics
. 2011 Feb 15;12 Suppl 1:S9.

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.
Duitama J, Kennedy J, Dinakar S, Hernández Y, et al.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S53.

Repeat-aware modeling and correction of short read errors.
Yang X, Aluru S, Dorman KS.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52.

Strobe sequence design for haplotype assembly.
Lo C, Bashir A, Bansal V, Bafna V.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S24.

Efficient study design for next generation sequencing.
Sampson J, Jacobs K, Yeager M, Chanock S, Chatterjee N.
Genet Epidemiol. 2011 Mar 2. doi: 10.1002/gepi.20575. [Epub ahead of print]

A comparative analysis of parallel computing approaches for genome assembly.
Ahmed M, Ahmad I, Khan SU.
Interdiscip Sci. 2011 Mar;3(1):57-63. Epub 2011 Mar 3.

Genomic DNA pooling strategy for next-generation sequencing-based rare variant discovery in abdominal aortic aneurysm regions of interest -- challenges and limitations.
Harakalova M, Nijman IJ, Medic J, Mokry M, et al.
J Cardiovasc Transl Res. 2011 Mar 1. [Epub ahead of print]

An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-seq.
Mercier E, Droit A, Li L, Robertson G, et al.
PLoS One. 2011 Feb 16;6(2):e16432.

Mutations in origin recognition complex gene ORC4 cause Meier-Gorlin syndrome.
Guernsey DL, Matsuoka M, Jiang H, Evans S, et al.
Nat Genet. 2011 Feb 27. [Epub ahead of print]

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RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiß S, Müller SA, Kalkhof S, et al.
RNA. 2011 Feb 28. [Epub ahead of print]

Refinement of the X-linked nonsyndromic high-grade myopia locus (MYP1) on Xq28 and exclusion of thirteen known positional candidate genes by direct sequencing.
Ratnamala U, Lyle R, Raval R, Singh R, et al.
Ophthalmol Vis Sci. 2011 Feb 25. [Epub ahead of print]

Identification of genetic susceptibility to childhood cancer through analysis of genes in parallel.
Plon SE, Wheeler DA, Strong LC, Tomlinson GE, et al.
Cancer Genet. 2011 Jan;204(1):19-25.

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis.
Ho JW, Bishop E, Kharchenko PV, Negre N, et al.
BMC Genomics. 2011 Feb 28;12(1):134. [Epub ahead of print]

Analysis of the lung microbiome in the "healthy" smoker and in COPD.
Erb-Downward JR, Thompson DL, Han MK, Freeman CM, et al.
PLoS One. 2011 Feb 22;6(2):e16384.

Using genomic sequencing for classical genetics in E. coli K12.
Lyons E, Freeling M, Kustu S, Inwood W.
PLoS One. 2011 Feb 25;6(2):e16717.

Genome-wide mapping of DNA strand breaks.
Leduc F, Faucher D, Bikond Nkoma G, Grégoire MC, et al.
PLoS One. 2011 Feb 25;6(2):e17353.

Deep sequencing of the nicastrin gene in pooled DNA, the identification of genetic variants that affect risk of Alzheimer's disease.
Lupton MK, Proitsi P, Danillidou M, Tsolaki M, et al.
PLoS One. 2011 Feb 25;6(2):e17298.

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Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.
Sun Z, Asmann YW, Kalari KR, Bot B, et al.
PLoS One. 2011 Feb 25;6(2):e17490.

Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants.
Harper MA, Chen Z, Toy T, Machado IM, et al.
PLoS One. 2011 Feb 18;6(2):e16517.

The GENCODE exome: sequencing the complete human exome.
Coffey AJ, Kokocinski F, Calafato MS, Scott CE, et al.
Eur J Hum Genet. 2011 Mar 2. [Epub ahead of print]

Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform.
Ram JL, Karim AS, Sendler ED, Kato I.
Syst Biol Reprod Med. 2011 Mar 1. [Epub ahead of print]

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.