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Papers of Note: Feb 15, 2011

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Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Handsaker RE, Korn JM, Nemesh J, McCarroll SA.
Nat Genet. 2011 Feb 13. [Epub ahead of print]


The genomic complexity of primary human prostate cancer.
Berger MF, Lawrence MS, Demichelis F, Drier Y, et al.
Nature. 2011 Feb 10;470(7333):214-20.


Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study.
Lee KT, Byun MJ, Kang KS, Park EW, et al.
PLoS One. 2011 Feb 2;6(2):e16356.


Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting.
Ehrich M, Deciu C, Zwiefelhofer T, Tynan JA, et al.
Am J Obstet Gynecol. 2011 Feb 9. [Epub ahead of print]


Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy.
Jordan DM, Kiezun A, Baxter SM, Agarwala V, et al.
Am J Hum Genet. 2011 Feb 11;88(2):183-92.


Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire.
Nguyen P, Ma J, Pei D, Obert C, et al.
BMC Genomics. 2011 Feb 11;12(1):106.


Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Turro E, Su SY, Goncalves A, Coin LJ, et al.
Genome Biol. 2011 Feb 10;12(2):R13.


Whole-genome amplified DNA from stored dried blood spots is reliable in high resolution melting curve and sequencing analysis.
Winkel BG, Hollegaard MV, Olesen MS, Svendsen JH, et al.
BMC Med Genet. 2011 Feb 9;12(1):22.


Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations.
De Leeneer K, Hellemans J, De Schrijver J, Baetens M, et al.
Hum Mutat. 2011 Jan 25. doi: 10.1002/humu.21428. [Epub ahead of print]


Large scale loss of data in low-diversity Illumina sequencing libraries can be recovered by deferred cluster calling.
Krueger F, Andrews SR, Osborne CS.
PLoS One. 2011 Jan 28;6(1):e16607.


A comparative transcriptomic analysis of uveal melanoma and normal uveal melanocyte.
An J, Wan H, Zhou X, Hu DN, et al.
PLoS One. 2011 Jan 28;6(1):e16516.


ReadDepth: A parallel R package for detecting copy number alterations from short sequencing reads.
Miller CA, Hampton O, Coarfa C, Milosavljevic A.
PLoS One. 2011 Jan 31;6(1):e16327.


Mayday SeaSight: Combined analysis of deep sequencing and microarray data.
Battke F, Nieselt K.
PLoS One. 2011 Jan 31;6(1):e16345.


Considering transposable element diversification in de novo annotation approaches.
Flutre T, Duprat E, Feuillet C, Quesneville H.
PLoS One. 2011 Jan 31;6(1):e16526.


Detection and removal of biases in the analysis of next-generation sequencing reads.
Schwartz S, Oren R, Ast G.
PLoS One. 2011 Jan 31;6(1):e16685.


A new testing strategy to identify rare variants with either risk or protective effect on disease.
Ionita-Laza I, Buxbaum JD, Laird NM, Lange C.
PLoS Genet. 2011 Feb 3;7(2):e1001289.


A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA.
Robertson AB, Dahl JA, Vågbø CB, Tripathi P, et al.
Nucleic Acids Res. 2011 Feb 7. [Epub ahead of print]


A multi-site study using high-resolution HLA genotyping by next generation sequencing.
Holcomb CL, Höglund B, Anderson MW, Blake LA, et al.
Tissue Antigens. 2011 Mar;77(3):206-217. doi: 10.1111/j.1399-0039.2010.01606.x.

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White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

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