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10.1186/s12859-017-1746-1 http://scihub22266oqcxt.onion/10.1186/s12859-017-1746-1 C5504728!5504728 !28697761     free     free     free Deprecated: Implicit conversion from float 219.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Warning: imagejpeg(C:\Inetpub\vhosts\kidney.de\httpdocs\phplern\28697761 .jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117       BMC+Bioinformatics 2017 ; 18 (1 ): 334 Nephropedia Template TP {{tp|p=28697761 |t=2017. HLA-check: evaluating HLA data from SNP information |pdf=|usr=}}{{28697761 }} gab.com Text HLA-check: evaluating HLA data from SNP information JO: BMC Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=28697761 #FOAvip BACKGROUND: The major histocompatibility complex (MHC) region of the human genome, and specifically the human leukocyte antigen (HLA) genes, play a major role in numerous human diseases. With the recent progress of sequencing methods (eg, Next-Generation Sequencing, NGS), the accurate genotyping of this region has become possible but remains relatively costly. In order to obtain the HLA information for the millions of samples already genotyped by chips in the past ten years, efficient bioinformatics tools, such as SNP2HLA or HIBAG, have been developed that infer HLA information from the linkage disequilibrium existing between HLA alleles and SNP markers in the MHC region. RESULTS: In this study, we first used ShapeIT and Impute2 to implement an imputation method akin to SNP2HLA and found a comparable quality of imputation on a European dataset. More importantly, we developed a new tool, HLA-check, that allows for the detection of aberrant HLA allele calling with regard to the SNP genotypes in the region. Adding this tool to the HLA imputation software increases dramatically their accuracy, especially for HLA class I genes. CONCLUSION: Overall, HLA-check was able to identify a limited number of implausible HLA typings (less than 10%) in a population, and these samples can then either be removed or be retyped by NGS for HLA association analysis. Twit Text FOAVip HLA-check: evaluating HLA data from SNP information ????BMC Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=28697761 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=28697761 #FOAvip English Wikipedia <ref>{{Cite pmid|28697761 }}</ref> HLA-check: evaluating HLA data from SNP information #MMPMID28697761 Jeanmougin M ; Noirel J ; Coulonges C ; Zagury JF BMC Bioinformatics 2017[Jul]; 18 (1 ): 334 PMID28697761 show ga BACKGROUND: The major histocompatibility complex (MHC) region of the human genome, and specifically the human leukocyte antigen (HLA) genes, play a major role in numerous human diseases. With the recent progress of sequencing methods (eg, Next-Generation Sequencing, NGS), the accurate genotyping of this region has become possible but remains relatively costly. In order to obtain the HLA information for the millions of samples already genotyped by chips in the past ten years, efficient bioinformatics tools, such as SNP2HLA or HIBAG, have been developed that infer HLA information from the linkage disequilibrium existing between HLA alleles and SNP markers in the MHC region. RESULTS: In this study, we first used ShapeIT and Impute2 to implement an imputation method akin to SNP2HLA and found a comparable quality of imputation on a European dataset. More importantly, we developed a new tool, HLA-check, that allows for the detection of aberrant HLA allele calling with regard to the SNP genotypes in the region. Adding this tool to the HLA imputation software increases dramatically their accuracy, especially for HLA class I genes. CONCLUSION: Overall, HLA-check was able to identify a limited number of implausible HLA typings (less than 10%) in a population, and these samples can then either be removed or be retyped by NGS for HLA association analysis. |*Polymorphism, Single Nucleotide [MESH] |*Software [MESH] |Alleles [MESH] |Genotyping Techniques/*methods [MESH] |HLA Antigens/*genetics [MESH] |Histocompatibility Antigens Class I/genetics [MESH] |Histocompatibility Testing [MESH] |Humans [MESH] |Linkage Disequilibrium [MESH]HLA-check: evaluating HLA data from SNP information (epmc).pdf DeepDyve Pubget Overpricing