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Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

Authors :
Matey-Hernandez, María Luisa
Maretty, Lasse
Jensen, Jacob Malte
Petersen, Bent
Andreas Sibbesen, Jonas
Liu, Siyang
Villesen, Palle
Skov, Laurits
Belling, Kirstine
Theil Have, Christian
Gonzalez-Izarzugaza, Jose Maria
Grosjean, Marie
Bork-Jensen, Jette
Grove, Jakob
Als, Thomas D.
Huang, Shujia
Chang, Yuqi
Xu, Ruiqi
Ye, Weijian
Rao, Junhua
Guo, Xiaosen
Sun, Jihua
Cao, Hongzhi
Ye, Chen
Beusekom, Johan v.
Espeseth, Thomas
Flindt, Esben N.
Friborg, Rune M.
Halager, Anders Egerup
Le Hellard, Stephanie
Hultman, Christina M.
Lescai, Francesco
Li, Shengting
Lund, Ole
Løngren, Peter
Mailund, Thomas
Mors, Ole
Pedersen, Christian N. S.
Sicheritz-Pontén, Thomas
Sullivan, Patrick F.
Ali , Syed
Westergaard, David
Yadav, Rachita
Li, Ning
Xu, Xun
Hansen, Torben
Krogh, Anders
Bolund, Lars
Sørensen, Thorkild I. A.
Pedersen, Oluf
Gupta, Ramneek
Besenbacher, Søren
Børglum, Anders D.
Wang, Jun
Eiberg, Hans
Kristiansen, Karsten
Brunak, Søren
Schierup, Mikkel Heide
Izarzugaza, Jose M. G.
Source :
Matey-Hernandez, M L, Brunak, S, Izarzugaza, J M G & Danish Pan-Genome Consortium (Jakob Grove, member of-) 2018, ' Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios ', BMC Bioinformatics, vol. 19, no. 1, 239 . https://doi.org/10.1186/s12859-018-2239-6, BMC Bioinformatics, BMC Bioinformatics, Vol 19, Iss 1, Pp 1-12 (2018), Matey-Hernandez, M L, Danish Pan Genome Consortium, Brunak, S, Izarzugaza, J M G, Sørensen, L M, Petersen, B, Sibbesen, J A, Liu, S, Belling, K G, Have, C T, Bork-Jensen, J, Sun, J, Hansen, T, Krogh, A, Sørensen, T I A, Pedersen, O B, Wang, J, Eiberg, H R L & Kristiansen, K 2018, ' Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios ', BMC Bioinformatics, vol. 19, 239, pp. 1-12 . https://doi.org/10.1186/s12859-018-2239-6, Matey-Hernandez, M L, Maretty, L, Jensen, J M, Petersen, B, Andreas Sibbesen, J, Liu, S, Villesen, P, Skov, L, Belling, K, Theil Have, C, Gonzalez-Izarzugaza, J M, Grosjean, M, Bork-Jensen, J, Grove, J, Als, T D, Huang, S, Chang, Y, Xu, R, Ye, W, Rao, J, Guo, X, Sun, J, Cao, H, Ye, C, Beusekom, J V, Espeseth, T, Flindt, E N, Friborg, R M, Halager, A E, Le Hellard, S, Hultman, C M, Lescai, F, Li, S, Lund, O, Løngren, P, Mailund, T, Matey-Hernandez, M L, Mors, O, Pedersen, C N S, Sicheritz-Pontén, T, Sullivan, P F, Ali, S, Westergaard, D, Yadav, R, Li, N, Xu, X, Hansen, T, Krogh, A, Bolund, L, Sørensen, T I A, Pedersen, O, Gupta, R, Besenbacher, S, Børglum, A D, Wang, J, Eiberg, H, Kristiansen, K, Brunak, S, Schierup, M H, Brunak, S & Izarzugaza, J M G 2018, ' Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios ', B M C Bioinformatics, vol. 19, 239 . https://doi.org/10.1186/s12859-018-2239-6
Publication Year :
2018

Abstract

BACKGROUND: The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods.RESULTS: We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles.CONCLUSIONS: Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.

Details

Language :
English
Database :
OpenAIRE
Journal :
Matey-Hernandez, M L, Brunak, S, Izarzugaza, J M G & Danish Pan-Genome Consortium (Jakob Grove, member of-) 2018, ' Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios ', BMC Bioinformatics, vol. 19, no. 1, 239 . https://doi.org/10.1186/s12859-018-2239-6, BMC Bioinformatics, BMC Bioinformatics, Vol 19, Iss 1, Pp 1-12 (2018), Matey-Hernandez, M L, Danish Pan Genome Consortium, Brunak, S, Izarzugaza, J M G, Sørensen, L M, Petersen, B, Sibbesen, J A, Liu, S, Belling, K G, Have, C T, Bork-Jensen, J, Sun, J, Hansen, T, Krogh, A, Sørensen, T I A, Pedersen, O B, Wang, J, Eiberg, H R L & Kristiansen, K 2018, ' Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios ', BMC Bioinformatics, vol. 19, 239, pp. 1-12 . https://doi.org/10.1186/s12859-018-2239-6, Matey-Hernandez, M L, Maretty, L, Jensen, J M, Petersen, B, Andreas Sibbesen, J, Liu, S, Villesen, P, Skov, L, Belling, K, Theil Have, C, Gonzalez-Izarzugaza, J M, Grosjean, M, Bork-Jensen, J, Grove, J, Als, T D, Huang, S, Chang, Y, Xu, R, Ye, W, Rao, J, Guo, X, Sun, J, Cao, H, Ye, C, Beusekom, J V, Espeseth, T, Flindt, E N, Friborg, R M, Halager, A E, Le Hellard, S, Hultman, C M, Lescai, F, Li, S, Lund, O, Løngren, P, Mailund, T, Matey-Hernandez, M L, Mors, O, Pedersen, C N S, Sicheritz-Pontén, T, Sullivan, P F, Ali, S, Westergaard, D, Yadav, R, Li, N, Xu, X, Hansen, T, Krogh, A, Bolund, L, Sørensen, T I A, Pedersen, O, Gupta, R, Besenbacher, S, Børglum, A D, Wang, J, Eiberg, H, Kristiansen, K, Brunak, S, Schierup, M H, Brunak, S & Izarzugaza, J M G 2018, ' Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios ', B M C Bioinformatics, vol. 19, 239 . https://doi.org/10.1186/s12859-018-2239-6
Accession number :
edsair.doi.dedup.....897a97a82c5d3fd8bfeac61457eafd0b