BACKGROUND: High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation. RESULTS: Here, we report on DR2S, an R package that leverages the strengths of two sequencing technologies-the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio's SMRT sequencing or ONT's nanopore sequencing-to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised for HLA and KIR genes, DR2S is applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition, DR2S integrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases. CONCLUSIONS: DR2S is a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such as HLA or KIR. It has been used by biologists to successfully characterise and submit more than 500 HLA alleles and more than 500 KIR alleles to the IPD-IMGT/HLA and IPD-KIR databases.
BACKGROUND: High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation. RESULTS: Here, we report on DR2S, an R package that leverages the strengths of two sequencing technologies-the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio's SMRT sequencing or ONT's nanopore sequencing-to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised for HLA and KIR genes, DR2S is applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition, DR2S integrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases. CONCLUSIONS:DR2S is a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such as HLA or KIR. It has been used by biologists to successfully characterise and submit more than 500 HLA alleles and more than 500 KIR alleles to the IPD-IMGT/HLA and IPD-KIR databases.
Authors: Sarah Cooley; Daniel J Weisdorf; Lisbeth A Guethlein; John P Klein; Tao Wang; Steven G E Marsh; Stephen Spellman; Michael D Haagenson; Koy Saeturn; Martha Ladner; Elizabeth Trachtenberg; Peter Parham; Jeffrey S Miller Journal: J Immunol Date: 2014-04-18 Impact factor: 5.422
Authors: Stephanie J Lee; John Klein; Michael Haagenson; Lee Ann Baxter-Lowe; Dennis L Confer; Mary Eapen; Marcelo Fernandez-Vina; Neal Flomenberg; Mary Horowitz; Carolyn K Hurley; Harriet Noreen; Machteld Oudshoorn; Effie Petersdorf; Michelle Setterholm; Stephen Spellman; Daniel Weisdorf; Thomas M Williams; Claudio Anasetti Journal: Blood Date: 2007-09-04 Impact factor: 22.113
Authors: Roger Horton; Laurens Wilming; Vikki Rand; Ruth C Lovering; Elspeth A Bruford; Varsha K Khodiyar; Michael J Lush; Sue Povey; C Conover Talbot; Mathew W Wright; Hester M Wain; John Trowsdale; Andreas Ziegler; Stephan Beck Journal: Nat Rev Genet Date: 2004-12 Impact factor: 53.242
Authors: Ines Wagner; Daniel Schefzyk; Jens Pruschke; Gerhard Schöfl; Bianca Schöne; Nicole Gruber; Kathrin Lang; Jan Hofmann; Christine Gnahm; Bianca Heyn; Wesley M Marin; Ravi Dandekar; Jill A Hollenbach; Johannes Schetelig; Julia Pingel; Paul J Norman; Jürgen Sauter; Alexander H Schmidt; Vinzenz Lange Journal: Front Immunol Date: 2018-12-04 Impact factor: 7.561