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Methods in Molecular Biology 1310 Peter Bugert Editor Molecular Typing of Blood Cell Antigens M M B ETHODS IN OLECULAR IOLOGY Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hat fi eld, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Molecular Typing of Blood Cell Antigens Edited by Peter Bugert Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Wurttemberg – Hessen, Heidelberg University, Mannheim, Germany Editor Peter B ugert Institute of Transfusion Medicine and Immunology Medical Faculty Mannheim, German Red Cross Blood Service Baden-Wurttemberg – Hessen Heidelberg University Mannheim, Germany ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-2689-3 ISBN 978-1-4939-2690-9 (eBook) DOI 10.1007/978-1-4939-2690-9 Library of Congress Control Number: 2015938771 Springer New York Heidelberg Dordrecht London © Springer Science+Business Media New York 2 015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Humana Press is a brand of Springer Springer Science+Business Media LLC New York is part of Springer Science+Business Media (www.springer.com) Prefa ce Blood cells are characterized by the surface expression of a variety of antigens that are defi ned by their capacity to induce an immune response in the autologous or allogenic set- ting. Antigens on red blood cells are designated as blood groups, and the more than 300 blood group antigens are assigned to currently 35 blood group systems by the International Society for Blood Transfusion (ISBT). In 1990, the ABO blood group system was the fi rst that was characterized on the molecular level. Since then the molecular basis of all blood group systems has been discovered. In clinical diagnosis of blood group antigens and anti- bodies, serological methods are still the gold standard widely used all over the world. However, molecular blood grouping is an upcoming fi eld with increasing portion of com- mercialized techniques and methods. In contrast to blood groups, molecular typing is more advanced in the area of human leukocyte antigens (HLA). This rapid progress was driven by the fact that serological HLA phenotyping had a much lower diagnostic value compared to genotyping. Nowadays, low to high resolution HLA genotyping is the gold standard in matched organ or stem cell transplantation. In addition to red and white cell antigens blood platelets represent another cellular component carrying a variety of antigens. The molecular basis of the clinically most relevant human platelet antigens (HPA) is known. Genotyping is straightforward since the antigens are defi ned by diallelic single nucleotide polymorphisms (SNPs) in glycoprotein genes. Very similar is true for the human neutrophil antigens (HNA). Thus, SNP typing is also an important topic of this book. The majority of molecular antigen typing methods and techniques are performed on genomic DNA involving PCR-based amplifi cation of the target genes. Many of the methods have been developed for diagnostic use with particular requirements for robustness and quality control. The detailed protocols described in this book can be applied to introduce the methods in the lab. The validation of such a new method or the ongoing quality control is important for the diagnostic use. The fi rst chapter of this book gives a short overview of the minimal demands with regard to fi rst time or ongoing validation. Such diagnostic systems have a great relevance in blood transfusion and organ transplantation. The aim of this volume about Molecular Typing of Blood Cell Antigens is to bring together a variety of protocols useful for the DNA-based typing of blood cell antigens. The methodological spectrum ranges from rather simple approaches with low technical complexity to highly sophisticated modern developments. In transfusion medicine the blood group genotyping methods need to be fl exible for the individual diagnosis of patients on one side. On the other side techniques are required that allow a high-throughput and com- plex analysis of multiple blood group systems in large numbers of blood donors. The HLA genetics is characterized by a limited number of gene loci, however, each with a remarkably high number of gene variants mostly based on exonic SNPs. This kind of molecular genetic complexity is challenging for genotyping techniques. Therefore, many technical and methodological developments can be observed in the HLA fi eld including in silico methods to deduce HLA types from RNA sequencing data. The review about novel approaches and technologies in molecular HLA typing (s ee Chapter 1 8 ) is highly recommended. v vi Preface This book summarizes contributions from leading international experts in the fi eld of DNA typing for blood cell antigens. As editor of this volume I am very grateful indeed to them for their willingness to provide an insight into their knowledge and to provide the detailed step-by-step protocols. I also wish to thank my colleagues Karin Janetzko and Erwin Scharberg for many fruitful discussions and their considerable input. Mannheim, Germany P eter B ugert Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x 1 Validation of Genotyping Protocols for Diagnostic Use. . . . . . . . . . . . . . . . . . 1 Paul M etcalfe 2 H igh-Resolution Melting Analysis of Single Nucleotide Polymorphisms . . . . . 5 Carol M. B ruzzone and Clifford J. S teer 3 H igh-Speed Droplet-Allele-Specific Polymerase Chain Reaction for Genotyping of Single Nucleotide Polymorphisms. . . . . . . . . . . . . . . . . . . . 29 Kazuyuki Matsuda and Takayuki H onda 4 B lood Grouping Based on PCR Methods and Agarose Gel Electrophoresis. . . . . 3 7 Ana Maria S ell and J eane Eliete L aguila V isentainer 5 P arallel Donor Genotyping for 46 Selected Blood Group and 4 Human Platelet Antigens Using High-Throughput MALDI-TOF Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Stefan Meyer , N adine T rost , B eat M . F rey , and Christoph G assner 6 P CR with Sequence-Specific Primers for Typing of Diallelic Blood Groups. . . . . . 7 1 Gabriele Rink , Erwin A . Scharberg , and Peter Bugert 7 H igh-Resolution Melting Analysis for Genotyping Duffy Blood Group Antigens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 3 Ewa Łukasik , Kazimiera W aśniowska , Magdalena G rodecka , Edyta M ajorczyk , and Marcin C zerwiński 8 M olecular RHD-RHCE Analysis by Multiplex PCR of Short Fluorescent Fragments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Yann F ichou and Claude F érec 9 M icroarrays in Blood Group Genotyping . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 05 Stephanie A. Boccoz , G aëlle L e Goff , Loïc J . B lum , and C hristophe A. M arquette 10 Next-Generation Sequencing for Antenatal Prediction of KEL1 Blood Group Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 15 Klaus Rieneck , F rederik B anch Clausen , and M orten Hanefeld Dziegiel 11 454-Sequencing™ for the KEL, JR, and LAN Blood Groups. . . . . . . . . . . . . . 1 23 Carola W ieckhusen and Peter B ugert 12 N oninvasive Prenatal Blood Group Genotyping . . . . . . . . . . . . . . . . . . . . . . . 1 35 Andrea Doescher and T homas H . Müller 13 Genotyping of Human Platelet Antigens by BeadChip Microarray Technology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 Gerald Bertrand and Fabiana C onti vii viii Contents 14 Sequence-Based Typing for Platelet alloantigens . . . . . . . . . . . . . . . . . . . . . . . 1 67 Shun-Chung P ai and L iang-In L in 15 M iniaturized Technology for DNA Typing: Cassette PCR. . . . . . . . . . . . . . . . 1 75 Dammika P. Manage and L inda M . Pilarski 16 G eno- and Phenotyping of Human Neutrophil Antigens. . . . . . . . . . . . . . . . . 1 93 Angelika Reil and J ürgen Bux 17 A llelic Discrimination by TaqMan-PCR for Genotyping of Human Neutrophil Antigens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205 Rudi Steffensen , John B aech , and Kaspar R . Nielsen 18 N ovel Approaches and Technologies in Molecular HLA Typing . . . . . . . . . . . 2 13 Paul P. J . Dunn 19 L uminex-Based Methods in High-Resolution HLA Typing. . . . . . . . . . . . . . . 2 31 Manuela Testi and Marco Andreani 2 0 In Silico HLA Typing Using Standard RNA-Seq Sequence Reads . . . . . . . . . . 2 47 Sebastian B oegel , Jelle Scholtalbers , M artin L öwer , U gur Sahin , and John C . C astle Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 59 Contributors MARCO ANDREANI • Laboratory of Immunogenetics and Transplant Biology – IME Foundation, P olyclinic of Tor Vergata University , R ome , I taly JOHN B AECH • Department of Clinical Immunology , A alborg Hospital , A alborg , D enmark GERALD B ERTRAND • Histocompatibilty and Immunogenetics Laboratory , E tablissement Français du Sang (EFS) Bretagne , Rennes, France LOÏC J . B LUM • Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Equipe Génie Enzymatique, Membranes Biomimétiques et Assemblages Supramoléculaires (GEMBAS) UMR 5246 ICBMS, Université Lyon1 - CNRS , V illeurbanne, France STEPHANIE A. BOCCOZ • AXO Science SAS , Villeurbanne, France SEBASTIAN B OEGEL • TRON gGmbH – Translational Oncology at Johannes Gutenberg- University Medical Center gGmbH , Mainz , G ermany ; U niversity Medical Center of the Johannes Gutenberg-University , M ainz , G ermany CAROL M. BRUZZONE • Department of Medicine, U niversity of Minnesota Medical School , Minneapolis, M N , U SA PETER BUGERT • Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, G erman Red Cross Blood Service Baden-Württemberg – Hessen, Heidelberg University , Mannheim, G ermany JÜRGEN BUX • German Red Cross Blood Service West, Hagen , G ermany JOHN C. C ASTLE • 4-Antibody AG, Basel, Switzerland; TRON gGmbH – Translational Oncology at Johannes Gutenberg-U niversity Medical Center gGmbH , M ainz , G ermany FREDERIK BANCH C LAUSEN • Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital , C openhagen, D enmark FABIANA C ONTI • Section of Transfusion Medicine and Cellular Therapy, Department of Hemotherapy , Hospital Albert Einstein , São Paulo, B razil MARCIN CZERWIŃSKI • Ludwik Hirszfeld Institute of Immunology and Experimental Therapy , P olish Academy of Sciences , W rocław, Poland ; F aculty of Physical Education and Physiotherapy, Opole University of Technology , O pole , P oland ANDREA DOESCHER • German Red Cross Blood Transfusion Service NSTOB , O ldenburg, Germany PAUL P .J. D UNN • University Hospitals Leicester NHS Trust, Leicester General Hospital , Leicester, U K MORTEN H ANEFELD DZIEGIEL • Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital , C openhagen, D enmark CLAUDE F ÉREC • Etablissement Français du Sang (EFS) – Bretagne , Brest, F rance ; Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1078 , Brest, F rance ; Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale , B rest , France ; L aboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Régional Universitaire (CHRU) , H ôpital Morvan , B rest , F rance YANN FICHOU • Etablissement Français du Sang (EFS) – Bretagne , B rest , F rance ; I nstitut National de la Santé et de la Recherche Médicale (INSERM), UMR 1078 , Brest, F rance BEAT M . FREY • Department of Molecular Diagnostics and Research (MOC), Blood Transfusion Service Zurich, Swiss Red Cross , Schlieren, Switzerland ix