Molecular Typing of Blood Cell Antigens

275 Pages·2015·8.084 MB·English

by  Peter Bugert

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
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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 meth-
ods 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 sys-
tems 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 com-
plexity 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 meth-
odological 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