US20140213480A1

US20140213480A1 - Method for the simultaneous determination of blood group and platelet antigen genotypes

Info

Publication number: US20140213480A1
Application number: US14/247,383
Authority: US
Inventors: Gregory A. Denomme
Original assignee: Canadian Blood Services
Current assignee: Canadian Blood Services
Priority date: 2004-02-06
Filing date: 2014-04-08
Publication date: 2014-07-31
Also published as: EP1718661A1; CA2554845A1; EP2298785A1; US20100112574A1; EP2298784A1; US20080261205A1; US8728735B2; EP2298785B1; EP1718661A4; CA2554845C; EP2298784B1; CA2897983A1; WO2005075496A1; EP1718661B1; US20100105047A1; US20140213481A1

Abstract

RBC and platelet (Plt) alloimmunization requires antigen-matched blood to avoid adverse transfusion reactions. Some blood collection facilities use unregulated Abs to reduce the cost of mass screening, and later confirm the phenotype with government approved reagents. Alternatively, RBC and Plt antigens can be screened by virtue of their associated single nucleotide polymorphisms (SNPs). We developed a multiplex PCR-oligonucleotide extension assay using the GenomeLab SNPStream platform to genotype blood for a plurality of blood group antigen-associated SNPs, including but not limited to: RhD (2), RhC/c, RhE/e, S/s, K/k, Kp^a/b, Fya/b, FY0, Jk^a/b, Di^a/b, and HPA-1a/b.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a Continuation application of currently pending U.S. Utility application Ser. No. 12/551,881, filed on Sep. 1, 2009, which is a Continuation of U.S. Utility application Ser. No. 10/588,631, filed Nov. 27, 2007, which is a 371 National Stage of International Application No. PCT/CA2005/000250 filed on Feb. 7, 2005, which designated the U.S., and which claims benefit under 35 U.S.C. §119(e) of the U.S. provisional application Ser. No. 60/541,932, filed Feb. 6, 2004. The content of these applications is incorporated herewith in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Mar. 26, 2014, is named Sequence_Listing.txt and is 7,202 bytes in size.

TECHNICAL FIELD

This invention relates to an ultra high throughput (UHT) multiplex PCR genotyping method. More specifically, the present invention relates to an automated method of determining a plurality of blood group and platelet antigen, preferably human platelet antigen (HPA), genotypes simultaneously from a single sample through the detection of single nucleotide polymorphisms (SNPs) for various blood group and platelet antigens.

BACKGROUND OF THE INVENTION

At present, there are 29 blood group systems and 6 HPA systems recognized by the International Society of Blood Transfusion (ISBT), wherein, with a few exceptions, a blood group ‘system’ may be defined by a single gene at a given locus of the human genome (Daniels, G. L. et al. Vox Sang 2003; 84:244; Metcalfe P. et al., Vox Sang. 2003; 85:240). Most people know their ABO and Rh blood group. However, the ABO and Rh blood group systems expressed on red cells simply represent antigens from only two of the 29 blood group systems, and more systems are being discovered each year. Some examples of blood group systems are the ABO, Rh (D, C, c, E, e), P, Lutheran, Kell (K, k), Lewis, Duffy (Fy^a, Fy^b), or Kidd (Jk^a, Jk^b). Moreover, there are over 250 blood group and 12 human platelet antigens assigned to one of the blood group or HPA systems, respectively. A system is defined by a gene or group of genes at a specific locus of the human genome. The alleles or genotype of a person for each blood group or HPA system represent the unique nucleotide gene sequences that express specific blood group or platelet antigens (for a review see Denomme, G. et al., Approaches to Blood Group Molecular Genotyping and Its Applications: in Stowell, C. and Dzik W., editors; Emerging Technologies in Transfusion Medicine, AABB 2003, Ch 4).
A blood group or HPA system maps to a specific region of the human genome, termed a locus. Nearly all blood group or HPAs can be identified by the presence of its unique nucleotide sequence, termed an ‘allele’, at the locus of interest. Every person has two alleles for any given autosomal gene. Some individuals are homozygotes for a specific allele, i.e. they have two identical alleles, while others are heterozygotes for a specific allele, i.e. they have two different alleles. By definition, alleles that represent different blood group or HPAs differ by at least one nucleotide; sometimes they differ by several nucleotides. For example, a deoxythymidine (T) or a deoxycytidine (C) nucleotide can be found at cDNA position 196 of the glycoprotein IIa (GP3A) gene that expresses the HPA-1 (Newman P. J. et al., J Clin Invest 1989; 83:; 1778). The allele containing the deoxthymidine nucleotide expresses the HPA-1a antigen and the allele containing the deoxycytidine nucleotide expresses the HPA-1b antigen. We refer to the T/C nucleotide difference between the two alleles as a single nucleotide polymorphism (SNP).
Blood group alleles for a given blood group system represent genetic variations of the same gene. For example, the ABO blood group system has 3 common alleles, that confer 6 genotypes within this blood group system. Moreover, many alleles within a blood group system express different blood group ‘antigens’, that is to say, dependent on the allelic genotype the corresponding antigenic phenotype is accordingly expressed. Alleles differ in their nucleotide sequence, and the difference between one allele and another, usually within a single blood group system, may be one single nucleotide variation. Therefore, two alleles can differ by one nucleotide, i.e. a SNP and represent a co-dominant bi-allelic system. Alternatively, alleles can differ by a few to several dispersed nucleotides, or by a stretch of nucleotides, any one of which can be used to identify the alleles. Regardless of whether the variations in the nucleotide are due to single or multiple nucleotide differences, the phenotype associated with a specific genotype (the specific nucleotide sequence) will result in the expression of a specific blood group or platelet antigen on the red cell or platelet surface, respectively.
Normally, all blood donations are blood grouped for ABO and RhD. However, sometimes a previously transfused recipient will require more blood that is antigen-matched with one of their own antigens because they have made antibodies to a different blood group or platelet antigen. The gold standard in the industry is to ‘phenotype’ blood for the presence of specific blood group and platelet antigens using government regulated antisera (antibodies) performed by single-test methods or by an automated platform, which is a cost ineffective method for a blood collection facility that routinely performs tests on a high volume basis.
Blood group phenotypes are presently determined using commercially available government-regulated serological reagents and human red cells. These known tests rely on the principle of antibody binding and red cell agglutination to identify clinically important blood group phenotypes. The presently known tests were originally devised some 60 years ago and today require the use of government regulated (for example, Health Canada) approved serological reagents. Some of the tests being employed today have been automated (for example, ABO and Rh typing) while some have been semi-automated (for example, RhC/c and RhE/e). However, many of the presently used tests are performed manually by highly-trained laboratory technologists and are done on a test-by-test basis. In other words, a technologist must perform four separate tests to determine, for example, the Fy^a, Fy^b, Jk^aand Jk^bphenotype of a single blood donation. Essentially, the current tests which employ government-approved reagents in a manual, single-test driven method are a very cost ineffective method for a blood collection facility that is often required to perform such tests on a high volume basis.
In an effort to reduce costs, a blood collection facility will often use non-regulated antisera to ‘screen’ blood donations for important blood group phenotypes and then confirm the phenotype with the regulated antisera. However, since much of the blood is sent to hospitals within 24-48 hours after collection, manual blood group phenotyping cannot meet the short turn-around time required to provide the end user with the information required before blood must be shipped. Therefore, hospital blood banks must perform their own tests on the blood that they have in their inventories. It would be advantageous to provide a cost effective blood screening method that would provide quick and reliable results relating to the clinically important blood group phenotypes.
The prior art uses two basic techniques to detect SNPs; polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) (Chaudhuri A., et al. 1995; 85:615), and sequence specific primer (SSP)-PCR (McFarland J. G. et al., Blood 1991; 78:2276). For PCR-RFLP analysis, restriction enzymes are used to digest PCR amplified genomic DNA fragments. In brief, DNA is extracted from nucleated blood cells manually for each blood sample to be analyzed. The PCR is set up manually; a separate PCR is performed on each sample for each SNP of interest. The PCR amplified fragments are digested with a specific restriction enzyme and the digested products are separated on a gel. The pattern of digested DNA fragments viewed from the gel predicts the presence or absence of either nucleotide of a SNP of interest. In SSP-PCR, two PCRs are set up in separate tubes for each SNP of interest. One tube contains a universal primer and a primer with a sequence that is specific to detect one nucleotide of a SNP. The other tube contains the same universal primer and a primer specific for the other nucleotide of a SNP. Prior art has used two pair or three pair PCR to analyze a nucleotide for a given SNP, with at least one pair acting as an internal control to ensure DNA is available for PCR amplification. The prior art does not provide the use of multiple DNA sequences as primer pairs that work simultaneously on a single sample. Moreover, the prior art does not employ novel DNA sequences to detect blood group SNPs in an automated high-throughput fashion.
St-Louis M., et al. (Transfusion 2003; 43:11126-32) have used allele-specific PCR-ELISA to detect blood group SNPs, wherein some of the PCR primers were publicly known and all primers were labeled with digoxigenin; SNPs were detected by oligonucleotide hybridization using solid-phase microplate wells coated with individual blood group-specific complementary oligonucleotides. An abstract by Buffleir E. et al. (Transfusion 2003; 43:92 A) outlines a combined HPA-1 and HPA-5 genotyping method that uses biotin labeled PCR-amplified targets and allele specific oligonucleotide probes arrayed on the bottom of 96 well microplates. Specific hybridization is detected with the use of an enzyme conjugate which produces a specific colourimetric signal. An array of several oligonucleotides reportedly can be used to detect HPA SNPs. The publications, cited above, do not use multiplex PCR primers, nor do they use extension probes, and rely on a less sensitive and more error-prone allele-specific hybridization to detect the SNPs. There are a few other publications that refer to the multiplex PCR amplification of the RHD gene alone, or together with sex determination, or with internal control primers designed to confirm the presence of DNA in various blood group PCR applications. U.S. Pat. No. 5,723,293 describes a diagnostic method and kit for determining Rh blood group genotypes, wherein there is provided a method for directly determining D and associated CcEe genotypes using restriction fragment length polymorphisms (RFLPs) for diagnosis. U.S. Pat. No. 5,804,379 describes a diagnostic method and kit for determining Kell blood group genotype, wherein there is provided a method for determining the K1/K2 genotype using RFLPs for diagnosis. U.S. Pat. No. 5,780,229 provides polynucleotides for determining the Pen polymorphism of human platelet membrane glycoprotein IIa, and generally describes diagnostic and therapeutic uses relating to the “Pen” human platelet polymorphism (HPA-4) and differs from the teachings of the present invention. United States patent application 20020098528 describes methods and apparatus for blood typing with optical bio-disc, and essentially describes a method for determining the ABO blood cell type of an individual with optical bio-discs and a disc-reading apparatus.
In the SSP-PCR application by St. Louis et al. (Transfusion 2003; 43:1126), two PCR primer pairs are set up, each in a separate well, to detect the nucleotides of a SNP of interest. For example, one primer pair containing a universal primer and a sequence specific primer is set up in a tube to detect a nucleotide of a SNP. Another primer pair containing the same universal and another sequence specific primer is set up in another tube to detect the alternate nucleotide for the same SNP. In addition, each tube includes a primer pair that detects a universal sequence contained in all human DNA. Contained in the PCR tube is digoxigenin-dUTP that is incorporated into the amplified DNA fragment if the sequence specific primer detects the appropriate nucleotide of an SNP. For the detection phase, one of each primer pair contains the chemical tag biotin, which is used to capture the DNA amplified fragment in sets of microtitre wells containing streptavidin. An optical colorimetric assay is used to detect the presence of digoxigenin-dUTP in each of the wells; anti-digoxigenin peroxidase conjugated antibody detects the presence of digoxigenin dUTP and the peroxidase can convert a substrate added to the well into a colored end product. Therefore, the presence of a nucleotide of a SNP is detected by the presence of a color in the microtitre well. Such assays are routinely designed in a 96-well microtitre plate format to facilitate semi-automation. The colorimetric results are evaluated by the operator to determine the presence or absence of the nucleotides for a SNP. The deficiencies of these test systems are the use of a single PCR reaction for each nucleotide of a given nucleotide of each SNP, and the pooling of samples prior to the detection phase and manual post-analyte data analysis.
No prior art has used a multiple, or 12, primer pair multiplexed PCR that successfully works in a single tube, nor has prior art employed novel DNA sequences as probes to detect both nucleotides of a plurality of blood group and HPA genotypes simultaneously, such as the detection of all 12 blood group and HPA SNPs in these mixtures using an automated high-throughput platform.
Accordingly, there is a need for a high-throughput automated multiple blood-group associated SNP analysis of genomic DNA that is capable of rapidly and accurately determining the genotypes and associated phenotypes of a plurality of blood group systems in a single test sample.

SUMMARY OF THE INVENTION

The present invention provides a method of detecting the presence or absence of nucleotides relating to various SNPs for the determination of a specific genotype and accordingly the inferred phenotype. More specifically, the present invention allows for the detection of the presence or absence of two nucleotides of a plurality of different SNPs, and more preferably of the 12 SNPs in a preferred embodiment of the present invention.
The present invention accordingly provides an automated, or robotic, high-throughput ‘screening’ tool for blood group and platelet antigens by evaluating the alleles of the genes that express these antigens on red cells and platelets, respectively. This is done by identifying the unique nucleotides associated with the specific alleles that occupy the gene locus using a testing platform, which requires novel and specific compounds that we designed. Our robotic high-throughput platform provides important blood group and HPA genotype information within 24 hours from the start of the test. We identified the alleles of blood group antigens for; RhD, RhC, Rhc, RhE, Rhe, S, s, Duffy (Fy)^a, Fy^b, K, k, Kp^a, Kp^b, Diego (Di)^a, Di^b, Kidd (Jk)^a, Jk^b, and the platelet antigens, Human Platelet Antigen (HPA)-1a and HPA-1b, representing, but not limited to 19 of the most clinically important antigens in red cell and platelet transfusion. Additional genotyping tests for other clinically important blood group and platelet antigens may be developed, and are encompassed in the teachings of the present invention. When performed on all blood donations for all clinically important blood group and platelet antigens, our invention will provide a comprehensive database to select and confirm the antigens when required using government regulated antisera. The use of this platform as a screening tool will lessen the number of costly government regulated tests to be done by the collection facility and end user (the hospital blood bank), and meet the demand of antigen-matched blood for specific transfusion recipients.
The invention discloses a method for DNA-based blood group genotyping for clinically important blood group and platelet antigens. The technology uses an ultra high-throughput multiplex PCR design to detect specific SNPs that represent clinically important blood group antigens: RhD, RhC, Rhc, RhE, Rhe, S, s, Duffy (Fy)^a, Fy^b, K, k, Kp^a, Kp^b, Diego (Di)^a, Di^b, Kidd (Jk)^a, Jk^b, and the platelet antigens, Human Platelet Antigen (HPA)-1a and HPA-1b. It should be noted however that the present invention is not limited to the detection of SNPs for only the SNPs listed, but additionally comprises the detection of SNPs for all blood group and platelet antigens. The invention discloses novel DNA sequences of PCR primers that are specifically designed to avoid inter-primer pair cross-reactions and post-PCR probes that make multiple analyses possible. The invention represents a novel approach to screening multiple blood group and HPA genotypes at once and addresses a clear need in the art for novel, rapid, cost-effective and reliable genotyping. This additionally replaces the use of expensive and difficult-to-obtain serological reagents, which can be reserved for use to confirm only the donors identified by the screening process.
More specifically, the present invention analyzes the HPA-1 GP3A mutation incorporated into our SNP assay, and the other blood group antigen SNPs in a method according to the present invention.
The invention addresses the need for an automated, accurate, rapid and cost-effective approach to the identification of multiple blood group antigens. The multiplex SNP assay design and automated genotyping platform allows one trained research technician to identify a plurality of blood group alleles, and more specifically, 19 blood group alleles, overnight on 372 to 2232 individual blood samples. In one application of the present invention, the multiplex PCR and SNP detection platform analyzed the nucleotides of 12 SNPs overnight on 372 individual blood samples. The cost using current standard blood group serology for 372 samples is estimated at CDN$99,500, which reflects a reagent cost of CDN$54,000 (excluding new capital equipment investments) and an operator cost of CDN$45,500 to analyse each of the antigens by Gel Card technology (n=5), immediate spin tube test (n=2), indirect antiglobulin tube test (n=8), and platelet GTI® test (n=1). Approximate 10 to 15 fold cost savings are obtained in the simultaneous DNA-based determination of these blood group alleles. It should be noted that the present invention is not limited to the detection of only 12 SNPs, and may be optimally used for the detection a plurality of SNPs for potentially all blood group and platelet alleles. Accordingly, the products, methods, platform and teachings of the present invention can detect all blood group and HPA SNP variations on a great number of samples, such as 744 samples overnight, as further described below.
The present invention overcomes the deficiencies of the prior art because the entire test, i.e. all steps of the method of the present invention, from PCR to computation analyses can be automated and multiplexed so that the nucleotides of a plurality of SNPs, and more preferably, the 12 SNPs of the present invention, can be identified simultaneously. This automated multiplex high throughput analysis can meet the demand of testing hundreds of blood samples, and the turn-around time of less than 24 hours, to provide valuable information to a blood collection facility before blood is shipped to the end user. This platform has the advantage over existing technology in that it reduces operator handling error. In addition, there are significant cost reductions compared with the current government-regulated serological analysis. It should be noted that present prior art technologies relating to PCR-RFLP and SSP-PCR for blood group and platelet antigens are not routinely used since they are no more cost efficient than serology. The present invention overcomes the deficiencies of the prior art and fulfils an important need in the present art for the automated, accurate, rapid and cost-effective identification of multiple blood group and HPA SNPs.
The invention provides the opportunity to screen all blood donors to obtain a daily or ‘live’ repository of the genotypes or combinations of genotypes currently available for specific transfusion needs. Accordingly, the present invention fulfills a need relating to the collection and antigen screening of blood and blood products.
For convenience, some terms employed in the present specification are noted below. Unless defined otherwise, all technical and scientific terms used herein have the meanings commonly understood by one of ordinary skill in the present art.
The present invention provides a method or screening assay for the determination of blood genotypes of the various blood group and HPA systems through the ultra high throughput multiplex PCR analysis of SNPs in an automated platform (Petrick J. Vox Sang 2001; 80:1). A platform, as referred to herein, refers to a system of machine(s) and protocol(s) capable of analyzing multiplex PCR amplified SNPs, wherein said platform is not limited to, but may comprise the GenomeLab SNPStream (Beckman Coulter Inc., Fullerton, Calif.), the SNPSTREAM™ UHT (Orchid BioSciences, Princeton, N.J.), the SNPSTREAM™ 25K (Orchid BioSciences, Princeton, N.J.), the MALDI-TOF/Mass-Spectrophotometer Spectro CHIP (Sequenom, San Diego, Calif.), and the Gene Chip Microarray (Affymetrix, Inc., Santa Clara, Calif.), Nano Chip (Nanogen, San Diego, Calif.) and the Random Ordered Bead Arrays (Illumina, Inc., San Diego, Calif.) or any other system, machine or protocol capable of analyzing multiplex PCR amplified SNPs. Accordingly, the present invention provides a platform, or system and protocols, for the evaluation and detection of SNPs, for the purpose of typing (determining the genotype and corresponding phenotype) blood group and platelet, preferably, human platelet antigen (HPA) SNP analysis. A preferred platform that can be used in accordance with the present invention is the Orchid SNP-IT system for HLA typing (Orchid Bioscience, Princeton, N.J.), wherein a preferred embodiment of the present invention comprises the use of the primer pairs of Table 1 for the specific oligonucleotide primer extension of blood group and platelet, preferably, human platelet antigen (HPA) SNPs, and the probes of Table 2 for the specific hybridization thereof, and the simultaneous analysis of the absence or presence of a plurality of blood group and platelet, preferably, human platelet antigen (HPA) SNPs using a platform as described herein, or using any SNP analysis system capable of detecting multiplex PCR amplified SNPs.
For the purposes of the present disclosure, SNPs, may refer to any blood group and HPA SNPs, and more preferably refers to any of the SNPs specified in Table 1, or any other known blood group or HPA SNPs or single nucleotide changes including, but not limited to, nucleotide substitutions, deletions, insertions or inversions, that can be defined as a blood group or HPA SNP due to nucleotide differences at the specified position in a gene sequence.
Ultra high throughput (UHT) refers to the implementation of the platform in a rapid and optimized form, that is to say, through the analysis of multiple SNPs. That is to say, UHT analysis refers to the rapid and simultaneous evaluation of a plurality of samples for a plurality of markers, in this case SNPs. For example, the analysis of 12 SNPs (equivalent to 12 C and 12 T nucleotides) for 372 samples, would result in the generation of 8928 (i.e. 2×12×372) determinations that are analysed, an evaluation that far exceeds the number of evaluation points possible with manual or automated serological methods.
Phenotype in the context of red cell blood group and Human Platelet Antigen (HPA) refers to the expressed moiety of an allele for a given gene, and is also referred to in this document as ‘antigen’. Genotype refers to the two alleles of an autosomal gene that occupy a given locus or alternatively to either one or two alleles of an X-linked gene that occupies a given locus.
Antigen refers to a red cell or platelet membrane carbohydrate, protein or glycoprotein that is expressed as a polymorphic structure among the human population, that is to say a moiety that is immunogenic in another animal, or human, due differences in its amino acid or carbohydrate composition. Blood group or red cell, or HPA or platelet antigen refers to a moiety expressed on red cells or platelets that has been assigned a blood group or Human Platelet Antigen (HPA) designation, or provisional or workshop designation. The present invention comprises a method and for the determination of the antigen genotype and corresponding phenotype of any blood group or red cell, or HPA or platelet antigen using multiplex PCR SNP analysis. The following two tables (Table A and Table B) list most of the known human blood group and platelet antigens. Many of the antigens can be identified by their unique nucleotide sequence.

TABLE A

Human Red Cell Blood Group Systems

			Component	Associated
ISBT Name (ISBT	Chromosome	Gene Name	Name	Blood Group
Number)	Location	ISGN (ISBT)	(CD Number)	Antigens

ABO (001)	9q34.2	ABO (ABO)	Carbohydrate	A, B, A, B, A1
MNS (002)	4q28.2-q31.1	GYPA (MNS)	GPA (CD235a)	M, N, Vw,
		GYPB (MNS)	GPB (CD235b)	S, s, U, He +
				36 more
P (003)	22q11.2-qter	P1 (P1)	Carbohydrate	P1
Rh (004)	1p36.13-p34.3	RHD (RH)	RhD (CD240D)	D, G, Tar
		RHCE (RH)	RhCE	C, E, c, e, V,
			(CD240CE)	Rh17 + 39 more
Lutheran (005)	19q13.2	LU (LU)	Lutheran glyco-	Lu^a, Lu^b, Lu3,
			protein	Lu4, Au^a, Au^b+
			B-CAM (CD239)	13 more
Kell (006)	7q33	KEL (KEL)	Kell glycoprotein	K, k, Kp^a, Kp^b,
			(CD258)	Ku, Js^a, Js^b+
				17 more
Lewis (007)	19p13.3	FUT3 (LE)	Carbohydrate	Le^a, Le^b, Le^ab,
			Adsorbed form	Le^bh, ALe^b, BLe^b
			plasma
Duffy (008)	1q22-q23	DARC (FY)	Fy glycoprotein	Fy^a, Fy^b, Fy3,
			(CD234)	Fy4, Fy5, Fy6
Kidd (009)	18q11-q12	SLC14A1 (JK)	Kidd	Jk^a, Jk^b, Jk3
			glycoprotein
Diego (010)	17q21-q22	SLC4A1 (DI)	Band 3, AE1	Di^a, Di^b, Wr^a,
			(CD233)	Wr^b, Wd^a, Rb^a+
				14 more
Yt (011)	7q22	ACHE (YT)	Acetyl-	Yt^a, Yt^b
			cholinesterase
Xg (012)	Xp22.32	XG (XG)	Xg^aglycoprotein	Xg^a
		MIC2	CD99	CD99
Scianna (013)	1p34	ERMAP (SC)	ERMAP	Sc1, Sc2, Sc3, Rd
Dombrock (014)	12p13.2-p12.1	DO (DO)	Do glycoprotein;	Do^a, Do^b, Gy^a,
			ART 4	Hy, Jo^a
Colton (015)	7p14	AQP1 (CO)	Channel-forming	Co^a, Co^b, Co3
			integral protein
Landsteiner-	19p13.3	LW (LW)	LW glycoprotein	LW^a, LW^ab, LW^b
Wiener (016)			(ICAM-4)
			(CD242)
Chido/Rodgers	6p21.3	C4B, C4A	C4B, C4A	CH1, CH2, Rg1 +
(017)		(CH/RG)		6 more
Hh (018)	19q13.3	FUT1 (H)	Carbohydrate	H
			(CD173)
Kx (019)	Xp21.1	XK (XK)	Xk glycoprotein	Kx
Gerbich (020)	2q14-q21	GYPC (GE)	GPC	Ge3, Ge4, Wb,
			GPD (CD236)	Ls^a, Dh^aGe2,
				Ge3, An^a
Cromer (021)	1q32	DAF (CROM)	DAF (CD55)	Cr^a, Tc^a, Tc^b,
				Tc^c, Dr^a, Es^a,
				IFC,
				WES^a, WES^b,
				UMC, GUTI
Knops (022)	1q32	CR1 (KN)	CR1 (CD35)	Kn^a, Kn^b, McC^a,
				Sl^a, Yk^a
Indian (023)	11p13	CD44 (IN)	Hermes antigen	In^a, In^b
			(CD44)
OK (024)	19pter-p13.2	CD147 (OK)	Neurothelin,	Ok^a
			basogin (CD147)
RAPH (025)	11p15.5	MER2 (MER2)	Not defined	MER2
JMH (026)	15q22.3-q23	SEMA-L (JMH)	H-Sema-L	JMH
			(CD108)
I (027)	6p24	CGNT2 (IGNT)	Carbohydrate	I
Globoside (028)	3q25	B3GALT3	Carbohydrate	P
		(βGalNAcT1)	(Gb₄, globoside)
GIL (029)	9p13	AQP3 (GIL)	AQP3	GIL

ISGN = International Society for Gene Nomenclature

TABLE B

Human Platelet Antigen Systems

		Chromo-
	Gene	some		Associated
System	Name	Location	Component Name (CD)	Antigens

HPA-1	GP3A	17q21.32	Integrin β3 (CD61)	Pl^A1/2
HPA-2	GP1BA	17pter-	Glycoprotein Ibα	Ko^a/b
		p12	(CD42b)
HPA-3	GP2B	17q21.32	Integrin α2b (CD41)	Bak^a/b
HPA-4	GP3A	17q21.32	Integrin β3 (CD61)	Pen^a/b
HPA-5	GP1A	5q23-q31	Integrin α2 (CD49b)	Br^a/b
HPA-6w	GP3A	17q21.32	Integrin β3 (CD61)	Ca^a/Tu^a
HPA-7w	GP3A	17q21.32	Integrin β3 (CD61)	Mo^a
HPA-8w	GP3A	17q21.32	Integrin β3 (CD61)	Sr^a
HPA-9w	GP2B	17q21.32	Integrin α2b (CD41)	Max^a
HPA-	GP3A	17q21.32	Integrin β3 (CD61)	La^a
10w
HPA-	GP3A	17q21.32	Integrin β3 (CD61)	Gro^a
11w
HPA-	GP1BB	22q11.2	Glycoprotein Ibβ	Ly^a
12w			(CD42c)
HPA-	GP1A	5q23-q31	Integrin α2 (CD49b)	Sit^a
13w
HPA-	GP3A	17q21.32	Integrin β3 (CD61)	Oe^a
14w
HPA-15	AF410459	6q13	GPI-linked GP (CD109)	Gov^a/b
HPA-	GP3A	17q21.32	Integrin β3 (CD61)	Duv^a
16w
?	GPV	?	Glycoprotein V	Pl^T
?	GPIV	7q11.2	Glycoprotein IV (CD36)	Vis^a/Nak^a

Note:
HPA numbers on the left ending with a ‘w’ represent ISBT workshop designations and are tentative HPA systems.

A single nucleotide polymorphism (SNP) refers to any blood group or HPA allele that defines a specific red cell or platelet antigen by virtue of its unique nucleotide sequence as defined in Garratty et al. Transfusion 2000; 40:477 and as updated from time-to-time by the International Society of Blood Transfusion.
It is understood that the presently disclosed subject matter is not limited to the particular methodology, protocols, cell lines, vectors, and reagents described as these can vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the presently disclosed subject matter.
Unless defined otherwise, all technical and scientific terms used herein are intended to have their meanings as understood by one skilled in the present art. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the presently disclosed subject matter, the preferred embodiments, methods, devices and materials described.
It is also understood that the articles ‘a’ and ‘an’ are used herein to refer to one or to more than one (i.e. to at least one) of the grammatical object of the article. Accordingly, ‘an element’ means one element or more than one element.
Our novel platform simultaneously performs automated multiple blood group-associated SNP analyses using genomic DNA and the Thermus aquaticus polymerase chain reaction (PCR) to infer the presence of specific blood group genotypes. This automated high-throughput platform has particular application in the blood donation industry since it represents a novel screening tool for the expression of blood group antigens or phenotypes.
Our platform provides important genotypic information within 24 hours of donation. When performed on all blood donations for all important blood group phenotypes, our invention will provide a comprehensive database to select and confirm blood group phenotypes using government regulated antisera. The use of this platform as a screening tool will lessen the number of regulated blood group phenotype tests done by the collection facility and end user, and meet the end user demand for antigen-matched blood for transfusion recipients.
Unique to this invention is the assay design for the simultaneous identification of a plurality of blood group or HPA alleles. The present invention provides novel assay for the simultaneous identification of a plurality of blood group or HPA alleles, and more preferably of 19 blood group alleles using a plurality of SNPs, and more preferably, 12 SNPs. In one embodiment, the genotyping platform queries genetic variants using multiplexed single nucleotide primer extension coupled with two-laser fluorescence detection and software for automated genotype calling. Each of the relevant gene regions are PCR amplified from purified genomic DNA in a single reaction using the following oligonucleotide primer designs:


Gene	Primer	Sequence (5′ - 3′)

RHD Exon	RHDe4S	AGACAAACTGGGTATCGTTGC
4		(SEQ ID NO: 1)
	RHDe4A	ATCTACGTGTTCGCAGCCT (SEQ ID NO:
		2)

RHD Exon	RHDe9S	CCAAACCTTTTAACATTAAATTATGC
9		(SEQ ID NO: 3)
	RHDe9A	TTGGTCATCAAAATATTTAGCCTC
		(SEQ ID NO: 4)

RHCE Exon	RHCEe2S	TGTGCAGTGGGCAATCCT (SEQ ID NO:
2		5)
	RHCEe2A	CCACCATCCCAATACCTG (SEQ ID NO:
		6)

RHCE Exon	RHCEe5S	AACCACCCTCTCTGGCCC (SEQ ID NO:
5		7)
	RHCEe5A	ATAGTAGGTGTTGAACATGGCAT
		(SEQ ID NO: 8)

GYPB Exon	GYPBe4S	ACATGTCTTTCTTATTTGGACTTAC
4		(SEQ ID NO: 9)
	GYPBe4A	TTTGTCAAATATTAACATACCTGGTAC
		(SEQ ID NO: 10)

KEL Exon	KELe6S	TCTCTCTCCTTTAAAGCTTGGA
6		(SEQ ID NO: 11)
	KELe6A	AGAGGCAGGATGAGGTCC (SEQ ID NO:
		12)

KEL Exon	KELe8S	AGCAAGGTGCAAGAACACT
8		(SEQ ID NO: 13)
	KELe8A	AGAGCTTGCCCTGTGCCC (SEQ ID NO:
		14)

FY	FYproS	TGTCCCTGCCCAGAACCT (SEQ ID NO:
Promoter		15)
	FYproA	AGACAGAAGGGCTGGGAC (SEQ ID NO:
		16)

FY Exon	FYe2S	AGTGCAGAGTCATCCAGCA
2		(SEQ ID NO: 17)
	FYe2A	TTCGAAGATGTATGGAATTCTTC
		SEQ ID NO: 18)

JK Exon	JKe9S	CATGAACATTCCTCCCATTG
9		(SEQ ID NO: 19)
	JKe9A	TTTAGTCCTGAGTTCTGACCCC
		(SEQ ID NO: 20)

DI Exon	DIe19S	ATCCAGATCATCTGCCTGG
18		(SEQ ID NO: 21)
	DIe19A	CGGCACAGTGAGGATGAG (SEQ ID NO:
		22)

GP3A	GP3Ae3S	ATTCTGGGGCACAGTTATCC
		(SEQ ID NO: 23)
	GP3Ae3A	ATAGTTCTGATTGCTGGACTTCTC
		(SEQ ID NO: 24)

The above primer pairs comprise the corresponding forward and reverse primers, and may be referred to herein as SEQ ID NOs 1-24.
Multiplexed single nucleotide primer extension is performed using the following 5′ tagged extension primers:

	RHD Exon 4
	(SEQ ID NO: 25)
	GTGATTCTGTACGTGTCGCCGTCTGATCTTTATCCTCCGTTCCCT

	RHD Exon 9
	(SEQ ID NO: 26)
	GCGGTAGGTTCCCGACATATTTTAAACAGGTTTGCTCCTAAATCT

	RHCE Exon 2
	(SEQ ID NO: 27)
	GGATGGCGTTCCGTCCTATTGGACGGCTTCCTGAGCCAGTTCCCT

	RHCE Exon 5
	(SEQ ID NO: 28)
	CGACTGTAGGTGCGTAACTCGATGTTCTGGCCAAGTGTCAACTCT

	GYPB Exon 4
	(SEQ ID NO: 29)
	AGGGTCTCTACGCTGACGAT TTGAAATTTTGCTTTATAGGAGAAA

	KEL Exon 6
	(SEQ ID NO: 30)
	AGCGATCTGCGAGACCGTATTGGACTTCCTTAAACTTTAACCGAA

	KEL Exon 8
	(SEQ ID NO: 31)
	AGATAGAGTCGATGCCAGCTTTCCTTGTCAATCTCCATCACTTCA

	FY Promoter
	(SEQ ID NO: 32)
	GACCTGGGTGTCGATACCTAGGCCCTCATTAGTCCTTGGCTCTTA

	FY Exon 2
	(SEQ ID NO: 33)
	ACGCACGTCCACGGTGATTTGGGGGCAGCTGCTTCCAGGTTGGCA

	JK Exon 9
	(SEQ ID NO: 34)
	CGTGCCGCTCGTGATAGAATAAACCCCAGAGTCCAAAGTAGATGT

	DI Exon 19
	(SEQ ID NO: 35)
	GGCTATGATTCGCAATGCTTGTGCTGTGGGTGGTGAAGTCCACGC

	GP3A Exon 3
	(SEQ ID NO: 36)
	AGAGCGAGTGACGCATACTTGGGCTCCTGTCTTACA

	GP3A Exon 3
	(SEQ ID NO: 37)
	GCCCTGCCTC

The above probes may be referred to herein as SEQ ID NOs 25-37. The DNA bases are represented by their single letter equivalents (A,C,G or T) and SEQ ID NOs: 36 and 37 are joined together by a C3 (phosphoramidite) spacer between the two sequences represented by letter X as follows AGAGCGAGTGACGCATACTTGGGCTCCTGTCTTACAXGCCCTGCCT (SEQ ID NO. 36 X SEQ ID NO. 37).
In this embodiment, the 12 bolded nucleotides in the 5′ region of the extension probes are hybridized to a complementary DNA sequence that has been micro-arrayed onto microplates so that specific blood group SNPs are individually identified and reported.
Proof of principle experiments have been performed using 372 consent qualified samples (please refer to Appendix A). Collection of serological data for samples has been constant and the success rates based upon the expected allele frequencies have been performed.
In the preceding example, one preferred embodiment has been described. However, it should be obvious to one skilled in the art that other methodologies and/or technologies for SNP identification could be used, providing that the novel DNA sequences disclosed above are also used.
The teachings and method of the present invention are superior to the teachings of the prior art for a number of reasons, one of which is that the complete method of the present invention, from DNA extraction to result computation analyses can be automated and multiplexed so that many SNPs can be determined simultaneously. This automated multiplex high throughput analysis can meet the demand (hundreds of blood donations can be tested) and the turn-around time (<24 hours) to collate and provide valuable information to the blood collection facility before blood is shipped to the end user. This platform and method has the further advantage over existing technology in that it reduces operator handling error.
In addition, there are significant cost reductions compared with the current technology. The invention addresses the need for an automated, accurate, rapid and cost-effective approach to the identification of multiple blood group SNPs. According to an embodiment, a multiplex SNP assay of the present invention detected 12 SNPs overnight on 372 individual blood samples. In accordance with the teachings of the present invention, the platform, products and methods of the present invention can detect all SNP variations for all blood group antigens, for example, as shown below on 744 samples.

BRIEF DESCRIPTION OF THE DRAWINGS

Further features and advantages of the present invention will become apparent from the following detailed description, taken in combination with the appended drawings, in which:

FIG. 1 A computer screen display of a typical UHT SNP scatter plot to sort the fluorescence of a C/T SNP analysis of GP3A Exon 3 for HPA-1a/b genotyping.

FIG. 2 Representative samples of GP3A Exon 3 HPA-1a/b) genotyping by manual PCR-RFLP analysis using MspI restriction enzyme analysis (A) and the tabulated comparative results with the UHT SNP analysis (B).

FIG. 3 Representative samples JK genotyped by manual PCR-RFLP analysis using MnlI (A) and the tabulated comparative results with the UHT SNP analysis (B).

FIG. 4 A-L Computer screen displays of typical UHT SNP scatter plots to sort the fluorescence of a C/T SNP for various blood group and HPA genotypes.

Appendix A provides a tabulated summary of the multiplex SNP assay detection of 12 possible SNPs on 372 individual blood samples.
It will be noted that throughout the appended drawings, like features are identified by like reference numerals.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

RBC and platelet (Plt) alloimmunization requires antigen-matched blood to avoid adverse transfusion reactions. Some blood collection facilities use unregulated Abs to reduce the cost of mass screening, and later confirm the phenotype with government approved reagents. Alternatively, RBC and Plt antigens can be screened by virtue of their associated single nucleotide polymorphisms (SNPs). The present invention provides a multiplex PCR-oligonucleotide extension assay using the GenomeLab SNPStream platform, or any other SNP analysis system, to genotype blood for a plurality of common antigen-associated SNPs, including but not limited to: RhD (2), RhC/c, RhE/e, S/s, K/k, Kp^a/b, Fya/b, FY0, Jk^a/b, Di^a/b, and HPA-1a/b. According to one example of the present invention, a total of 372 samples were analysed for 12 SNPs overnight. Individual SNP pass rates varied from 98-100% for 11 of 12 SNPs. Of the Rh-pos, 98.6% were correctly identified. Six of 66 Rh-neg (9%) were typed as RHD-pos; 5 of 6 were subsequently demonstrated to contain an non-RHDψ gene by SSP-PCR. Eleven of 12 R1R1 and 1 of 1 r″r were correctly identified. HPA-1b was identified in 4, which was confirmed by PCR-RFLP (n=4) and serology (n=1). PCR-RFLP on selected samples (n<20) for K/k, Fy^a/b, and Jk^a/bwere 100% concordant. Confirmation of some of the results is provided. The platform has the capacity to genotype thousands of samples per day for all SNP variations. The suite of SNPs can provide collection facilities with real-time genotypic data for all donors at an annual cost (excluding RhD) estimated to equal the current cost of phenotyping 5-10% of the donors.

Methods and Reagents

Methodology Specific to the Invention.

We have designed a novel blood group and HPA SNP and detection system that employ the use of two sets of novel compounds (reagents) that are specifically designed to work in a multiplex format.
In brief, genomic DNA is harvested the salting out procedure using the Qiagen (Qiagen Inc. Valencia, Calif.) Blood DNA Isolation Kit. Our invention can use any good quality DNA harvested by any one of a variety of methods. For the multiplex PCR, the DNA regions containing all 12 SNPs of interest were PCR-amplified in a single reaction well. Tables 1 and 2 outline the novel PCR primers and extension probes, respectively, used in the assay. Note that the concentration of the various reagents may be adjusted to optimize DNA amplification, and is dependent on but is not limited to: the concentration and quality of the genomic DNA, the concentration of the PCR primers or the type of thermal cycler used for the PCR.
Our current genotyping technology identifies SNPs using single base-pair primer extension using the novel products and protocols of the present invention. In brief, the genomic region surrounding the SNP of interest is PCR-amplified as described above, preferably using one or more, or all of the primer pairs of Table 1. Then, the amplified DNA fragments are used as a template for DNA hybridization using one or more or all the corresponding novel probes of Table 2, and single nucleotide extension (synthesis) based on the nucleotide present at each of the specific SNP sites. The PCR primers pairs in Table 1 represent sequences complementary to DNA regions containing SNPs of interest; of which the exact sequences of each primer pair and mixture of primer pairs have been specifically optimized to amplify genomic DNA of interest as a mixture of 12 primer pairs. Although noted above, Table 2 further summarizes 12 novel extension primers specifically used together to detect the nucleotides of blood group and platelet antigen or HPA SNPs, simultaneously. The extension primers represent a group of 12 novel nucleotide sequences, of which each are a combination of: 1) a unique 5′ region necessary to direct hybridization to a micro-arrayed tag located in a specific spot in each microplate well, and 2) a 3′ region complementary to and adjacent to a SNP of a PCR-amplified DNA region containing the SNP of interest.

TABLE 1

The PCR primers used in the 12-pair multiplex PCR format for multiple SNP
detection.

		Primer		Product	Size
Antigen	SNP	Name	Sequence	5′-3′	Target	(bp)

RhD/RhCE	C/T	RHDe4S	AGACAAACTGGGTATCGTTGC	RHD	111
		RHDe4A	ATCTACGTGTTCGCAGCCT	Exon	4

RhD/RhCE	A/G	RHDe9S	CCAAACCTTTTAACATTAAATTATGC	RHD		98
		RHDe9A	TTGGTCATCAAAATATTTAGCCTC	Exon	9

RhC/Rhc	T/C	RHCEe2S	TGTGCAGTGGGCAATCCT	RHCE		90
		RHCEe2A	CCACCATCCCAATACCTG	Exon	2

RhE/Rhe	C/G	RHCEe5S	AACCACCCTCTCTGGCCC	RHCE	107
		RHCEe5A	ATAGTAGGTGTTGAACATGGCAT	Exon	5

GYPBS/GYPBs	T/C	GYPBe4S	ACATGTCTTTCTTATTTGGACTTAC	GPYB		103
		GYPBe4A	TTTGTCAAATATTAACATACCTGGTAC	Exon 4

K/k	T/C	KELe6S	TCTCTCTCCTTTAAAGCTTGGA	KEL	142
		KELe6A	AGAGGCAGGATGAGGTCC	Exon	6

Kp^a/Kp^b	T/C	KELe8S	AGCAAGGTGCAAGAACACT	KEL		100
		KELe8A	AGAGCTTGCCCTGTGCCC	Exon	8

Fy/Fy0	T/C	FYproS	TGTCCCTGCCCAGAACCT	Duffy		90
		FYproA	AGACAGAAGGGCTGGGAC	Promoter

Fy^a/Fy^b	G/A	FYe2S	AGTGCAGAGTCATCCAGCA	Duffy	122
		FYe2A	TTCGAAGATGTATGGAATTCTTC	Exon	2

Jk^a/Jk^b	G/A	JKe9S	CATGAACATTCCTCCCATTG	Kidd	130
		JKe9A	TTTAGTCCTGAGTTCTGACCCC	Exon	9

Di^a/Di^b	T/C	DIe19S	ATCCAGATCATCTGCCTGG	Diego		90
		Die19A	CGGCACAGTGAGGATGAG	Exon 19

HPA-1a/b	T/C	GP3Ae3S	ATTCTGGGGCACAGTTATCC	GP3A	114
		GP3Ae3A	ATAGTTCTGATTGCTGGACTTCTC	Exon	3

The above primers correspond to SEQ ID NOs 1-24, respectively, as outlined herein above.

TABLE 1A

Additional Blood Group and Platelet Antigen
SNPs for Clinically Relevant Antigens.

		Product
Antigen	SNP	Target	Size (bp)

A/O	G/T	ABO
GalNAc/Del		Exon 6
A/B	C/G	ABO
(GalNAc/Gal)		Exon 7
A/B	G/A	ABO
(GalNAc/Gal)		Exon 7
A/B	C/A	ABO
(GalNAc/Gal)		Exon 7
A/B	G/C	ABO
(GalNAc/Gal)		Exon 7
M/N	G/A	MNS
		Exon 2
M/N	T/G	MNS
		Exon 2
MNS/MiI	C/T	MNS
		Exon 3
RHD/Weak D	T/G	RHD
Type 1		Exon 6
RHD/Weak D	G/C	RHD
Type 2		Exon 9
RHD/Weak D	C/G	RHD
Type 3		Exon 1
RHD/D nt602	C/G	RHD
Variants		Exon 4
RHD/‘DAR’	T/C	RHD
Variant		Exon 7
RHD/Weak D	C/A	RHD
Type 5		Exon 3
RHD/D_el	G/A	RHD
		IVS3 + 1
RHD/D_el	G/T	RHD
		Exon 6
RHD/D_el	G/A	RHD
		Exon 9
RHD/RHD_ψ	A/T	RHD
nt506		Exon 4
RHCE/RhC	T/C	RHCE
		IVS2 + 1722
RHCE/RhC	C/T	RHCE
		IVS2_1751
RHCE/	C/G	RHCE
VS variant		Exon 5
Lu^a/Lu^b	A/G	LU
		Exon 3
Au^a/Au^b	A/G	LU
		Exon 12
Js^a/Js^b	C/T	KEL
		Exon 17
Js/Js_null	G/T	JK
		IVS7 + 1
FY/Fy^x	C/T	FY
		Exon 2
FY/Fy^x	G/A	FY
		Exon 2
Wr^a/Wr^b	A/G	DI
		Exon 16
Yt^a/Yt^b	C/A	YT
		Exon 2
Sc1/Sc2	G/A	SC
		Exon 3
Do^a/Do^b	C/T	DO
(nt 378)		Exon 2
Do^a/Do^b	T/C	DO
(nt 624)		Exon 2
Do^a/Do^b	A/G	DO
(nt 793)		Exon 2
Co^a/Co^b	C/T	CO
		Exon 1
In^a/In^b	C/G	IN
		Exon 2
Ok(a+)/Ok(a−)	G/A	OK
		Exon 4
GIL/GIL_null	G/A	GIL
		IVS5
HPA-2a/b	C/T	GP1BA
		Exon 2
HPA-3a/b	T/G	GP2B
		Exon 26
HPA-4a/b	G/A	GP3A
		Exon 4
HPA-5a/b	G/A	GP1A
		Exon 13
Gov^a/Gov^b	A/C	CD109
		Exon 19

Each antigen listed on the left represents a blood group or HPA genotype and the single nucleotide polymorphism (SNP). Some genotypes are evaluated using more than one SNP because they differ by more than one nucleotide. Each PCR primer pair consists of a sense (Primer Name ending in S) and antisense (Primer Name ending in A) oligonucleotide (Sequence 5′-3′) designed to amplify the DNA region containing the SNP for the antigen of interest. The target region (Product Target) and the amplified fragment (Size (bp)) are shown on the right. Note that 12 SNPs are evaluated for 19 different blood group and platelet antigens because some antigens have more than one SNP. In some cases an A or G SNP is included since the complementary DNA strand can be evaluated as it will contain the T or C SNP of interest.

TABLE 2

Extension probes used to detect the nucleotides of blood group and HPA SNPs.

Name	Sequence	5′-3′

RHD	GTGATTCTGTACGTGTCGCC GTCTGATCTTTATCCTCCGTTCCCT
Exon
4

RHD	GCGGTAGGTTCCCGACATAT TTTAAACAGGTTTGCTCCTAAATCT
Exon
9

RHCE	GGATGGCGTTCCGTCCTATT GGACGGCTTCCTGAGCCAGTTCCCT
Exon
2

RHCE	CGACTGTAGGTGCGTAACTCGATGTTCTGGCCAAGTGTCAACTCT
Exon
5

GYPB	AGGGTCTCTACGCTGACGAT TTGAAATTTTGCTTTATAGGAGAAA
Exon
4

KEL	AGCGATCTGCGAGACCGTAT TGGACTTCCTTAAACTTTAACCGAA
Exon
6

KEL	AGATAGAGTCGATGCCAGCT TTCCTTGTCAATCTCCATCACTTCA
Exon
8

FY	GACCTGGGTGTCGATACCTA GGCCCTCATTAGTCCTTGGCTCTTA
Promoter

FY Exon	ACGCACGTCCACGGTGATTT GGGGGCAGCTGCTTCCAGGTTGGCA
2

JK Exon	CGTGCCGCTCGTGATAGAAT AAACCCCAGAGTCCAAAGTAGATGT
9

Di Exon	GGCTATGATTCGCAATGCTT GTGCTGTGGGTGGTGAAGTCCACGC
19

GP3A	AGAGCGAGTGACGCATAC TTGGGCTCCTGTCTTACAXGCCCTGCCTC
Exon
3

The above probes correspond to SEQ ID NOs 25-36, respectively, as identified herein above. The DNA bases are represented by their single letter equivalents (A, C, G or T) and the letter X in GP3A, Fxon 3, between the SEQ ID NO: 36 AND SEQ ID NO: 37 represents a C3 (phosphoramidite) spacer between the two adjacent DNA bases.

The present invention also provides novel hybrid probes, wherein the preferred probes are listed in Table 2, but limited to said listing. Each extension probe is designed in two parts: (1) the 5′ portion: the 5′ nucleotides indicated in boldface of the extension primer are complementary to unique and specific DNA sequences which are micro-arrayed onto the bottom of microplates in a specified location of each microplate well. Thus, the 5′ portion of the extension probes in table 2 represent, but are not limited to, 12 unique complementary sequences used together to identify the individual SNPs through hybridization to the micro-arrayed tags in the microplate wells. The 12 unique 5′ portions can be interchanged with each of the 3′ regions specified below, which contain DNA sequences complementary to and adjacent to the SNPs of interest, or they can be interchanged with other additional unique 5′ portions as specified by the micro-arrayed tags in the microplate wells provided they are used to identify blood group or HPA SNPs; and (2) the 3′ portion: the 3′ nucleotides are complementary to and precisely adjacent to the SNP site of the PCR-amplified DNA, which enables the detection of either or both nucleotides of the SNP. Thus, the extension probe is a unique sequence that can hybridized to a specific location and to the PCR-amplified DNA and be extended by a single fluorescent-labeled dideoxy-nucleotide using PCR thermal cylers. The extension probe products are hybridized to the complementary micro-arrayed DNA sequence on the microplate and the incorporation of Bodipy- and Tamra-labeled dideoxy-nucleotides are detected by laser-microplate fluorescence for each individual blood group SNP. The presence of the nucleotides for a given SNP is displayed by automated imaging and analysis software. In one variation of the detection reaction, a dideoxyguanidine tri-nucleotide labeled with the Bodipy-fluorochrome is added in the extension reaction. If a deoxycytidine is present in the PCR-amplified DNA fragment, then the nucleotide will be incorporated into the nascent DNA fragment. In another variation of the reaction, a dideoxyadenine nucleotide labeled with the Tamra-fluorochrome is added to the extension assay. If the PCR-amplified fragment contains a deoxythimidine, then an extension will occur. In each case, the flurochrome is detected after the extension reaction has been completed. Again, these reactions proceed in the same tube along with the other extension reactions. The laser-detection apparatus can identify and evaluate each specified extension due to the location of each micro-arrayed DNA sequence.
Each extension primer has a region complementary to a tag that is been bound to the surface of a microplate well (Bold nucleotides) and a region (Italicized nucleotides) that is complementary to the region and immediately adjacent to the SNP site.
It should be noted that the teachings, products and methods of the present invention are not limited to the above-specified primer pairs and probes, but additionally comprise all primer pairs and probes specific to the blood group and HPA SNPs, wherein said primer pairs and probes are optimized for use in a multiplex PCR reaction for the simultaneous identification of more than one, or all, blood group or HPA genotypes and their corresponding phenotypes.

EXAMPLES

Although the following examples may provide preferred methods, products, platforms or protocols of the present invention, it will be understood by one skilled in the art that the presently provided examples are not limited to the specified parameters of each example, and may be varied provided that the resulting outcome of the methods or protocols are in accordance with the teachings of the present invention, and the products are functionally equivalent or relating to the teachings of the present invention.

Example 1

A preferred protocol for the multiplex blood group and HPA SNP Genotyping is provided. Although the present example analyzes 12 SNP extension primers, the present invention is not limited to the analysis of a maximum of 12 SNPs, but may include a plurality of SNPs relating to more than one or all of the blood group or HPA SNPs.
Additional blood group and platlet antigen SNPs for clinically relevant antigens embodied by the present invention appear in Table 1A. Primer pairs and probes, such as those exemplified in Tables 1 and 2, corresponding to these SNPs of clinical relevance, can be prepared according to the teachings of the present invention. Target primers may be initially identified from existing databases (e.g. autoprimer.com) based on information corresponding to the SNP of interest and the corresponding flanking regions, and subsequently optimized as herein disclosed for use in accordance with the present invention.

I (a). PCR Primer Pooling

Step

Action



	1	Dilute each of 12 PCRS and PCRA primer (forward and
		reverse primers) pairs to final concentration of
		240 uM (only required upon arrival of new primers)
	2	Generate working primer pool by combining 5 ul of
		each of the 24 individual PCR primers

I (b). SNP Extension Primer Pooling

Step

Action



	1	Dilute each of 12 SNP extension primers to final
		concentration of 120 uM (only required upon arrival
		of new primers)
	2	Generate working SNP extension primer pool by
		combining 10 ul of each of the 12 individual SNP
		extension primers

II. Multiplex PCR from purified DNA templates

Step

Action

1	Prepare 10 ul multiplex PCR master mix for use with
	96 well plates containing PCR primers (synthesized
	by Integrated DNA Technologies, Coralville, IA,
	USA), dNTPs (MBI Fermentas, Hanover, MD, USA),
	MgCl₂, 10X PCR Buffer, and Amplitaq Gold (Applied
	Biosystems, Branchburg, NJ, USA):

	Initial	Final	Volume
Component	Concentration	Concentration	(ul/well)
PCR primer pool	10 uM each	50 nM each	0.05
dNTPs	2.5 mM each	75 uM each	0.33
MgCl₂	25 mM	5 mM	2.00
10x PCR Buffer	10x	1x	1.00
AmpliTaq Gold	5 U/ul	0.075 U/ul	0.15
dH₂O			4.47

2	For each DNA Sample, transfer 2 ul of 4 ng/ul stock
	DNA to each well of 96 well plates. Use Biomek FX
	(Beckman Coulter Inc., Fullerton, CA, USA) Script
	‘2ul96well Transfer’ automated program
3	Place Multiplex PCR Master Mix in Biomek FX station
	1. Place 96 well plates of DNA in Biomek FX station
	5-8.
4	Transfer 8 ul Multiplex PCR master mix to DNA samples
	using Biomek FX Script: ‘8 ul PCR Transfer’
5	After addition of master mix seal tightly with MJ
	Microseal A film (MJ Research, Inc., Waltham, MA,
	USA)
6	Spin down in centrifuge for 30 sec at 1500 rpm
7	Place in MJ Tetrad Thermal cyclers (MJ Research,
	Inc., Waltham, MA, USA)and run ‘UHT-MPX’ CBS
	multiplex PCR program:
	Thermal cycle conditions ‘UHT-MPX’:

	Denature	94° C. 1:00 (min)
	35 cycles of:	94° C. 0:30 (min)
		55° C. 0:33 (min)
		72° C. 1:00 (min)
	Hold Temperature	4° C. ∞

III. Post PCR Cleanup

Step

Action

1	Prepare ExonucleaseI (ExoI; USB Corporation,
	Cleveland, OH, USA) and Shrimp Alkaline Phosphatase
	(SAP; USB Corporation, Cleveland, OH, USA) master
	mix:

Component	Final concentration	Volume per well (ul)
ExoI	2 U	0.4
SAP	1 U	2.0
10x SAP buffer	1x	0.6
dH₂O		3.0

2	Add Exo/SAP master mix to grooved reservoir and
	place on Multimek (Beckman Coulter Inc., Fullerton,
	CA, USA) Station 3
3	Add UHT (ultra high-throughput) salt solution
	(provided) to grooved reservoir and place on
	Multimek Station 4
4	Transfer 8 ul Exo/SAP master mix to amplified PCR
	products using Multimek Script: EXO96-2.SCI (two 96
	well plates, at Multimek stations 1 and 2
5	After Multimek addition of Exo/SAP seal tightly with
	MJ Microseal A film
6	Spin down in centrifuge for 30 sec at 1500 rpm
7	Place in MJ Tetrad Thermal cyclers and run
	‘UHTCLEAN’ program:
	Thermal cycle conditions ‘UHTCLEAN’:

	Temp	Time (min)
	37° C.	30:00
	100° C.	10:00
	4° C.	∞

IV. SNP-IT Assay using the GENOMELAB SNPSTREAM ™ (Beckman

Coulter Inc. Fullerton, CA, USA)

Step	Action

1	Prepare SNP-IT extension mix containing extension
	primers (synthesized by Integrated DNA Technologies,
	Coralville, IA, USA), C/T ddNTPs, Extension mix
	diluent, and DNA polymerase (Beckman Coulter Inc.,
	Fullerton, CA, USA)

	Component	Volume per well (ul)
	SNP Extension primer pool	3.22
	C/T ddNTP Extension mix	21.43
	Extension mix diluent	402.98
	DNA polymerase	2.24
	dH2O	318.22

2	Add SNP-IT mix to grooved reservoir and place on
	Multimek Station 3
3	Add UHT salt solution (provided) to grooved
	reservoir and place on Multimek Station 4
4	Transfer 7 ul SNP-IT extension mix to UHT-CLEAN PCR
	products using Multimek Script: 7UL96-2.SCI (two 96
	well plates, at Multimek stations 1 and 2
5	After Multimek addition of SNP-IT extension mix seal
	tightly with MJ Microseal A film
6	Spin down in centrifuge for 30 sec at 1500 rpm
7	Place in MJ Tetrad Thermal cyclers and run ‘UHT-
	SNPIT’ program:
	Thermal cycle conditions ‘UHTSNPIT’:

	Temp	Time (min)
Denature	96° C.	3:00
45 cycles of:	94° C.	0:20
	40° C.	0:11
Hold Temperature	4° C.	∞

V. Post-extension Transfer and Hybridization

Step

Action

1	Preheat incubator to 42° C.
2	Make sure there is adequate 20x dilution of SNPWare
	UHT Wash Buffer in washer Carboy B. If required
	dilute 20x stock solution with water and refill
	Carboy B

3	Run SAMI/EL 405 Script ‘Prime B’
4	Place all Tag Array plates in Row 1 of the Carousel,
	starting with Hotel 1, with subsequent plates in
	Hotel 2, 3, etc., preferably with their barcodes
	facing inwards.
5	Place all PCR plates directly below their
	corresponding Tag Array Plates. PCR plates
	corresponding to Quadrants 1-4 should be placed in
	Rows 2-5 of the proper Hotel, respectively. For all
	PCR plates, the “ABC . . . ” lettered edge of the plates
	should face inwards on the Carousel.
6	Place grooved reservoir with solubilized UHT Salt
	Solution in Multimek Station 4
7	Place grooved reservoir with Hybridization solution
	master mix in Multimek Station 3
	Hybridization Solution master mix:

	Component	Volume per Tag Array plate (ul)
	2x Hybridiaztion Soluton	3500.00
	Hybridization Additive	203.7

8	Run SAMI Script ‘Post-extension
	Transfer_Hybridization 1x384.smt’:
	This automated program prepares the tag array plate
	by washing it 3x with SNPWare UHT wash buffer; adds
	8.0 ul of Hybridization solution master mix to each
	SNP extension reaction and subsequently transfers
	8.0 ul of this mixture to the prepared tag array
	plate.
9	Place Tag Array plates in humidified 42° C. incubator
	for 2 hours

VI. Post-Hybridization Wash

Step

Action



	1	Make sure there is adequate 64x dilution of SNPWare
		UHT Stringent Wash Solution in washer Carboy C. If
		required dilute 64x stock solution with water and
		refill Carboy C
	2	Run SAMI/EL 405 Script ‘Prime C’
	3	Run SAMI/EL 405 Script ‘Post-hyb 3x Wash’
	4	Completely dry Tag Array plates using vacuum/pipette
		tip

	5	Run SAMI/EL405 script ‘Prime A’ several times to
		clean plate washer pins

VII. UHT (Ultra high through-put) Tag Array Plate Reading

Step

Action



1	Turn on lasers, turning both keys 90 degrees
	clockwise, and allow at least 30 minutes to warm up
2	Turn on SNPScope Reader and Twister.
3	Activate lasers: Flip two switches on laser box
	from ‘Standby’ to ‘Operate’/‘Laser’
4	Open UHT Run Manager Software and ‘Initialize’
	SNPScope system
5	Stack Tag Array plates in Twister carousel 1, with
	‘Assay Test Plate’ on top. Make sure all barcodes
	are facing outwards, and plates are pushed towards
	the reader
6	Select ‘SNPTEST_W_BC_run’ from UHT RUN Manager
	Software, enter the number of plates to be read
	(including the test plate).
7	Select ‘RUN’

The SNPScope plate reader will excite and capture images of Bodipy-fluorescein and Tamra-labeled ddNTPs separately. All genotype calls are subsequently automatically generated using the SNPStream Software Suite of MegaImage, UHTGetGenos and QCReview.
It should be noted that the specific steps associated with the protocol exemplified in Example 1 are not intended to limit the teachings and methods of the present invention to the specific above protocol. Example 1 is provided to specify a preferred method in accordance with the present invention wherein a plurality of blood group and HPA SNPs are simultaneously analysed in a ultra high throughput multiplex automated system for the determination of the specific genotypes and accordingly the phenotypes associated therewith. Accordingly, it should be understood by one skilled in the art that the steps of Example 1 may be varied provided that such variations yield the preferred results of the present invention.

Results

1. GP3A Exon 3 SNP Scatter Plots.

The robotic UHT platform produces laser-fluorescence values for each sample which are represented in ‘scatter plots’ for the operator to review. A sample scatter plot is shown in FIG. 1 for the SNP analysis GP3A Exon 3, which represents the HPA-1a and HPA-1b antigens. As can been seen in FIG. 1 and FIG. 4, results are graphed using logarithmic and XY scatter plots (upper right). Green O, orange □ or blue O sample designations represent CC, TC and TT SNP genotype calls, respectively, with corresponding graphical summaries appearing in the respective legends of each figure. No fluorescence represents an assay failure (FL) for that sample.
Scatter plots (as shown in FIG. 1 and FIG. 4) are generated preferably using SNPStream software suite and viewed through QCReview. It should be additionally noted that the present analysis is not limited to SNPstream or QCReview, and may be carried out using any SNP analysis software. Individual TT, TC and CC genotype calls are represented as dark blue, orange and green open circles, respectively. Sample failures and water controls are represented by yellow and light blue filled circles respectively. Logarithmic (left) and XY scatter (upper right) plots are generated using the relative fluorescence of the Bodipy-fluorescein and Tamra labels obtained during SNPScope plate imaging and analysis.

2. SNP Data Manipulation and Analysis.

The SNP results of a scatter plot are electronically exported to a spreadsheet and examined for total sample failure and individual SNP failure rates. SNP results for 372 DNA samples are summarized in Table 3 (provided in Appendix A). Accordingly, Table 3 provides the Pass and Failure Rates for 12 blood group and HPA SNP analyses. 372 DNA samples were analyzed for several antigens, including the blood group RhD (RHD Exon 4 and RHD Exon 9) and platelet HPA-1a/b (GP3A Exon 3) genotypes. Sample success or pass rates are indicated on the right and individual SNP success or pass rates are shown at the bottom. Three hundred and fifty seven of 372 samples (96%) had results for at least one SNP. Individual SNP results (i.e. minus the sample failures) ranged from 80-100%; only two SNPs had success rates <98%. Individual SNP failures do not affect the results of a sample for other SNPs that do not fail.

3. SNP Allele Result Compared to the Serological Result

RhD status was compared between the serological result and the SNP analysis for RHD Exon 4 and RHD Exon 9. Table 4 summarizes the comparison. 287 of 291 (98.6%) RhD positive units and 55 of 66 (83.3%) RhD negative units were identified correctly using the UHT SNP platform. It is important to note that the 6 incorrect calls suggesting the presence of the RHD gene in a serologically RhD-negative sample may be due to one of the non-functional RHD genes present in the random population (Singleton B. K. et al., Blood 2000; 95:12; Okuda H., et al., J Clin Invest 1997; 100:373; Wagner F. F. et al., BMC Genet 2001; 2:10).

TABLE 4

A comparison of the SNP genotype result and the serological
result obtained with government-regulated antisera.

D-		RHD Exon	RHD Exon
positive:	Assay	4	9	No	Percent

N = 291		pos	Pos	287	98.6%
		neg	Neg	4	1.4%
	Total			291

D-
negative:	Assay	RHD4	RHD9	No	Percent

N = 66		neg	Neg	55	83.3%
		neg	FL	5	7.6%
		pos	Pos
	6	9.1%
	Total			66

NOTE:
CBS laboratory regulations do not allow copies of serological results of blood donors to be made from their laboratory information system. Therefore, the results of the CBS serological phenotypes were reviewed by research personnel and the results tabulated and compared to the SNP data.

4. SNP Genotype Frequency Analysis.

The SNP results then were compared with published phenotype frequencies for Caucasians and Blacks and are summarized in Table 5 below. The data clearly shows that the allele frequencies are consistent with the accepted published frequencies for Caucasians and Blacks. The data show that the SNP genotype frequencies match the published population phenotype frequencies.

TABLE 5

Table 5. A summary of the UHT SNP analysis of genotype
frequencies for several SNPs analyzed and compared to
published phenotype frequencies for Caucasians and
Blacks. The ethnicity of the samples analyzed is not known.
UHT Genotyping Analysis
FL = assay failure

Phenotype	Caucasians	Blacks	Observed	(%)

K− k+

91%

98%

326

91.3

KEL Exon6

K− k+	91%	98%	326	91.3
K+ k−	0.2%	rare	0	0
K+ k+	8.8%	2%	28	7.8
Fails			3	0.8

No of FL	18
No. of Pass	354
Call Rate	95.2%

An independent assay as described in Molecular Protocols in Trans-

fusion Medicine was performed using the UHT SNP Stream System.

Seven samples were tested (Four KEL 2/KEL 2, Three KEL1/KEL 2).

All samples showed a 100% correspondence with the UHT genotype

results.

KEL Exon8

Kp(a+ b−)	Rare	0%	0	0
Kp(a− b+)	97.7%	100%	354	99.2
Kp(a+ b+)	2.3%	rare	1	0.3
Fails			2	0.6

No of FL	17
No. of Pass	355
Call Rate	95.4%

DI Exon18

Di(a+ b−)	<0.01%	<0.01%	0	0
Di(a− b+)	>99.9%	>99.9%	353	98.9
Di(a+ b+)	<0.1%	<0.1%	2	0.6
Fails			2	0.6
No of FL	17
No. of Pass	355
Call Rate	95.4%

FY PRM

wt/wt	348	97.5
wt/mut	7	20
mut/mut	2	0.5
Fails	0	0
No of FL	15
No. of Pass	357
Call Rate	96.0%

An independent assay as described in Molecular Protocols in Trans-

fusion Medicine was performed using the UHT SNP Stream System.

Thirteen samples were tested (six wt/wt, five wt/mut and two

mut/mut for the GATA site).

All samples showed a 100% correspondence with the UHT genotype

results.

FY Exon 2

Fy(a+ b−)	17%	9%	89	24.9
Fy(a− b+)	34%	22%	112	31.4
Fy(a+ b+)	49%	1%	155	43.4
Fails			1	0.3
No of FL	16
No. of Pass	356
Call Rate	95.7%

An independent assay as described in Molecular Protocols in Trans-

fusion Medicine was performed using the UHT SNP Stream System

Eleven samples were tested (eight FY2/FY2, three FY1/FY2 and one

FY1/FY1).

All samples showed a 100% correspondence with the UHT genotype

results.

GP3A Exon 3

HPA-1a/1a	80%	84%	263	73.7
HPA-1a/1b	18%	64%	89	24.9
HPA-1b/1b	2%	0%	4	1.1
Fails			1	0.3
No of FL	16
No. of Pass	356
Call Rate	95.7%

An independent assay as described in Molecular Protocols in Trans-

fusion Medicine was performed using the UHT SNP Stream System.

Eighteen samples were tested (Seven HPA-1a, Seven HPA-1a/1b and

Four HPA-1b).

All samples showed a 100% correspondence with the UHT genotype

results.

JK9

Jk(a+ b−)	26.3%	51.1%	90	25.2
Jk(a− b+)	23.4%	8.1%	87	24.4
Jk(a+ b+)	50.3%	40.8%	178	49.4
Fails			2	0.5
No of FL	17
No. of Pass	355
Call Rate	95.4%

An independent assay as described in Molecular Protocols in Trans-

fusion Medicine was performed using the UHT SNP Stream System.

Nineteen samples were tested (Seven JK1, Seven JK1/JK2 and Five

JK2).

All samples showed a 100% correspondence with the UHT genotype

results.

5. HPA-1a/HPA-1b PCR-RFLP Analysis.

The GP3A Exon 3 SNP detection method for HPA-1a/b genotyping (Appendix A) was compared to a subset of samples (n=18) using conventional PCR-RFLP analysis performed independently (FIG. 2). The results of the two assays were 100% concordant. In addition, a 217G nucleotide mutation 21 basepairs downstream of the GP3A SNP was present in sample 8. This mutation does not affect HPA-1b expression but is detected in the PCR-RFLP and is prone to interpretation error in the conventional PCR-RFLP assay. However, the sample was correctly genotyped as HPA-1b in our SNP assay. Accordingly, the present invention eliminates or minimizes error in HPA-1 results obtained since no confusing or confounding information results from the gel readings of the present invention. That is to say, the conventional RFLP detected the presence of an additional DNA fragment at ˜180 bp which represents a heterozygous HPA-1b/1b^G217allele and was correctly genotyped as HPA-1b/b by the present invention.

Example 2

However, it should be obvious to one skilled in the art that other methodologies and/or technologies for SNP identification could be used, providing that the novel DNA sequences disclosed above are also used. Other embodiments could include the following but without limitation to micro-arrays on glass slides or silica chips, the use of mass spectrometry, or oligo-ligation and extension techniques to detect the SNPs of interest.
A preferred method of the present invention relates to a method for the detection of blood group and HPA genotypes. The present invention also provides novel DNA sequences that are used as primers in a multiplex PCR format according to the present invention to amplify the genomic regions of interest. The present invention also provides novel combinations of DNA sequences that are used in said multiplex PCR format, and for novel DNA sequences that are used to detect blood group and platelet SNPs.
A preferred application of the present invention is in the blood collection and blood banking industry without limitation to red blood cell, platelet, and bone marrow donations. Canada has over 850,000 blood donations yearly, many from repeat donors. Eventually, after all repeat donors are tested (each donor is tested once), the analyses will be performed only on the blood of new donors. With over 29 blood group and 6 HPA systems encompassing over 250 antigens, the platform will find wide application in this industry.
The present invention additionally encompasses various embodiments relating to the detection of various SNPs for the determination of the various genotypes in a sample and for the determination of the corresponding phenotype. In a preferred embodiment, the present invention utilizes a platform to analyzes a cytidine-to-thymidine (C→T) single nucleotide polymorphism. The invention may also employ the multiplex detection of, but not limited to, C→A, A→T, and G→C SNPs, or any other nucleotide SNP related to blood group or platelet antigens.
The present invention may additionally include methods and products for the detection of clinically relevant blood group antigens whereby an antigen of interest is characterized by a genotypic identifier that exceeds a single nucleotide polymorphism. Specifically, the present invention may extend to include clinically relevant insertions or deletions or other nucleotide changes that characterize a blood group antigen of interest, such a multiple base pair insertion in an allele of interest. For example, a genotypic identifier corresponding to a blood group antigen of interest may be pre-characterized, suitable primers and probes for detection thereof may be prepared and a blood sample screened according to the teachings of the present invention.
The present invention provides DNA sequences corresponding to the PCR primer pairs optimized for multiplex use to identify blood group and platelet antigens simultaneously. Accordingly, the present invention provides the novel primer pair sequences listed in Table 1.
The present invention additionally provides novel DNA sequences used to identify the single nucleotide polymorphisms (SNPs) that represent underlying DNA blood group and platelet antigens. Accordingly, the present invention provides the novel extension probes listed in Table 2.
The present invention provides a method of a combined analysis of blood group and HPA SNP analyses.
The present invention advantageously utilizes PCR, the variant and unique SNPs for the variant alleles that infer blood group phenotypes, and single base extension and detection chemistry as a foundation for the novel products and methods of the present invention. Accordingly, the present invention provides a high throughput, multiplexed, DNA-based method of blood group genotyping that replaces the current manual, semi-automated and automated serological screening process used to determine blood group phenotypes.
Accordingly, the present invention provides a method for the identification of rare blood group genotypes due to the suite of SNPs as described above, and in some instances replaces the current state of the art in which most rare blood group genotypes are identified serendipitously (propositus and their relatives) and enabling significant advances over current serological technologies. For example, by analyzing the SNP for the RhC allele in Rh negative blood, we can identify RhC homozygotes and thereby, the rare RhD-negative and Rhc-negative blood.
The present invention additionally provides a method of use in tissue compatibility matching for the purposes, without limitation, of organ transplantation, bone marrow transplantation and blood transfusion related to blood group and platelet antigens.
The present invention additionally provides novel components and constituents that are beneficial for the analyses relating to the present invention. More specifically, the group of currently developed SNPs representing a ‘suite’, or the presently known set of SNPs that relate to clinically important blood group and HPA genotypes for red blood cell and platelet antigens, respectively are provided. The present invention is not limited to the presently listed SNPs, but is understood to comprise all blood group and platelet antigen, and preferably HPA SNPs that may be analyzed in accordance with the teachings of the present invention and using the products, protocols and methods of the present invention.
The present invention also provides the DNA primer sequences optimized for use in a multiplex PCR format.
The present invention also provides novel DNA probe sequences used to detect the SNPs of interest.
The present invention provides a method for the simultaneous detection of a plurality of blood group SNPs. More specifically, the present invention provides a method for the simultaneous detection of at least 19 blood group SNPs; RHD (2), RHC/c, RHE/e, S/s, Duffy (a/b), Kidd (a/b), Diego (a/b), Kell K1/K2, Kell K3/K4, and HPA-1a/b simultaneously. The method of the present invention provides (1) DNA sequences corresponding to the PCR primer pairs optimized for multiplex use to identify a plurality of blood group and platelet antigens simultaneously; (2) Novel DNA sequences used to identify the single nucleotide polymorphisms (SNPs) that represent underlying DNA blood group and platelet antigens; and (3) The combination of SNP analyses including blood group and platelet antigens.
To support and validate the teachings of the present invention various experimental tests have been completed and analyzed. Numerous validating experimental data has been recorded, however, for the purpose of simplicity the following example is provided. Each step in the validating experiment is noted below:
(1) Ultra high throughput (UHT) Multiplex SNP analyses on 372 unrelated blood donor specimens for RHD (2), RHC/c, RHE/e, S/s, FY1/FY2 (2), JK1/JK2, DI1/DI2, KEL1/KEL2, KEL3/KEL4, and HPA-1A/B genotypes and corresponding phenotypes was examined, and data was recorded (please refer to Appendix A for the raw data accumulated, and Table 5 for a Summary of the results obtained).
(2) Manual PCR-RFLP analyses was performed on some of the 372 specimens for some of the blood group SNPs to for comparison to the results obtained in Step (1).
(3) Serological analyses was also performed on some of the 372 specimens for each of the blood group and HPA SNPs using Health Canada regulated reagents performed by licensed medical technologists in a provincially licensed laboratory.
(4) Serological analyses was also performed on some of the 372 specimens for each of the blood group and platelet antigens by unlicensed research technologists using Health Canada regulated reagents and methodologies in an unlicensed laboratory.
The results obtained from the above validating experimental data is provided below by way of supportive Figures and Tables.

1. SNP Platform Data Generation.

The robotic platform produces fluorescence for each sample which are presented in ‘scatter plots’ (as illustrated in FIG. 1) for the operator to review. Sample genotype results are shown for each blood group SNP and are graphed using logarithmic and XY scatter plots (upper right). Green, orange or blue sample designations represent CC, TC and TT genotype calls respectively. No fluorescence represents an assay failure (FL) for that sample.

2. SNP Data Manipulation and Analysis.

The SNP results of a scatter plot are electronically exported to a spreadsheet and examined for total sample failure and individual SNP failure rates. Twelve SNP results for 372 DNA samples are summarized in Table 3 with sample failure rates (shown on the right) and individual SNP success rates (shown at the bottom). Three hundred and fifty seven of 372 samples (96%) had results for at least one SNP. Individual SNP results ranged from 80% to 100%; only one SNP result success rate was <98%. Individual SNP failures do not affect the results of a sample for other SNPs that do not fail.

3. SNP Allele Frequency Analysis.

The SNP results where then compared with published phenotype frequencies for Caucasians and Blacks and are summarized in Table 5 above. The data shows that the allele frequencies are consistent with the accepted published frequencies for Caucasians and Blacks.

3.1 SNP Allele Result Compared to the Serological Result.

RhD status was compared between the serological result and the SNP analysis for RHD exon 4, and 9 (RHD Exon 4, RHD Exon 9, respectively). Table 4 summarizes the comparison. 287 of 291 (98.6%) RhD positive units and 55 of 66 (83.3%) RhD negative units were identified correctly using the UHT SNP platform.

3.2 SNP Analysis Compared to Manual PCR-RFLP.

Some of the UHT SNP genotype results were compared with manual PCR-RFLP analysis performed independently. The results show 100% concordance. A representative PCR-RFLP is shown in FIG. 3.
The genotyping technology provided in the present invention queries and analyzes SNPs using single base-pair primer extension. In brief, the genomic region surrounding the SNP of interest is amplified and used as a template for the ensuing hybridization and single nucleotide extension of the SNP specific extension primer. The extension primer is designed to hybridize adjacent to the polymorphic nucleotide(s) and enables us to query bi-allelic polymorphisms, small insertions, deletions or inversions. The 5′ extension primer tags are hybridized to the complementary DNA sequence on micro-arrayed plates and incorporation of Bidopy- and Tamra-labeled ddNTPs are detected by laser-microplate fluorescence for each individual blood group and HPA SNP. Individual sample genotypes are generated through automated imaging and analysis software as shown in the genotype scatter plots of FIG. 1.
The embodiment(s) of the invention described above is(are) intended to be exemplary only. The scope of the invention is therefore intended to be limited solely by the scope of the appended claims.

APPENDIX A

Genotype Results for updated 12 SNP CBS Panel

Sample

Pass

ID

RHD4

RHD7

RHD9

RHCE2

RHCE5

KEL6

KEL8

DI18

FYP

FY2

GP3A

JK9

FL

Rate

BB24401

FL

12

0.0%

BB24402

TT

FL

CC

TC

CC

TT

CC

TC

CC

1

91.7%

BB24407

TC

TT

TC

CC

TT

TC

0

100.0%

BB24408

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24409

TC

TT

TC

CC

TT

CC

TC

0

100.0%

BB24410

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24415

TC

TT

TC

FL

CC

TT

TC

1

91.7%

BB24416

FL

12

0.0%

BB24417

TC

TT

TC

FL

TC

CC

TT

CC

TT

TC

1

91.7%

BB24420

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24421

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24422

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24423

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24424

TC

TT

TC

FL

TC

CC

TT

CC

TT

TC

1

91.7%

BB24425

TC

TT

TC

CC

TT

TC

0

100.0%

BB24426

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24427

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24428

TC

TT

TC

CC

TT

TC

0

100.0%

BB24429

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24430

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24431

TC

TT

TC

CC

TC

CC

TT

TC

TT

0

100.0%

BB24432

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24433

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24434

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24435

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24436

TT

FL

CC

TC

CC

TT

TC

TT

TC

1

91.7%

BB24437

TC

TT

TC

CC

TT

0

100.0%

BB24438

TC

TT

TC

CC

TT

0

100.0%

BB24439

TC

TT

TC

CC

TT

TC

0

100.0%

BB24440

TC

TT

TC

FL

TC

CC

TT

CC

TT

TC

1

91.7%

BB24444

TC

TT

TC

CC

TC

CC

TT

TC

TT

TC

0

100.0%

BB24448

TT

FL

CC

FL

CC

TT

TC

TT

CC

2

83.3%

BB24461

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24462

TT

FL

CC

TC

CC

TT

TC

TT

CC

1

91.7%

BB24463

TC

TT

TC

CC

TT

TC

0

100.0%

BB24464

TC

TT

TC

CC

TT

TC

0

100.0%

BB24465

TC

TT

TC

CC

TT

TC

0

100.0%

BB24466

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24467

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24468

TC

TT

TC

FL

TC

CC

TT

CC

TT

TC

1

91.7%

BB24469

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24470

TT

FL

CC

TC

CC

TT

CC

1

91.7%

BB24471

TC

TT

TC

CC

TT

TC

0

100.0%

BB24472

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24473

TC

TT

TC

CC

TT

CC

0

100.0%

BB24474

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24475

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24476

TC

TT

TC

CC

TT

TC

0

100.0%

BB24477

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24478

TC

TT

TC

CC

TT

TC

0

100.0%

BB24479

TC

TT

TC

CC

TT

TC

0

100.0%

BB24480

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24481

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24482

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24483

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24484

TC

TT

TC

CC

TT

CC

TC

0

100.0%

BB24485

TT

FL

CC

FL

TC

CC

TT

TC

2

83.3%

BB24486

TT

FL

CC

TC

CC

TT

1

91.7%

BB24487

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24488

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24489

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24491

TC

TT

TC

CC

TT

TC

0

100.0%

BB24492

TT

FL

CC

TC

CC

TT

CC

TT

CC

1

91.7%

BB24493

TT

FL

CC

TC

CC

TT

TC

TT

TC

1

91.7%

BB24494

FL

12

0.0%

BB24495

TC

TT

TC

CC

TT

TC

0

100.0%

BB24496

TC

TT

TC

CC

TT

CC

0

100.0%

BB24497

TC

TT

TC

CC

TT

TC

0

100.0%

BB24499

TC

TT

TC

CC

TT

CC

0

100.0%

BB24504

TC

TT

TC

CC

TT

TC

0

100.0%

BB24505

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24506

TC

TT

TC

CC

TT

TC

0

100.0%

BB24507

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24512

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24513

TC

TT

TC

FL

TC

CC

TT

CC

TT

CC

1

91.7%

BB24516

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24517

TT

FL

CC

TC

CC

TT

TC

TT

1

91.7%

BB24518

TC

TT

TC

CC

TT

CC

TC

0

100.0%

BB24519

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24522

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24523

FL

12

0.0%

BB24524

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24525

TC

TT

TC

FL

TC

CC

TT

TC

TT

1

91.7%

BB24526

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24527

TT

FL

CC

TC

CC

TT

CC

TT

TC

1

91.7%

BB24528

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24529

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24530

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24531

FL

12

0.0%

BB24532

TC

TT

TC

CC

TT

TC

0

100.0%

BB24533

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24534

TC

TT

TC

FL

TC

CC

TT

1

91.7%

BB24535

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24536

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24537

TC

TT

TC

CC

TT

TC

0

100.0%

BB24538

TC

TT

TC

CC

TT

TC

0

100.0%

BB24539

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24540

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24541

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24542

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24543

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24547

FL

12

0.0%

BB24548

TT

FL

CC

TC

CC

TT

CC

TT

TC

1

91.7%

BB24549

TT

FL

CC

FL

CC

TT

TC

TT

TC

2

83.3%

BB24550

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24552

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24553

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24554

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24555

TC

TT

TC

CC

TT

0

100.0%

BB24556

TC

TT

TC

CC

TT

0

100.0%

BB24557

TC

TT

TC

CC

TT

TC

0

100.0%

BB24558

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24559

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24560

TT

FL

CC

TT

CC

TT

CC

1

91.7%

BB24561

TC

TT

TC

FL

TC

CC

TT

CC

TC

1

91.7%

BB24562

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24563

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24564

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24565

TC

TT

TC

CC

TT

TC

0

100.0%

BB24566

TT

FL

CC

TC

CC

TT

TC

TT

TC

1

91.7%

BB24567

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24568

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24569

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24570

TC

TT

TC

FL

TC

CC

TT

TC

CC

1

91.7%

BB24571

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24572

TT

FL

CC

TC

CC

TT

TC

TT

TC

1

91.7%

BB24573

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24574

TT

FL

CC

TC

CC

TT

TC

TT

CC

1

91.7%

BB24575

TT

FL

CC

TC

CC

TT

TC

TT

CC

1

91.7%

BB24576

TC

TT

TC

CC

TT

TC

0

100.0%

BB24577

TC

TT

TC

CC

TT

CC

0

100.0%

BB24578

TC

TT

TC

CC

TT

TC

0

100.0%

BB24579

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24580

TT

FL

CC

TC

CC

TT

TC

TT

CC

2

83.3%

BB24581

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24586

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24587

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24594

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24600

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24601

TC

TT

TC

FL

TC

CC

TC

TT

CC

1

91.7%

BB24602

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24603

TC

TT

TC

FL

TC

CC

TT

TC

TT

1

91.7%

BB24604

TC

TT

TC

CC

TT

TC

0

100.0%

BB24605

TC

TT

TC

CC

TT

TC

0

100.0%

BB24606

TC

TT

TC

CC

TT

CC

0

100.0%

BB24607

TC

TT

TC

CC

TC

TT

TC

CC

0

100.0%

BB24608

TC

TT

TC

CC

TT

CC

0

100.0%

BB24609

TC

TT

TC

FL

TC

CC

TT

CC

TC

CC

1

91.7%

BB24610

TT

FL

CC

TC

CC

TT

TC

TT

1

91.7%

BB24611

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24612

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24613

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24614

TC

TT

TC

CC

TT

0

100.0%

BB24615

TC

TT

TC

CC

TC

CC

TT

CC

0

100.0%

BB24616

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24617

TC

TT

TC

FL

TC

CC

TT

TC

TT

1

91.7%

BB24618

TC

TT

TC

CC

TC

TT

TC

0

100.0%

BB24619

TC

TT

TC

FL

CC

TT

TC

2

83.3%

BB24620

TC

TT

TC

FL

CC

TT

CC

TT

TC

2

83.3%

BB24621

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24622

TC

TT

TC

FL

TC

CC

TT

CC

TT

TC

1

91.7%

BB24623

TT

FL

CC

TC

CC

TT

TC

TT

CC

1

91.7%

BB24624

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24625

TC

TT

TC

CC

TT

0

100.0%

BB24626

TC

TT

TC

CC

TT

TC

0

100.0%

BB24627

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24628

TC

TT

TC

CC

TT

TC

0

100.0%

BB24629

FL

12

0.0%

BB24630

TC

TT

TC

CC

TT

0

100.0%

BB24631

TC

TT

TC

FL

TC

CC

TT

CC

TT

TC

1

91.7%

BB24632

TC

TT

TC

CC

TC

TT

TC

0

100.0%

BB24633

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24634

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24635

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24636

TC

TT

TC

FL

TC

CC

TT

CC

TT

CC

1

91.7%

BB24637

TC

TT

TC

FL

TC

CC

TT

1

91.7%

BB24638

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24639

TT

FL

CC

TC

CC

TT

CC

TT

TC

1

91.7%

BB24640

TC

TT

TC

CC

TT

CC

0

100.0%

BB24641

TT

FL

CC

TC

CC

TT

1

91.7%

BB24642

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24643

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24644

TT

FL

TC

FL

CC

TT

TC

TT

CC

4

66.7%

BB24645

TC

TT

TC

CC

TT

CC

0

100.0%

BB24646

TT

FL

CC

TC

CC

TT

1

91.7%

BB24647

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24648

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24649

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24650

FL

12

0.0%

BB24651

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24652

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24653

TC

TT

TC

CC

TT

CC

TC

TT

0

100.0%

BB24654

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24655

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24656

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24657

FL

12

0.0%

BB24658

TT

FL

CC

TC

CC

TT

CC

TT

TC

1

91.7%

BB24659

TC

TT

TC

CC

TT

TC

0

100.0%

BB24660

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24661

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24662

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24663

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24664

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24665

TT

FL

CC

TC

FL

CC

FL

TT

TC

CC

TC

4

66.7%

BB24666

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24667

TC

TT

TC

CC

TT

TC

0

100.0%

BB24668

TC

TT

TC

CC

TT

TC

0

100.0%

BB24669

TC

TT

TC

CC

TC

CC

TT

CC

TC

CC

0

100.0%

BB24670

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24672

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24673

TC

TT

TC

CC

TT

TC

0

100.0%

BB24674

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24675

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24676

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24678

TT

FL

CC

TC

CC

TT

TC

TT

TC

1

91.7%

BB24679

TC

FL

TC

CC

TT

CC

TT

1

91.7%

BB24680

TC

TT

TC

CC

TT

0

100.0%

BB24681

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24682

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24683

TT

FL

CC

TC

CC

TT

TC

TT

1

91.7%

BB24684

TC

TT

TC

CC

TT

TC

0

100.0%

BB24685

TC

TT

TC

CC

TT

CC

0

100.0%

BB24686

TC

TT

TC

CC

TT

CC

TC

0

100.0%

BB24687

TC

TT

TC

CC

TT

CC

TC

TT

0

100.0%

BB24688

TT

FL

CC

TC

CC

TT

TC

TT

1

91.7%

BB24689

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24690

TC

TT

TC

CC

TT

CC

TC

CC

0

100.0%

BB24691

TC

TT

TC

CC

TT

CC

0

100.0%

BB24692

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24693

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24694

TT

FL

CC

TC

CC

TT

TC

TT

TC

1

91.7%

BB24695

TT

FL

CC

TC

CC

TT

CC

1

91.7%

BB24696

TC

TT

TC

CC

TT

TC

0

100.0%

BB24697

TC

TT

TC

CC

TT

0

100.0%

BB24698

TC

TT

TC

CC

TT

TC

0

100.0%

BB24699

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24700

FL

12

0.0%

BB24701

TT

FL

CC

TC

CC

TT

CC

1

91.7%

BB24702

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24703

TT

FL

CC

TC

CC

TT

TC

TT

CC

1

91.7%

BB24704

TC

TT

TC

FL

TC

CC

TT

CC

TT

TC

1

91.7%

BB24705

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24706

TT

FL

CC

TC

CC

TT

CC

TT

TC

2

83.3%

BB24707

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24708

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24709

TC

TT

TC

CC

TT

0

100.0%

BB24710

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24711

TC

FL

TC

CC

TT

TC

TT

CC

1

91.7%

BB24712

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24713

TC

FL

TC

FL

TC

CC

TT

CC

TT

2

83.3%

BB24714

TT

FL

CC

TC

CC

TT

TC

TT

1

91.7%

BB24715

TT

FL

CC

TC

CC

TT

TC

TT

TC

1

91.7%

BB24716

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24717

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24718

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24719

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24720

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24721

TC

TT

TC

CC

TT

TC

0

100.0%

BB24722

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24723

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24724

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24725

TT

FL

CC

TC

CC

TT

CC

TT

CC

1

91.7%

BB24726

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24727

TC

TT

TC

CC

TT

TC

0

100.0%

BB24728

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24729

TC

TT

TC

FL

TC

CC

TT

CC

TT

CC

1

91.7%

BB24730

TC

FL

TC

CC

TT

TC

TT

1

91.7%

BB24731

TC

TT

TC

CC

TT

TC

0

100.0%

BB24732

TT

FL

CC

TC

CC

TT

CC

1

91.7%

BB24733

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24734

TC

TT

TC

CC

TC

CC

TT

TC

TT

TC

0

100.0%

BB24735

TT

FL

CC

TC

CC

TT

1

91.7%

BB24736

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24737

TC

TT

TC

FL

TC

CC

TT

1

91.7%

BB24738

TT

FL

CC

TC

CC

TT

TC

CC

1

91.7%

BB24739

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24740

FL

12

0.0%

BB24741

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24742

TC

TT

TC

CC

TC

TT

0

100.0%

BB24743

TC

TT

TC

CC

TT

0

100.0%

BB24744

TC

TT

TC

CC

TT

TC

0

100.0%

BB24745

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24746

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24747

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24748

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24749

TT

FL

CC

TT

TC

TT

1

91.7%

BB24750

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24751

TC

TT

TC

CC

TC

TT

TC

0

100.0%

BB24752

TC

TT

TC

CC

TT

TC

0

100.0%

BB24753

FL

12

0.0%

BB24754

TC

TT

TC

CC

TT

TC

FL

1

91.7%

BB24755

TT

FL

CC

TC

CC

TT

TC

TT

1

91.7%

BB24756

TC

FL

TC

CC

TT

TC

TT

1

91.7%

BB24757

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24758

TC

TT

TC

CC

TT

CC

TC

0

100.0%

BB24759

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24760

TC

TT

TC

CC

TT

TC

0

100.0%

BB24761

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24762

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24763

TC

TT

TC

FL

TC

CC

TT

CC

FL

TC

2

83.3%

BB24764

TT

FL

CC

TC

CC

TC

CC

TT

CC

1

91.7%

BB24765

TC

FL

TC

CC

TT

CC

1

91.7%

BB24766

TC

TT

TC

FL

TC

CC

TT

TC

TT

TC

1

91.7%

BB24767

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24768

TC

TT

TC

FL

TC

CC

TT

TC

1

91.7%

BB24769

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24770

TT

FL

CC

TT

CC

TT

CC

1

91.7%

BB24771

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24772

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24773

TC

TT

TC

CC

TT

TC

0

100.0%

BB24774

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24775

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24776

TC

TT

TC

CC

TT

TC

0

100.0%

BB24777

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24778

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24779

TC

FL

TC

CC

FL

CC

TT

2

83.3%

BB24780

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24781

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24782

TC

TT

TC

CC

TT

CC

TT

CC

0

100.0%

BB24783

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24784

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24785

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24786

TC

TT

TC

CC

TT

TC

0

100.0%

BB24787

TC

TT

TC

CC

TT

TC

0

100.0%

BB24788

TC

TT

TC

CC

TT

TC

0

100.0%

BB24789

TC

TT

TC

CC

TT

0

100.0%

BB24790

TT

FL

CC

TC

CC

TC

TT

TC

1

91.7%

BB24791

TT

FL

CC

FL

TC

CC

FL

CC

TT

TC

TT

CC

3

75.0%

BB24792

TC

TT

TC

CC

TC

CC

TT

TC

0

100.0%

BB24793

TT

FL

CC

FL

CC

TT

TC

2

83.3%

BB24794

TC

TT

TC

CC

TT

CC

TC

CC

0

100.0%

BB24795

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24796

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24797

TC

TT

TC

CC

TC

TT

0

100.0%

BB24798

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24799

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24800

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24801

FL

12

0.0%

BB24803

TC

TT

TC

CC

TT

CC

TT

FL

1

91.7%

BB24804

TT

FL

CC

TC

CC

TT

TC

TT

CC

1

91.7%

BB24805

TC

TT

TC

CC

TT

0

100.0%

BB24806

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24807

TC

TT

TC

FL

TC

CC

TC

TT

CC

1

91.7%

BB24808

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24809

TC

TT

TC

CC

TT

TC

CC

0

100.0%

BB24810

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24811

FL

12

0.0%

BB24812

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24815

TC

TT

TC

CC

TT

TC

0

100.0%

BB24817

TC

TT

TC

CC

TT

CC

TT

0

100.0%

BB24818

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24819

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24820

TC

TT

TC

CC

TT

CC

TC

CC

0

100.0%

BB24821

TT

FL

CC

TC

CC

TT

CC

TT

1

91.7%

BB24823

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24824

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24826

TC

TT

TC

CC

TT

TC

TT

TC

0

100.0%

BB24827

TT

FL

CC

TC

CC

TT

CC

TT

1

91.7%

BB24830

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24831

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24832

TT

FL

CC

TC

CC

TT

TC

1

91.7%

BB24833

TC

TT

TC

CC

TT

TC

0

100.0%

BB24834

TC

TT

TC

CC

TT

TC

TT

CC

0

100.0%

BB24836

TC

TT

TC

CC

TT

CC

0

100.0%

BB24837

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24838

TC

TT

TC

CC

TT

CC

TT

TC

0

100.0%

BB24839

TC

TT

TC

CC

TC

CC

TT

TC

TT

CC

0

100.0%

BB24841

TC

TT

TC

CC

TT

TC

0

100.0%

BB24842

TC

TT

TC

CC

TT

TC

TT

0

100.0%

BB24843

TT

FL

TC

FL

CC

FL

TT

FL

TC

6

50.0%

BB24844

FL

12

0.0%

BB24847

TC

TT

TC

CC

TC

CC

TT

0

100.0%

Q1H2O

FL

12

0.0%

Q2H2O

FL

12

0.0%

Q3H2O

FL

12

0.0%

Q4H2O

FL

12

0.0%

	RHD4	RHD7	RHD9	RHCE2	RHCE5	KEL6	KEL8

Sample FL	15	86	20	54	23	18	17
Sample Pass	357	286	352	318	349	354	355
Call Rate	95.97%	76.88%	94.62%	85.48%	93.82%	95.16%	95.43%
Genotypes (N)
XX (TT)	64	286	0	0	0	0	0
XY (TC)	293	0	293	260	246	28	1
YY (CC)	0	0	59	58	103	326	354
Allele Freq
X (p)	58.96%	100.00%	41.62%	40.88%	35.24%	3.95%	0.14%
Y (q)	41.04%	0.00%	58.38%	59.12%	64.76%	96.05%	99.86%

	DI18	FYP	FY2	GP3A	JK9

Sample FL	17	15	16	16	17
Sample Pass	355	357	356	356	355
Call Rate	95.43%	95.97%	95.70%	95.70%	95.43%
Genotypes (N)
XX (TT)	0	348	112	263	87
XY (TC)	2	7	155	89	178
YY (CC)	353	2	89	4	90
Allele Freq
X (p)	0.28%	98.46%	53.23%	86.38%	49.58%
Y (q)	99.72%	1.54%	46.77%	13.62%	50.42%

Claims

1-19. (canceled)

20. A probe comprising (i) at least one of the nucleotide sequence of nucleotide positions 1 to 20 of any one of SEQ ID NO: 25 to 35 and nucleotide position 1 to 18 of SEQ ID NO: 6 and (ii) the nucleotide sequence of nucleotide positions 21 to 45 of as set forth in SEQ ID NO: 31.

21. The probe of claim 20 for use as an extension probe for the detection of a T/C SNP in an exon 8 of a KEL gene.

22. A blood group/platelet antigen typing kit comprising a first oligonucleotide having a nucleotide sequence as set forth in SEQ ID NO: 13, a second oligonucleotide having a nucleotide sequence as set forth in SEQ ID NO: 14 and a probe having the nucleotide sequence as defined in claim 1.

23. A method of detecting a Kp^a/bblood group antigen in a sample, said method comprising:

(a) providing genomic DNA from said sample;

(b) submitting the genomic DNA of step (a) to a PCR amplification with at the first oligonucleotide as defined in claim 3 and the second oligonucleotide as defined in claim 22 to obtain at least one amplification product; and

(c) analyzing the at least one amplification product of step (b) to detect the blood group antigen in the sample.

24. The method of claim 23, wherein the at least one amplification product is digested with a restriction enzyme.

25. The method of claim 24, wherein said restriction enzyme is Exonuclease I or shrimp alkaline phosphatase.

26. The method of claim 23, further comprising, in step (c), generating at least one extension product from the at least one amplification product.

27. The method of claim 26, further comprising hybridizing the at least one extension production with a probe having the sequence of nucleotide positions 21 to 45 of as set forth in SEQ ID NO: 31.

28. The method of claim 27, wherein the probe has the sequence as defined in claim 1.

29. The method of claim 27, wherein said extension product is hybridized to a tag-arrayed microplate.