The subject invention lies in the field of haemostasis and in particular is directed at the aspect of thrombosis. More particularly the invention is directed at a method for screening and diagnosis of thrombophilia, especially hereditary thrombophilia. The method according to the invention can then be used for determining the risk for thrombosis in individuals.
Deep vein thrombosis is a common disease. Well established risk factors include recent surgery, malignant disorders, pregnancy and labour, long term immobilisation, and deficiency of one of the main inhibitors of the clotting system (Ref.1). The main inhibitors are known to be protein C, protein S and antithrombin. The causes of deep vein thrombosis in many patients remain unclear. It has recently been established however that a poor anticoagulant response to activated protein C (APC) is present in several families with a hereditary tendency to venous thrombosis (Ref.2).
The anticoagulant property of APC resides in its capacity to inactivate the activated cofactors Va and VIIIa by limited proteolysis (Ref. 3). This inactivation of cofactors Va and VIIIa results in reduction of the rate of formation of thrombin, the key enzyme of coagulation. In vitro, this effect can be visualised by adding APC to normal plasma and accordingly determining the effect thereof in a coagulation test, for example in a test determining the APTT (activated partial thromboplastin time). Activation of protein C occurs at the surface of endothelial cells via the thrombin-thrombomodulin complex (Ref.27). Thrombomodulin is a membrane glycoprotein that can bind thrombin. By this binding thrombin loses the ability to convert fibrinogen to fibrin and the ability to activate blood platelets. In other words thrombin loses its coagulant properties and reduces its further own production (so-called negative feed-back) by activating protein C. In vivo (in the presence of calcium) the activation of protein C is almost completely dependent on the availability of thrombomodulin on the endothelium. APC is subsequently neutralized by formation of complexes with APC inhibitor (PCI) and xcex11 antitrypsin, which means that in normal conditions it remains only for a short time in the circulation and the anticoagulant effect remains generally locally expressed.
It was generally accepted that the inactivation of the cofactors Va and VIIIa by APC proceeds only optimally in the presence of Ca2+, phospholipids and the APC cofactor protein S (Ref.4,28,29). More recently this view was, however, challenged by the finding that in systems of purified proteins protein S has little cofactor activity to APC (Ref. 5, Ref. 6). A possible solution for this apparent discrepancy between the observations in vivo (thrombotic tendency in hereditary protein S deficiency) and in vitro (poor APC cofactor activity of protein S in systems of purified proteins) could be offered by the finding of Dahlbxc3xa4ck et al (Ref.2) who reported patients with normal values for antithrombin activity, protein C (immunologically and functionally) and protein S (immunologically and functionally) without indications for abnormal plasminogen, abnormal fibrinogen or lupus anticoagulants, but with a reduced anticoagulant response to activated protein C. The latter was found with a new test developed by Dahlback (Ref.2) in which he studies the response (coagulation time, APTT) of a plasma after in vitro addition of purified human APC. The addition of activated protein C to the plasma of these thrombotic patients did not result in the expected prolongation of the activated partial thromboplastin time (APTT). After postulating a number of mechanisms for this phenomenon only one was considered to provoke the poor anticoagulant response to APC, namely the existence of a hitherto unknown cofactor to APC that is deficient in these patients.
The following mechanisms have to date been rejected as being causes of the poor anticoagulant response to APC:
1. The presence of an auto antibody against APC
2. A fast acting protease inhibitor reacting with APC
3. A functional protein S deficiency
4. Mutations in the Factor V or Factor VIII gene
Dahlbxc3xa4ck (Ref.2.7) postulated that in the families studied a hereditary shortage of a hereto unknown APC cofactor that purportedly works independently of protein S was the cause of APC resistance. Dahlbxc3xa4ck et al (Ref. 2) also described a test method for diagnosing the thrombo embolic disorders by addition of activated protein C to a patient sample containing coagulation factors followed by measurement of an enzyme activity that is influenced by addition of APC in an international patent aplication WO93/10261. It is state in the application of Dahlbxc3xa4ck et al that the experimental results presented indicated that the disorders in question are related to a hitherto unknown coagulation factor or factors or unknown interactions of known factors. The unknown factor is not Factor Va or VIIIa that is resistant to degradation by APC and neither is it an inhibitor of the immunoglobulin type for APC. Furthermore it is not related to protein S deficiency. Dahlbxc3xa4ck (Ret. 2) state that their invention is a method particularly useful for further diagnosis of thromboembolic diseases such as hereditary or non hereditary thrombophilia and for determining a risk or thrombosis in connection with pregnancy, taking anticonception pills, surgery etc. They describe their method as being characterized in that the coagulation system in a sample is activated, wholly or partly in a manner known per se and incubated with activated protein C, whereupon a substrate conversion reaction rate like clotting or conversion of a chromogenic substrate is determined. The conversion rate obtained is compared with values obtained for normal plasma samples. If the rate is enhanced it indicates that the individual from which the sample is derived may suffer from a clotting disease. The disease is not expressed by protein S deficiency or by formation of Factor Va or Factor VIIIa resistant to degradation by APC or by an inhibitor of the immunoglobulin type for APC. In the international application it is also stated by Dahlbxc3xa4ck et al that the data in the application indicated that the patient in question could not carry a detective Factor VIII/VIIIa in contrast to what they had previously stated in Thromb. Haemostas. 65. Abstract 39. 658 (1991), wherein addition of activated protein C to a plasma sample of a patient, and study of then effect produced was claimed to have illustrated a defective Factor VIIIa molecule not degraded by activated protein C. Furthermore in the international patent application the assay was used to directly measure the inhibition of Factors Va and VIIIa by APC. Using the Factor Xa based clotting assay described therein, the inhibition of patient Factor Va by APC was found to be normal suggesting that Factor Va in the patient""s plasma was degraded in a normal fashion by exogeneously added APC.
Following the publication by Dahlbxc3xa4ck et al (Ref.2) other groups started research in this area. In Blood Vol. 82. nr. 7. 1993 on page 1989-1993 Griffin et al describe the results of APC resistance tests carried out among 25 venous thrombotic patients with no identifiable blood coagulation abnormality and 22 patients previously identified with heterozygous protein C or protein S deficiency. The APC induced prolongation of the activated partial thromboplastin time assay for these patients was compared with results for 35 normal subjects. The results showed that this new defect in anticoagulant response to APC was surprisingly present in 52 to 64% of the 25 patients i.e. in the majority of previously undiagnosed thrombophilia cases. The deficiency was not present in 20 of 22 heterozygous protein C or protein S deficient patients. This suggested that the new factor is a risk factor independent of protein C or protein S deficiency. Mixing of normal blood plasma with each of two extremely defective plasmas (APC-induced prolongation of APTT less than 20 s) was performed and the APTT assays were made to assess the ability of normal plasma to correct the poor response of the detective plasmas. The results were similar to those of Dahlbxc3xa4ck et al (Ref.2). This also suggested that normal plasma contains a factor which is missing from the detective patients plasmas. Value are given in the article for the net calculated prolongation in APTT, simply defined as an APTT value in the presence of APO minus the APTT value in the absence of APC. The article also describes the ratio of the APTT with APC to the APTT without APC and the fact that this parameter was compared to values for the APC induced APTT prolongation. This comparison indicated an excellent correlation between these parameters for the normals, with an extremely low APTT ratio value being indicative of abnormal patients. Therefore it followed that either the parameter of APC-induced APTT prolongation or the parameter of the ratio of APTT values with versus without APC or both parameter can be used as diagnostic parameter. None of these parameters seemed more useful for this purpose than the other according to the article. Furthermore in the article it was stated that the APC-induced prolongation of the APTT assay used was reminiscent of the assay involving APC-induced inactivation of endogenous Factor VIII in the plasmas of patients with lupus anticoagulant reported by Potzsch et al (Ref. 19) in Blood 80: 267a 1992 (Abstract)). Based on this latter assay it was reported in the Griffin et al article that plasma from lupus anticoagulant patients with thrombosis gave a poor response to APC and that patients with thrombosis could thereby be distinguished from those without thrombosis. Griffin et al speculated that auto-antibodies against the new hypothesized APC-cofactor could play a role in the risk of thrombosis among patients with lupus anticoagulants. It is further stated by them that it is tempting to speculate that an a acquired deficiency of the new APC-cofactor could be associated with an acquired risk of thrombosis.
In the Lancet, Dec. 18, 1993, Vol. 342, an pages 1503-1506 Koster et al. have elaborated further on the link between APC-resistance and thrombosis by describing how a population based case control study was undertaken to test the clinical importance of the abnormality in the coagulation system that is characterized by a poor anticoagulant response to activated protein C (APC). From studies within families this poor response to APC appears to inherit as an autosomal dominant trait (Ref. 2, 7 and 47). Among patients referred to a coagulation unit because of unexplained thrombosis this abnormality was a major cause of thrombophilia with a prevalence of about 40% (Ref. 8 and 9). In the study described by Koster at al in the Lancet. Dec. 18, 1993, Vol. 342. pages 1503-1506, the clinical importance of this poor response to APC was investigated in unselected consecutive patients, aged less than 70 years, with a first objectively confirmed episode of deep vein thrombosis and without a underlying malignancy. The sensitivity of these patients plasma to APC was compared with that of matched healthy controls. The sensitivity of their plasma APTT to activated protein C (A) was measured essentially as described by Dahlbxc3xa4ck et al (Ref. 2) using the reagents and reaction conditions previously developed for the protein S activity assay (Ref. 11). The results were expressed as APC sensitivity ratios (APC-SR) defined as the value of APTT (+APC) over the APTT (xe2x88x92APC). In the Koster at al article (Lancet. Dec. 18, 1993, Vol. 342. pages 1503-1506) it was stated that reduced levels of prothrombin and/or Factor X ( less than 0.5 u/ml) will increase the APC-SR. For this reason the test cannot be used for the evaluation of plasma""s of patient on oral anticoagulant treatment. In a series of 98 samples a correlation was found between the APC-SR obtained with the test of Koster et al (Lancet, Dec 18, 1993. Vol. 342, pages 1503-1506) and those obtained with the test developed by Chromogenix as described in WO 93/10261. A reference range for the APC sensitivity ratio was derived from healthy control subjects. After logarithmic transformation of the data and exclusion of 10 subjects with values outside 3 standard deviations (SD) of the mean, the lower limit of normal was 2.17 (meanxe2x80x941.96 SD). An inverse relation between the risk of thrombosis and the degree of response was found. The 21% prevalence of a poor response to APC among thrombosis patients and the odds ratio for thrombosis of 6.6 led to the conclusion that a poor response to APC could be considered a common and strong risk factor for deep vein thrombosis. It was even speculated that subjects with APC sensitivity ratios around 1.10 could be homozygous or double heterozygous, whereas subjects with APC sensitivity ratios around 1.50 could be heterozygous for the abnormality. The prevalence of the abnormality was 5% among the healthy control subjects. Because the distribution of the APC-SR was clearly bimodal Koster et al believe that subjects really had abnormal responses to APC rather than too low values within a normal range. The relation between risk of thrombosis and their response to APC seemed therefore not to follow the model of a simple single gene defect. Because the abnormality was found to be so prevalent in healthy subjects it was considered unlikely by Koster et al that the defect in itself is sufficient to cause thrombosis as is true also for protein C deficiency (Ref. 15, Ref. 16). An additional causal factor seems to be required for the development of thrombosis within a particular patient. These may be acquired factors and also as yet unknown genetic defects or variations. However once other causal factors are present poor APC response presents a strong risk of thrombosis as witnessed by its six to sevenfold increase of relative risk. It was stated in the article that the underlying defect of the poor response to APC remained to be clarified even though a dominantly autosomally inherited deficiency of a cofactor to activated protein C had been postulated (Ref. 7). While a poor response to APC appears to be 5 to 10 times as frequent as deficiencies of protein C, protein S or antithrombin it confers an approximately similar relative risk of thrombosis (Ref. 17 and 18) which according to Koster et al could make it worthwhile to test all patients with venous thrombosis for this abnormality.
In summary in the state of the art it was ascertained that a defect in the protein C anticoagulant pathway is linked to a relatively high risk of thrombosis. The poor anticoagulant response to activated protein C has been discussed in great detail, however the cause of the poor anticoagulant response to activated protein C remains unclear. A number of theories have been postulated, however the only one that has been accepted is the presence of an unknown cofactor for APC which is apparently deficient in a patient exhibiting a poor anticoagulant response to activated protein C. The identity of the postulated cofactor for APC is unknown. Furthermore current tests for detecting altered response to APC cannot be used on test persons already using anticoagulants.
Surprisingly the identity of the unidentified cofactor responsible for a poor anticoagulant protein C response has been found. It has been discovered that one of the mechanisms that had been rejected is in fact responsible for the defect in the protein C anticoagulant pathway in a majority of thrombophilic patients. The cause of the deficiency has been linked to the presence of a mutation in the nucleic acid material encoding Factor V or Factor VIII which upon expression is correlated to a decrease in the degree of inactivation by APC of said Factor V and/or of Factor Va, (the product of activation of said Factor V) or of said Factor VIII and/or of Factor VIIIa (the product of activation of said Factor VIII). The deficiency is therefore not the result of a mutation in an as yet unidentified cofactor for APC, but is in fact due to a defect in Factor V or Factor VIII or more particularly in the activation products thereof.
As was already indicated in the state of the art the link between a risk of thrombosis and the presence of APC-resistence had already been made and it had also been suggested that screening for such a deficiency would in fact be extremely helpful in diagnosing patients with an increased risk of thrombosis. As it is now known which factors carry the genetic defect responsible it has also now become possible to actually screen the population with methods other than the Chromogenix test for determining APC-resistance.
It has become possible to use DNA techniques or to use antibodies for determining the presence of mutant proteins when screening for the mutated Factor V or Factor VIII associated with resistance to APC. The subject invention is therefore directed at a method for screening for the presence of a genetic defect associated with thrombosis and/or poor anticoagulant response to activated protein C (APC), said genetic defect being indicative of an increased risk of thrombosis or said genetic defect actually causing thrombosis in a patient, said method comprising determination of the presence of a mutation in the nucleic acid material encoding Factor V or factor VIII in a manner known per se, which mutation upon expression of the nucleic acid material is correlated to a decrease in the degree of inactivation by APC of said Factor V and/or of Factor Va (the product of activation of said Factor V) or of said Factor VIII and/or of Factor VIIIa (the product of activation of said Factor VIII) and/or comprising determination of a mutation present in the protein Factor V and/or Factor Va and/or present in the protein Factor VIII and/or Factor VIIIa by analysis of said Factor V and/or Factor Va or Factor VIII and/or Factor VIIIa or analysis of a proteolytic fragment of said Factor V and/or said Factor Va and/or Factor VIII and/or Factor VIIIa in a manner known per se, said mutation being correlated to a decrease in the degree of inactivation by APC of said Factor V and/or said Factor Va and/or Factor VIII and/or Factor VIIIa. In particular the method according to the invention is directed at a method wherein the mutation in the nucleic acid sequence encoding the Factor V and/or Factor VIII is located at the position within the part of the nucleic acid sequence encoding a binding site or a cleavage site of APC on Factor V and/or Va and/or Factor VIII and/or VIIIa and results in Factor V and/or Factor Va and/or Factor VIII and/or Factor VIIIa poorly inactivated by APC. There are known to be a number of binding and cleavage sites for APC in Factors V, VIII, Va and VIIIa. (see Table 1, refs. 34.35,36,48,49.52 the article by Odegaard B and Mann K. G., in J.Biol.Chem. 262, 11233-11238 (1987) and the abstract by Kalafatis M., Haley P. E. and Mann K. G. in Blood 82, Suppl. 1, p. 58a, 1993).
Binding sites are not always cleavage sites. However it is quite clear that any effect leading to reduced binding of APC to such a factor will also have an effect on the APC resistance of such a factor, as generally speaking the factor must be bound by APC before it can subsequently be cleaved by APC. The mutation affecting the binding and/or cleavage site car be present in the primary amino acid sequence of amino acids located at the binding site or can be due to a mutation elsewhere in the molecule resulting in a tertiary structure with a reduced affinity for APC binding and/or cleavage. As a number of sites for APC binding and/or cleavage have been clarified it is obviously easiest to screen for mutations at these locations rather than in the whole molecule. A number of cleavage sites of APC are known to be located on the heavy chains of the Factors V, Va, VIII and VIIIa preferably the mutation to be detected will be located at a position within the part of the nucleic acid sequence encoding a cleavage site of APC on the heavy chain.
The activation of Factors V and VIII can occur by thrombin Factor Xa, and in the case of factor V also by some snake venoms. For xe2x80x9cactivated by a particular factorxe2x80x9d a person skilled in the art can also read xe2x80x9cactivated via a particular factorxe2x80x9d. The resulting activated factors differ slightly due to the manner in which they have been activated. It is therefore possible that a mutation resulting in reduced binding and/or cleavage by APC of Factor Va activated by thrombin will not result in reduced binding and/or cleavage by APC of Factor Va activated by Xa and vice versa. Factor V has the following domain structure A1A2/BA3C1C2, Factor Va that has been activated by Xa has the structure A1A2/Bxe2x80x2A3C1C2, whereas Factor Va that has been activated by thrombin has the structure A1A2/A3C1C2. It is probable that the tertiary structure differs due to the variation in the structure of the light chains of the factors when they have been activated in different manners. In the example in this document it is illustrated that the particular mutation illustrated in fact only inhibited APC inactivation of Factor Va when activation was initiated via Xa and did not have an effect on APC inactivation of Factor Va that was activated via thrombin. This particular mutation was located on the heavy chain of Factor V and is therefore present in both Factor Va activated via thrombin and Factor Va activated via Xa but presumably does not exhibit the same effect in the two forms of activated Factor V due to a differing tertiary structure of the two forms of activated factors.
As in practice the inactivation by APC occurs on activated Factor V or activated Factor VIII the subject method is preferably directed at detection of a mutation resulting in a decrease of binding affinity for APC and/or a reduction in cleavage by APC on Factors Va or VIIIa. Generally speaking mutations present in Factors Va and Factors VIIIa will also be present on the Factor V or Factor VIII from which the activation product has been derived. Therefore analysis of the nucleic acid sequence encoding Factor V or Factor VIII will reveal mutations that can also be present in the activated Factors Va or VIIIa. The analysis according to the subject method can therefore be carried out at nucleic acid level e.g. at DNA and/or mRNA level of Factors V and VIII and at protein level on any of factors Va, VIIIa. V and VIII, or fragments derived from these.
Factor Va DNA has been cloned from HepG2 cells (Ref. 20) and human fetal liver (Ref. 21 and 22). The complete Factor V amino acid sequence is known (refs. 20,23) also the organisation of the factor V gene has been elucidated (Ref. 23). Shen et al (The Journal of Immunology, Vol. 150, 2992-3001, No. 7, Apr. 1, 1993) have described how they found a cellular source of human Factor V. They identified Factor V mRNA in human lymphoid cells by using reverse transcription followed by the polymerase chain reaction (RT-PCR). The results from the PCR were confirmed by independent cloning of Factor V cDNA from a T-cell cDNA library. The sequence of the Factor V cDNA was virtually identical to hepatic Factor V mRNA. A limited span of mRNA encoding part of the connecting region of the Factor V protein was found to contain nucleotide polymorphisms based on 6 nucleotide substitutions. Shen et al described that the amplified F7/F8 Factor V cDNA fragment, present in 14 independent clones derived after amplification, comprised 6 nucleotide base substitutions. 2 Substitutions were of thymine to cytosine and from cytosine to thymine at positions 2209 and 2236 respectively that were silent mutations. Four were guanine to adenine base substitutions that also resulted in a silent mutation at position 2302 and also amino acid changes from arginine to lysine at position 2573, from arginine to histidine at position 2595 and from glutamic acid to lysine at position 2773. These deduced amino acid changes are described in the article as conservative substitutions that did not significantly affect Factor V function. Half of the clones (7 of 14) in addition exhibited an adenine to guanine substitution at position 2290, another silent substitution which abolished the EcoR1 site. None of these mutations have been associated with a decreased affinity for APC binding or cleavage.
In the article by Shen et al it is illustrated that Factor V mRNA can be recovered from human lymphoid cells in sufficient amounts to carry out polymerase chain reactions for example. With this information a person skilled in the art will have no difficulty in retrieving nucleic acid from humans in a sufficient amount to carry out the method according to the subject invention. In the Shen et al article a number of oligonucleotides are presented which can be used in nucleic acid amplification of human Factor V nucleic acid.
Bruce Odegaard and Mann (The Journal of Biological Chemistry. Vol. 262, No. 23, August 15, pp. 11233-11238, 1987) described for both Factor V and Va that cleavage of Factor V by thrombin results in a heavy chain (D chain) of Mr=94.000 and a light chain (E chain) of Mr=74.000. Each chain in itself is susceptible to proteolysis by activated protein C and by Factor Xa. Cleavage of the E chain by either activated protein C or Factor Xa yields two major fragments Mr=30.000 and Mr=48.000. They also indicated that the activated protein C and Factor Xa cleave the E chain at the same position. The activated protein C cleavage of the D chain yields two products Mr=70.000 and Mr=24.000. The Mr=70.000 fragment has the same NH2-terminal sequence as intact D chain, the Mr=24.000 fragment does not. They illustrated that the cleavage of D chain by activated protein C was responsible for the partial inactivation of Factor Va. Evidence that the inactivation of Factor Va is associated with cleavage of its heavy chain, as the light chain is cleaved at a slower rate, is also present in Refs. 10,12,13,14, and 48.
Odegaard and Mann also disclosed that there is a large deal of similarity between Factor Va and Factor VIIIa. Factor VIIIa is another cofactor of the clotting cascade whose activity is regulated by proteolysis. Factors VIIIa and Va have many similar structural and functional characteristics. Both are produced from a large procofactor through cleavage by thrombin or factor Xa, both are about the same size and consist of a heavy chain and a light chain. Both contribute greatly to the activity of a proteolytic complex while not exhibiting proteolytic activity on their own, and both are inactivated by activated protein C. Underlying this commonality is also an apparent homology of primary structure (Ref. 24, 25 and 26). They also themselves identified further sequence homology between Factors V and VIII. In particular they stated there are clearly segments of sequence homology between bovine Factor V and human Factor VIII at positions in the Factor VIII molecule that correspond reasonably well to the positions in the Factor V molecule at which cleavages occur. The effect illustrated by us for human Factor V (in example 1) can due to the equivalence of Factor V and Factor VIII in certain aspects also be expected concomitantly for Factors VIII and/or VIIIa. Odegaard and Mann also indicated that even when no heavy chain remained after cleavage of Factor Va by APC there remained residual cofactor activity. This indicated that the inactivation of Factor Va was a more complex event than simply the cleavage of a single bond, which makes the illustration of the examples of this document that a mutation in an APC binding and/or cleavage site of a Factor V molecule is in fact sufficient to cause a reduction in affinity for inactivation by APC even more surprising. For Factor VIII the APC cleavage sites have been postulated at Arg 562, Arg 336 and Arg 740 (Ref. 49) and the APC binding site in the A3 domain on residues 2009-2018 (Refs. 35, 36) (see also Table 1).
The method according to the invention is directed at detecting one or more mutations at one or more of the cleavage and/or binding sites for APC of Factor V and/or Factor Va or at Factor VIII and/or VIIIa at either nucleic acid or protein level or both. In particular the APC binding and/or cleavage sites located on the heavy chain of the protein or on nucleic acid encoding the heavy chain are considered relevant.
Kalafatis et al (Blood 82, Suppl. 1, p. 58A, 1993) illustrated that membrane bound human Factor Va was inactivated by activated protein C after cleavage of the heavy chain at Arg 506 and Arg 306. They illustrated that the cleavage pattern of the heavy chain of human Factor Va was dependent on the presence or absence of PCPS vesicles. In the absence of a membrane surface or in the presence of phospholipid vesicles exclusively composed of PC, cleavage resulted in a fragment comprising residues 1-506 and a fragment starting with residue 507, which is further cleaved by APC at the COOH-terminus. In contrast, in the presence of PCPS vesicles the complete loss of activity is correlated with the cleavage of the Mr=75.000 fragment and the appearance of Mr=40.000 and Mr=30.000 fragments. The Mr=30.000 fragment corresponds to residues 307 to 506 demonstrating cleavage by APC at Arg 306. No cleavage of the light chain of the cofactor is observed in the presence as well as in the absence of PCPS vesicles after incubation with APC. Thus, a specific APC cleavage site is exposed when the cofactor is bound to PCPS. The presence of a membrane is essential for complete inactivation of human Factor Va by APC and cleavage at Arg 506 only partially inactivates the cofactor and cleavage at Arg 306 is anionic lipid dependent and is required for the complete inactivation of human Factor Va. Recently, similar data have been published for the inactivation of bovine factor Va by APC (Ref. 48). It is clear from the state of the art that there are thus at least two potential cleavage sites in human Factor Va for APC. Kalafatis et al have also detected an additional APC cleavage site at lysine 994 of human factor V (ref 52). Therefore the method according to the invention is directed at detecting mutations at one or more of these cleavage sites for APC in Factor V and/or Va at either nucleic acid or protein level, or both. The cleavage sites for APC are located at Arg 506 and Arg 306 on the heavy chain. A further site has been found to be present at amino acid Arg 679 and Lys 994.
In view of the above the method according to the invention for screening for the presence of a genetic defect associated with thrombosis and/or poor anticoagulant response to activated protein C (APC) said genetic defect being indicative of an increase risk of thrombosis or said genetic defect actually causing thrombosis in a patient, said method comprising determination of the presence of a mutation in the nucleic acid material encoding Factor V in a manner known per se which mutation upon the expression of the nucleic acid material is correlated to a decrease in the degree of inactivation of APC of said Factor V and/or of Factor Va is of particular interest when the Factor V has been derived from Factor V activated by Xa.
In particular the method according to the invention is directed at determination of the mutation in a nucleic acid sequence encoding human Factor V or Va with a mutated amino acid sequence comprising an altered amino acid at a position corresponding to amino acid 506 of the sequence of plasma Factor V (Ref. 21). In particular when the above-mentioned mutation is a mutation whereby the amino acid arginine has been replaced by the amino acid glutamine at amino acid 506 of the sequence of plasma Factor V. This is in particular the case when the second nucleotide of the codon for the amino acid corresponding to amino acid 506, nucleotide G is mutated. In particular when the nucleotide G is mutated to A at the position corresponding to the second nucleotide of the codon for the amino acid corresponding to amino acid 506 of the sequence of plasma Factor V.
As is apparent from the Examples the subject invention is also directed at a method for determining whether a test person is homozygous or heterozygous for a mutation in Factor V and/or Factor Va or Factor VIII and/or Factor VIIIa comprising carrying out a method known per se for determining whether a defect is present in anticoagulant response to APC, subsequently followed by determination of a value of a parameter known to be useful for diagnosis of the defect such as the (APTT+APC) over (APTTxe2x88x92APC) value and comparing the value obtained with a value obtained in the same manner for a sample from a normal individual or from an individual known to be homozygotic or heterozygotic, thereby establishing whether the test person is homozygotic or heterozygotic for a defect in anticoagulant response to APC, in combination with any known method for determining the presence and optionally the nature of a mutation in Factor V and/or Va or Factor VIII and/or Factor VIIIa in particular in the embodiment illustrated in Example 1 and anv equivalent embodiments of said Example for other mutations in Factors V, Va, VIII and/or VIIIa resulting in altered anticoagulant response to APC, most particularly due to a mutation in an APC binding and/or cleavage site.
The method according to the invention can be accomplished by detecting the mutation by carrying out a nucleic acid target amplification reaction. Such target amplification reactions are well known to a person skilled in the art. It is required to use one or more primers specific to recognize and hybridize to stretches of nucleic acid adjacent to the 5xe2x80x2 and 3xe2x80x2 end of the stretch of nucleic acid in which the mutation can be located, said hybridisation being to a degree sufficient for amplification of the stretch of nucleic acid in which the mutation can be located. The stringency of hybridisation required is also known to a person skilled in the art of target amplification of nucleic acid. There are a number of target amplification reactions that are generally carried out in the state of the art comprising NASBA (Nucleic Acid Sequence Based Amplification) PCR (Polymerase Chain Reaction), LCR (Ligase Chain Reaction) and RCR (Repair Chain Reaction). For PCR target amplification methods the AmplicorR reaction kits are commercially available. It is also possible to use a primer sufficiently specific to recognize and hybridize to the stretch of nucleic acids in which the mutation itself can be located. An alternative amplification method comprises branch chain amplification as commercially exploited by Chiron wherein the probe rather than the target is amplified.
After amplification of the nucleic acid, analysis of the amplified nucleic acid in a manner known per se for detecting the presence and optionally the nature of the mutation is to be carried out in the method according to the invention.
It is also possible to determine the mutation without amplification of the nucleic acid material. There are a number of techniques known to a person skilled in the art that were used before the target amplification reaction was developed for determining the presence of mutations on nucleic acid and these can all be used in various embodiments of the method according to the invention. For example the mutation to be determined can be detected by a hybridisation reaction to at least one nucleic acid sequence sufficiently specific to hybridise to at least part of the nucleic acid sequence encoding the factor to be analysed when using normal to stringent hybridisation conditions e.g. blotting techniques followed by analysis of the nucleic acid thus isolated in a manner known per se for detecting the presence and optionally the nature of the mutation.
The detection of the presence and optionally the nature of the mutation can occur by subjecting the nucleic acid thus isolated to sequence analysis by using for example the Sanger sequence reaction to ascertain the nucleic acid sequence and subsequently to compare the results of this sequencing with the sequence known for the non-mutated factor. It is also possible to subject the nucleic acid sequence isolated to a further hybridisation test. The further hybridisation test being carried out with a stretch of nucleic acid material with a corresponding complementary sequence of sufficient length and specificity to at least hybridize to a fragment of the nucleic acid material comprising the mutation to detect the presence and optionally the nature of the mutation. The first hybridisation step merely isolates nucleic acid encoding the factor whether this is mutated or not and the second hybridisation step actually comprises hybridising the isolated sequence to the complementary sequence of the actual mutated nucleic acid sequence one wishes to ascertain in order to determine the presence or absence of said mutation on the isolated nucleic acid material. This latter hybridisation reaction should be carried out under stringent conditions for reliable results whilst the other hybridisation steps can be carried out under normal to stringent conditions. Thus two classical methods for determining the presence of a mutation on a particular nucleic acid are hereby illustrated and it will be obvious to a person skilled in the art that a number of known techniques can be used. In various standard books for molecular biology such techniques are amply illustrated for example in Sambrook, J., Fritsch, E. F., Maniatis, T. Molecular Cloning: a Laboratory Manual. (Cold Spring harbor Laboratory Press, cold Spring Harbor, N.Y., 1989.
It is also possible to analyse the amplified nucleic acid material obtained in the screening method according to the invention by using subsequent analysis tests using sequencing reactions or hybridisation to a corresponding complementary sequence of sufficient length and specificity to at least hybridize to a fragment of the nucleic acid material comprising the mutation to detect the presence and optionally the nature of the mutation as was illustrated above for analysis of isolated nucleic acid material that had not been subjected to an amplification reaction.
In particular for analysis of the presence of mutations in Factor V the isolated and/or amplified nucleic acid material can be subjected to a hybridisation test to a stretch of nucleic acid material selected from sequences with sequence numbers 12 and 13 of the sequence listing. For example an extremely suitable primer or nucleic acid sequence for hybridisation comprises at least a part of intron 10 of the nucleic acid sequence encoding human Factor V or a derivative thereof capable of hybridizing to said part of intron 10 under stringent conditions. Such a derivative will preferably be more than 90% homologous to the corresponding part of intron 10. The nucleic acid sequence of human Factor V is known and in sequence number 1 of the sequence listing the nucleic acid sequence encoding human Factor V is illustrated. The sequence is derived from Ref. 21. Using the nucleic acid sequence for hybridisation comprising at least a part of intron 10 it is quite simple to isolate and/or amplify and/or subsequently detect a mutation present in nucleic acid encoding Factor V, in particular of nucleic acid encoding an APC binding and/or cleavage site. It is in particular suitable to detect a mutation located on the heavy chain (see sequences 10, 14). Further, primers of nucleic acid sequences for hybridisation and/or amplification purposes can be selected from sequences with sequence listing numbers 2-11 of the sequence listing. As is already indicated above a number of other oligonucleotide primers are also known from the state of the art. It is also possible to use these primers for amplification purposes or hybridisation reactions to isolate the nucleic acid encoding Factor V and/or Va. It lies within the reach of a person skilled in the art to select oligonucleotide sequences best suited to isolate and/or amplify and/or determine the presence and nature of the mutation he is screening for in a method according to the invention as the sequence encoding the normal factor is known, as is a sequence for a mutated factor.
In the method according to the invention, in particular when the nucleic acid to be analysed has been subjected to target amplification, the isolated and/or amplified and/or hybridised nucleic acid material is subjected to sequence analysis and the sequence is then compared to the nucleic acid sequence of the corresponding non-mutated factor. It is also possible to analyse the amplified or isolated and/or hybridised nucleic acid material through restriction fragment analysis. In particular for the mutation illustrated in the example with Factor V that is mutated, the enzyme that can be used is Mnl I. Naturally the restriction enzyme one can use for a restriction fragment analysis depends on the nature of the mutation to be detected and the location thereof. Determination hereof lies within the reach of a person skilled in the art without involving further inventive step, merely routine experimentation not placing an undue burden on a person skilled in the art.
As stated above the method according to the invention can also be carried out by analysing the protein rather than the nucleic acid sequence encoding the protein. In particular this is a useful embodiment of the invention when the mutation in the protein is located at a position within the part of the amino acid sequence providing a binding and/or a cleavage site of APC on Factor V or Va and results in Factor V and/or Factor Va poorly inactivated by APC or is located on the part of the nucleic acid sequence providing a binding and/or a cleavage site of APC of Factor VIII or VIIIa and results in Factor VIII and/or Factor VIIIa poorly inactivated by APC.
As stated above the presence of a mutation within the part of the amino acid sequence providing a cleavage site of APC on Factor V, Va, Factor VIII or VIIIa is a mutation that will quite clearly lead to an altered resistance of the mutated factor to inactivation by APC and therefore determination of such a mutation is a preferred embodiment of the method according to the invention. As already indicated in the state of the art, inactivation of Factor Va or Factor VIIIa generally ensues when APC cleaves the heavy chain of the factor. Therefore, detection of a mutation in such a cleavage site resulting in an amendment of a degree of cleavage of the mutated factor is a preferred embodiment of the invention. When analysing the protein for a mutation it is not only the primary amino acid sequence of the cleavage site itself that is relevant, but also the tertiary structure of the protein can be distorted due to a mutation somewhere in the primary sequence not immediately associated with the binding and/or cleavage site. It is well known that mutations located quite a long way away from the actual binding site or cleavage site of a protein can exhibit a large effect on the tertiary structure of the protein thereby also abolishing or reducing binding to said protein in this instance binding by APC. Therefore the method according to the subject invention is not only directed at detection of mutations in the primary nucleic acid sequence of the cleavage and/or binding sites for APC but also at detection of mutations resulting in a mutated factor having an altered tertiary structure resulting in reduced binding and/or cleavage of the factor by APC.
As the Factors V and VIII can both be activated by different mechanisms and the resulting activated factors are known to differ both in tertiary structure from the factors from which they have been derived it is apparent that the mutation in Factor V or Factor VIII could have no influence on the APC binding and/or cleavage sites of said molecules but could have an effect on those of the activated factors or vice versa. Nevertheless the mutation in primary amino acid sequence responsible for the altered binding and/or cleavage of the activated Factor V or VIII will also be present on Factor V or Factor VIII. When the detection of the mutated protein occurs by using a specific antibody it is possible to use an antibody specifically directed against the activated factor comprising the mutation for detection of the presence and optionally the nature of the mutation. Alternatively it is also possible to proteolytically cleave the protein to be analysed, thereby obtaining linear or partially linear structures making it possible to use antibodies specific for the mutation in the primary amino acid sequence of Factor V and/or Va or Factor VIII and/or VIIIa. Thus the detection method of the mutation need not be restricted to analysis of the activated factors but can in fact also occur on Factor V or Factor VIII that have not yet been activated.
If the mutation is present in a binding and/or cleavage site for APC then treatment of Factor V, Va, VIII, VIIIa with APC followed by analysis of the fragments in a manner known per se should reveal different fragments than when the Factor is normal.
For instance in the case of Factor V a mutation at amino acid 506 prevents cleavage and/or binding of APC there. Treatment with activated APC will thus result in cleavage at sites 306, 679 and 994, providing one fragment of aa 307-aa 679 and three other fragments comprising a sequence of 1-306, 680-994 and 995-terminus. The fragment of interest being 307-679. A normal Factor V will not comprise this fragment but will comprise two other fragments i.e. aa 307-506 and aa 507-679 due to the active cleavage site at aa 506. Thus detection of the aa 307-aa 679 indicates the presence of a mutated APC site at amino acid 506.
An extremely elegant test could comprise subjecting the Factor V after treatment with APC to the presence of 2 antibodies. Such a treatment with APC naturally occurs during preparation of serum. One antibody in the test being specific for a site of the protein upstream of amino acid 506, said site being located downstream of as 306, the most adjacent cleavage site upstream of aa 506. The second antibody being specific for a site of the protein downstream of amino acid 506, said site being located upstream of aa 679, the most adjacent cleavage site for APC downstream from aa 506. The test comprises detection of a fragment detected by both antibodies. Such a test can be a sandwich immunoassay. Preferably one antibody will be immobilized or can be immobilised and the other antibody will be provided with a detectable marker in a manner known per se for a person skilled in the art of immuno-assays. Use of an antibody specifically recognizing a part of the fragment 307-506 in such a test falls within the scope of the invention. An antibody specifically recognizing a part of the fragment 507-679 as such and the use thereof in a test as just described falls within the scope of the invention. Preferably the antibodies will be monoclonal antibodies. A suitable test can be carried out to detect a mutation in the APC cleavage site located at Arg 306 in an analogous manner using 2 antibodies, one specific for a part of fragment 1-306 and one specific for a part of fragment 307-506. Use of an antibody specifically recognizing a part of the fragment 307-506 in such a test falls within the scope of the invention. An antibody specifically recognizing a part of the fragment 1-306 as such and the use thereof in a test as just described falls within the scope of the invention. A test can also be carried out in an analogous manner to that described above for detection of a mutation in the APC cleavage site located at amino acid 679. For this mutation one antibody specific for a part of the fragment 507-679 is required and one antibody specific for a part of the fragment downstream of amino acid 680 is required. Use of an antibody specifically recognizing a part of the fragment 507-679 in such a test falls within the scope of the invention. An antibody specifically recognizing a part of the fragment 507-569 and an antibody specifically recognizing a part of the fragment 570-994 as such and the use of one or more of these antibodies in a test analogous to that described above falls within the scope of the invention. Analogously a test can be described for detection of a mutation at the APC cleavage site at lysine 994. The fragments 994-terminus and 680-994 are the relevant fragments, as are the antibodies capable of recognising them.
In general terms the test for a mutation in Factor V, Va, VIII or VIIIa can comprise use of 2 antibodies in an immunoassay in a manner known per se to detect the presence or absence of a mutation decreasing or inhibiting cleavage by APC at a particular APC cleavage site, wherein one antibody recognizes a fragment upstream of said APC cleavage site, the second antibody recognizes a fragment downstream of said APC cleavage site, and no other APC cleavage sites are located between the part of the Factor either antibody recognizes and the particular APC cleavage site for which the presence or absence of a mutation has to be determined. The various embodiments following from this principal of mutation detection will be obvious to a person skilled in the art of immunoassays. It will thus be obvious for example that one or more additional proteases can be used in combination with APC, said APC having to be added or already being present in the sample depending on which type of sample is used. The additional protease or proteases being selected such that the absence of the active APC cleavage site to be detected on the Factor results in the binding of both antibodies to the proteolytic fragment comprising the inactive APC cleavage site, whereas the presence of the active APC cleavage site to be detected results in proteolytic fragments such that the antibodies cannot both bind to a proteolytic fragment. This is most simply arrived at by selection of one or more proteases resulting in cleavage of the Factor upstream and downstream of the APC cleavage site to be analysed and one of the two antibodies recognising a part of the fragment upstream of the APC cleavage site to be determined and downstream of the location the protease cleaves upstream of the APC cleavage site and the other of the two antibodies recognising a part of the fragment downstream of the APC cleavage site to be determined and upstream of the location the protease cleaves downstream of the APC cleavage site and the protease or proteases cleaving the Factor such that their cleavage sites are located between the APC cleavage site to be determined and the adjacent APC cleavage site as present on a non mutated Factor. In yet a further embodiment one can apply in lieu of APC a protease capable of cleavage of the mutated APC cleavage site but not of the non mutated APC cleavage site or vice versa. Once the nature of the mutation to be determined is ascertained it is a matter of routine experimentation for a person skilled in the art to screen the recognition sites known for proteases for a suitable protease.
A further possibility for detection of the mutation lies in the older technique of amino acid sequence analysis. Once the amino acid sequence of the non-mutated factor is known it is quite simple to determine the amino acid sequence of the factor to be analysed and compare that sequence to the known sequence of the corresponding non-mutated factor. However, using antibodies is a simple and efficient way to analyse proteins for the presence of mutations, for example using ELISA""s or RIA""s or a variety of other immunological tests known to a person skilled in the art.
It is also possible that the activated forms of Factor V and Factor VIII only exhibit a reduction in APC binding and/or cleavage when activated by one particular mechanism. This is illustrated in Example 1 for Factor V, wherein the activated form that has been activated using thrombin does not exhibit any altered binding and/or cleavage capacity for APC whereas the activated form that has been activated by Factor Xa does exhibit a reduction in the binding and/or cleavage by APC. However, as stated above, it is of course possible to detect the presence of the mutation on either Factor V, Factor Va activated by thrombin or Factor Va activated by Xa, regardless of whether the effect of the mutation only occurs in one of the activated forms.
As is illustrated in Example 1 a specific mutation in Factor V has been discovered that is representative for a very large percentage of patients exhibiting thrombophilia without the cause thereof having been previously determined. This concerned a mutation of the amino acid at a position corresponding to amino acid 506 of the amino acid sequence of plasma Factor V (as disclosed in Ref. 21) and therefore a method wherein the mutation of amino acid 506 can be determined forms a preferred embodiment of the invention. In general a method wherein the mutation to be detected comprises an alteration of the arginine amino acid located in an APC cleavage site, in particular on a heavy chain of Factor V(a) and/or Factor VIII(a) is an embodiment of the subject method that can be suitably carried out.
For detecting the mutation one can use a specific antibody capable of binding to the mutant protein Factor V and/or Va or of binding to a linear proteolytic fragment of the mutant protein Factor V and/or Va, said antibody having a lower binding affinity for the non-mutated protein or for the corresponding proteolytic fragment of the non-mutated protein. The method with antibodies can also be used for protein Factor VIII and/or VIIIa and linear proteolytic fragments of said mutant protein Factor VIII and/or VIIIa.
It is also possible as an alternative to use an antibody capable of binding to a protein Factor V and/or Va or a protein Factor VIII and/or Factor VIIIa, said protein not exhibiting a decrease in the degree of inactivation by APC, said antibody having a lower binding affinity for the corresponding factor and/or for the proteolytic fragment thereof comprising a mutation resulting in the mutated protein exhibiting a decrease in the degree of inactivation by APC. In this instance a test can be developed whereby non-binding of the antibody to the isolated protein or proteolytic fragment is illustrative of the presence of a mutation. The invention is not only directed at methods using antibodies as described above but is also directed at the antibodies themselves.
In the method according to the invention it is possible to first screen a sample for an altered coagulation time upon addition of APC in comparison to that of a normal plasma standard, followed by analysis of the nucleic acid sequence encoding Factor V or Factor VIII and/or of amino acid sequence of Factor V, Va, VIII or VIIIa and/or analysis of Factor V, Va, VIII or VIIIa itself once the sample is diagnosed as exhibiting altered APC resistance in comparison to the standard. It is also possible to immediately subject a sample to analysis for the presence of a specific mutation, for example for the mutation in Factor V illustrated in the following Examples. The methods to be used will depend on the circumstances of the case and also the objective of the test. For example when screening a large population the cheapest method to be used will be preferred. In some instances the mutation to be detected will be difficult to determine using antibodies and then use of nucleic acid sequences or restriction fragment analysis can be preferred. Also if the enzyme to be used for a restriction fragment test is inexpensive then carrying out such a test is very simple and cheap to carry out and will obviously be suitable. The invention is therefore also directed at use of a test for determining whether a sample exhibits altered binding and/or cleavage by APC in comparison to a sample comprising normal Factor V and/or Factor VIII and/or Factor VIIIa and/or Factor Va, followed by further analysis of the mutation causing this alteration in a manner elucidated above.
Another aspect of the invention lies in the detection of a mutation in Factor V, Va, VIII or VIIIa being homozygous or heterozygous in the test person. This can be carried out using the test protocol as described by Koster et al in Lancet, Dec. 18, 1993, Vol. 34 for determining whether a test person exhibits APC resistance. Basically Koster describes use of 50 xcexcl undiluted plasma incubated with 50 xcexcl APTT reagent (Cephotest(copyright), batch 103029) for 360 seconds at 37xc2x0 C. before clot formation was started either with 50 xcexcl of a reagent containing 33 mM CaCl2, 25 mM Tris (pH 7.5), 50 mM NaCl and 0.05% ovalbumin (APTTxe2x88x92APC) or with 50 xcexcl of the same reagent also containing 2.0 xcexcg/ml human APC and 0.6% glycerol (APTT+APC). He expressed his results as APC sensitivity ratio""s (APC-SR) defined as the ratio of APTT (+APC) and APTT (xe2x88x92APC). Under these conditions the APC-SR is achieved for normal plasma. Reduced levels of prothrombin and/or Factor X ( less than 0.5 U/ml) will increase the APC-SR. This method therefore cannot be used for evaluation of patients on oral anticoagulant treatment. Koster further stated that with this test he found a good correlation between his results and those obtained using the Chromogenix assay (Pearson correlation coefficient 0.54) discussed in the introduction. Surprisingly we discovered that the Koster test when applied for assessing whether a subject is heterozygous or homozygous for mutation in Factor V detects abnormals a lot better than the Chromogenix test which misses approximately half the heterozygotes. FIG. 14 is the Koster test and FIG. 11 is the Chromogenix test. We carried out tests twice using the Koster method and the Chromogenix test as commercially available on samples from a random selection of individuals genotyped as 1691 GG (normals) or 1691 AG (heterozygotes). In the Chromogenix test there was a great deal of overlap between the sensitivity ratios obtained in normals and heterozygotes, so that more than 50% of the heterozygotes could not be identified as APC resistant with the Chromogenix test. We therefore have found an additional test suitable for determining whether a test person is abnormal or normal for Factor V mutation resulting in APC resistance. Whereas previously the Koster test was merely postulated to be useful to determine whether a test person is normal or abnormal with regard to APC resistance in general we have now discovered it in fact detects Factor V mutation leading to APC resistance and in addition it does so to a much higher degree of reliability than the Chromogenix test can. A value of less than 0.84 is abnormal in our test and no overlap occurs between normal subjects and heterozygotes. This is a significant improvement over the Chromogenix test. We believe the improvement is due to the use of a different activator and more importantly the use of a different calcium concentration than in the Chromogenix test. The improved test comprises applying a calcium concentration of more than 25 mM CaCl2 in the sample. Preferably less than 45 mM, more preferably 30-40 mM, in particular 31-35 mM. This higher concentration probably neutralizes citrate in the sample to a better degree than in the Chromogenix formula. A further improvement lies in the use of Cephotest reagent as activator. The method is further analogous to the Chromogenix test and must be considered a considerable improvement thereof. When values obtained for the APC sensitivity ratio have bean normalised (see Example 1) a value below 0.84 is indicative of abnormality and a value above 0.84 is indicative of normality regarding APC resistance, in particular related to Factor V mutation. For homozygotes determination a value below 0.50 must be registered, with heterozygotes exhibiting values between 0.50 and 0.70. This improved method however is not applicable on patients that have been subjected to treatment with anticoagulant.
In the example the mutation that was detected was the Gxe2x86x92A mutation at the codon for amino acid 506 of Factor V. The frequency of occurrence of the mutation and the associated high risk of thrombosis means that determination whether a test person is homozygous or heterozygous is extremely relevant when assessing the risks for parents for passing on the mutated factor to their progeny. In Example 2 we illustrate that the presence of a mutation in Factor V, in particular the Gxe2x86x92A mutation in fact is a risk factor for developing thrombosis. Moreover the preliminary observation that 6% of the patients with a first myocardial infarction is a carrier of the 1691 Gxe2x86x92A mutation, might indicate that this mutation is also a mild risk factor for arterial thrombosis (relative risk 1.5-2.0). The timely detection of an increased risk for heart attack can lead to a person adjusting life style and taking precautions to prevent such an event. The importance regarding venous thrombosis has already been discussed in the introduction.
The invention is also directed at kits comprising the elements necessary for carrying out the method according to the invention in all the embodiments illustrated. This comprises for example test kits comprising one or more of the specific antibodies described above, in particular the pairs of antibodies described recognizing sites between APC cleavage and/or binding sites and/or comprising one or more probes or primers or pairs of primers for target amplification reactions and/or hybridisation reactions as described above. Specifically the invention is directed at a kit comprising a primer or primers for amplifying the nucleic acid sequence comprising the mutation of the nucleic acid sequence coding for amino acid 506 of Factor V and/or Factor Va. The kit can comprise primers and/or antibodies for the detection of one particular mutation or for a number of mutations. Preferably the kit will comprise the components necessary to detect the major mutations leading to a decrease and/or abolition of binding and/or cleavage by APC that are prevalent in specific populations.