Means and Methods for Assessing a Quality of a Biological Sample

Abstract

The present invention relates to the field of diagnostic methods. Specifically, the present invention relates to a method for assessing a quality of a biological sample comprising the steps of: (a) providing a table comprising a number of entries, wherein each entry comprises a compound, at least one parameter, and a scoring factor, wherein, in case the compound is a natural compound it refers to an analyte, or in case the compound is an artificial compound it refers to a ratio of two analytes, wherein the at least one parameter is related to the compound, wherein the parameter related to the analyte is derived from at least one recorded value for the analyte while the parameter related to the ratio of the two analytes is derived from a ratio of at least one recorded value of the two analytes, and wherein the scoring factor is related to the compound; (b) determining for each of the compounds in the table a compound quality score, wherein the compound quality score is determined by taking a multiple value of the scoring factor related to the compound, wherein, depending on the actual value of the at least one parameter related to the compound, the multiple value is selected, wherein the multiple value comprises an integral number or a decimal number by which the scoring factor related to the compound is multiplied; (c) deriving at least one sample quality score by summing up the compound quality scores for the compounds in the table as determined in step (b); and (d) comparing the at least one sample quality score as derived in step (c) with at least one reference quality score, by which comparison the quality of the sample is assessed. The invention further relates to tools for performing the mentioned method, such as a device and a kit, as well as a use of components or a detection agent therefore for assessing the quality of a biological sample. The invention particularly provides for, preferably automatically, identifying a correct sample type and, concurrently, assessing the sample quality, in particular, with respect to its preanalytical phase.

Claims

1. A computer-implemented method for assessing the quality of a biological sample for assuring quality and suitability of the biological sample to be used for metabolite profiling or other analytical or diagnostic methods, comprising the steps of: (a) providing a table comprising a number of entries, wherein each entry comprises a compound, at least one parameter, and a scoring factor, wherein, in case the compound is a natural compound it refers to an analyte, or in case the compound is an artificial compound it refers to a ratio of two analytes, wherein the at least one parameter is related to the compound, wherein the parameter related to the analyte is derived from at least one recorded value for the analyte while the parameter related to the ratio of the two analytes is derived from a ratio of at least one recorded value of the two analytes, and wherein the scoring factor is related to the compound; (b) determining for each of the compounds in the table a compound quality score, wherein the compound quality score is determined by taking a multiple value of the scoring factor related to the compound, wherein, depending on the actual value of the at least one parameter related to the compound, the multiple value is selected, wherein the multiple value comprises an integral number or a decimal number by which the scoring factor related to the compound is multiplied; (c) deriving at least one sample quality score by summing up the compound quality scores for the compounds in the table as determined in step (b); and (d) comparing the at least one sample quality score as derived in step (c) with at least one reference quality score, by which comparison the quality of the sample is assessed.

2. The method of claim 1, wherein the numbers of entries in the table is selected by a number of compounds required to assess the quality of the sample.

3. The method of claim 1, wherein the at least one parameter comprises at least one cut-off level and a direction parameter related to the at least one cut-off level, wherein the direction parameter indicates whether a value below the at least one cut-off level contributes to a low sample quality or to a high sample quality.

4. The method of claim 1, wherein the comparing of the at least one sample quality score with the at least one reference quality score provides a classification of the sample into at least two members of a quality group at least comprising a high quality, a medium quality, and a low quality.

5. The method of claim 1, wherein the table comprises a number of natural compounds and a number of artificial compounds, wherein the at least one parameter related to the natural compound is derived from at least one recorded value related to the compound, and wherein the at least one parameter related to the artificial compound is determined by comparing one of the at least one recorded values of at least two natural compounds.

6. The method of claim 1, wherein the at least one recorded value is acquired by quantitative liquid-chromatography coupled mass spectrometry (LC-MS) or gas-chromatography coupled mass spectrometry (GC-MS) of the analyte.

7. The method of claim 1, wherein the at least one recorded value is acquired by using a chemical or biological assay, in particular by utilizing one or more of an RIA (radioimmunoassay), an ELISA (enzyme-linked immunosorbent assay), a sandwich enzyme immune test, a electrochemiluminescence sandwich immunoassays (ECLIA), a dissociation-enhanced lanthanide fluoro immuno assay (DELFIA), or a solid phase immune test for the analyte.

8. The method of claim 1, further comprising the step of checking for each analyte whether the recorded value is missing or considered as erroneous.

9. The method of claim 1, wherein the analyte is one of: a molecular species being present in the sample as metabolite, a molecular species derived from the metabolite, a stereoisomer or an enantiomer of the metabolite, a sum of isomers of a biological class of isomeric molecules.

10. The method of claim 1, wherein, for the analyte, the multiple value is selected by comparing the at least one parameter of the analyte with the at least one recorded value of the analyte, or wherein, for the ratio of the two analytes, the multiple value is selected by comparing the at least one parameter of the ratio of the two analytes with the at least one recorded value of the at least two analytes.

11. The method of claim 1, wherein the method is assisted or performed in an automatic manner.

12. The method of claim 1, wherein the biological sample comprises one of plasma, serum, and urine, wherein the plasma comprises one of EDTA plasma, citrate plasma, and heparin plasma.

13. A device for assessing the quality of a biological sample for assuring quality and suitability of the biological sample to be used for metabolite profiling or other analytical or diagnostic methods, comprising: (A) a receiving unit for receiving a data set comprising at least one recorded value corresponding to at least one parameter of a compound in a table; (B) an evaluation unit comprising a data processing unit and a data base, wherein the data base comprises at least one stored reference score and the table, wherein the table comprises a number of entries, wherein each entry comprises one of the compounds, the at least one parameter, and a scoring factor, wherein, in case the compound is a natural compound it refers to an analyte, or in case the compound is an artificial compound it refers to a ratio of two analytes, wherein the at least one parameter is related to the compound, wherein the parameter related to the analyte is derived from at least one recorded value for the analyte while the parameter related to the ratio of the two analytes is derived from a ratio of at least one recorded value of the two analytes, and wherein the scoring factor is related to the compound, wherein the data processing unit has tangibly embedded at least one algorithm for assessing the quality of a biological sample according to the method of claim 1.

14. (canceled)

15. A kit for assessing the quality of a biological sample according to the method of claim 1 comprising at least one detection agent for at least one analyte.

Description

EXAMPLES

[0091] The invention will now be illustrated by the following Examples which are not intended to restrict or limit the scope of this invention.

Example 1

[0092] As a first example for step (a) of the present method for assessing a quality of a biological sample, Table 1A which comprises four separate lines of entry is presented. Herein, each entry line comprises a compound reference number, an acronym of a respective compound, two parameters, i.e. a first parameter and a second parameter, related to the corresponding compound as well as a scoring factor also in relationship to the respective compound within the same entry line:

TABLE-US-00001 TABLE 1A Compound Cut-off Scoring Ref. No. Compound level Direction factor 478100072 ASP 5.00 Up 0 478100045 ASN 1.00 Up 0 478100010 CYS 0.50 Down 2 999999992 ASP/ASN 6.00 Up 3

[0093] According to the present invention, the biological sample is, in particularly, assessed for a metabolomics of a minimal-invasive matrix type, wherein the minimal-invasive matrix type may comprises one of plasma, serum, and urine. Accordingly, the respective compounds as selected for an application in the assessment procedure and, therefore, comprised within Table 1A (or Table 2A as mentioned below) may particularly be indicative for this specific purpose, i.e. particularly reflecting the quality of the blood plasma, the serum, or urine to be investigated according to the present method. In a particular example (not presented here) it may, therefore, be feasible to, additionally, include at least one additional compound into the respective table which may allow for discriminating between the possible minimal-invasive matrix types of a biological sample in question and, thus, for deciding which minimal-invasive matrix type may actually be present in the biological sample under assessment. Alternatively or in addition, an investigation of an abundance of the at least one additional compound may be used for verifying whether a known sample is actually of the minimal-invasive matrix type as expected.

[0094] Prior to performing the assessment according to the present invention, an additional step of checking for each natural compound whether the recorded value may be missing or may be considered as erroneous may be preferably performed. Such a procedure may be of particular importance when a large number of samples may be investigated. As a result, a warning message or an entry in a protocol or log file may be provided for such a defective entry.

[0095] In this particular example, the first parameters each comprises a cut-off level which constitutes a threshold, wherein a value above the threshold or a value below the threshold may indicate a contribution to a high sample quality or to a low sample quality. Herein, the threshold value for the three natural compounds as comprised in lines 1 to 3 of Table 1A constitute an abundance of the respective natural compound as acquired through a LC-MS or GC-MS device.

[0096] Whether a value above the threshold or below the threshold may indicate a contribution to a high or to a low sample quality depends on the second parameter, i.e. the direction. Here, the direction which equals “up” may indicate a contribution to a high sample quality for a recorded value above the cut-off level whereas the direction being equal to “down” may indicate a contribution to a high sample quality when the recorded value may be below the cut-off level.

[0097] Furthermore, in this particular example, the scoring factor of the first two natural compounds is selected to be equal to 0 (zero) while the scoring factor for the third and the fourth compounds are given as different from zero. Whereas the scoring factor for the third compound refers to a natural compound which may be of importance for the sample quality assessment, the scoring factor for the fourth compound relates to an artificial component as acquired by forming a ratio of a relative abundance of the two natural components as comprised within line 1 and line 2 of Table 1A. In this particular example, where each of the corresponding parameters of two particular natural compounds may be a value related to a peak in a mass spectrum, such as an amplitude or an intensity of the peak, the artificial compound may be derived by determining the ratio of the amplitudes or of the intensities of the two respective peaks in the mas spectrum. In this particular example, only the ratio of an abundance of the two mentioned natural components but not the abundance of the two mentioned natural components themselves may be of importance for the sample quality assessment. Consequently, the artificial compounds may, in addition to the natural compounds, contribute to provide further indications which may be relevant for the quality of the sample.

[0098] With regard to this example, according to step (b) of the present method, a compound quality score is now determined for the four compounds as comprised within Table 1A. According to the present invention, the compound quality score is determined by taking a multiple value of the scoring factor being related to the compound. Herein, the multiple value is specified by the parameters related to the compound. Within this particular example, the respective dependence of the multiple value on the parameters may be represented by an algorithm which may take the values as indicate in the following Supplementary Table 1B:

TABLE-US-00002 SUPPLEMENTARY TABLE 1B Direction “up” “down” Value < Cut-off level 2 1 Value ≧ Cut-off level 1 2

[0099] With regard to lines 1 to 3 of Table 1A, which each comprise a natural compound, the given cut-off level is, therefore, compared with a recorded value in relationship to the natural compound which may constitute a recorded abundance of the respective natural compound as, for example, acquired by means of an LC-MS or GC-MS device. However, since the scoring factor of the natural components as comprised in lines 1 to 2 of Table 1A are equal to zero for the reasons as explained above, lines 1 to 2 of Table 1A may be disregarded since a multiplication of an arbitrary number with zero will always provide zero and, thus, only line 3 of Table 1A may further be taken into account.

[0100] With regard to line 3 of Table 1A, a recorded value of 0.28 may have been acquired through an LC-MS or GC-MS device, irrespective whether the recorded value may be a single value as actually recorded or, alternatively, a mean value as derived from a number of different, preferably subsequent, recordings. Within this regard, it is mentioned that the recorded value may be a characteristic value of the natural compound, in particular a peak in a mass spectrum, wherein the peak may comprise information on the natural compound, such as a mass vs. atomic number (m/z) information or an intensity value related to the abundance, i.e. its amount, of the natural compound in the sample. For this purpose, preferably, gas-chromatography coupled mass spectrometry (GC-MS) and/or liquid-chromatography coupled mass spectrometry (LC-MS) are used. As described above in more detail, liquid chromatography is a technique allowing a separation of analytes in a liquid or a supercritical phase, wherein the compounds in a mobile phase pass through a stationary phase at different rates to become separated in time, whereas in gas chromatography the analytes present in a gaseous volume pass a column comprising solid support materials which serves as a stationary phase, wherein each compound may exhibit a specific time required for passing through the column. For quantification .sup.13C labelled standards may be employed.

[0101] From line 3 of Table 1A it may, first, be derived that the recorded value of 0.28 as mentioned above is below the given cut-off level of 0.5. Secondly, the direction as presented in line 3 of Table 1A indicates “down”. Consequently, the corresponding multiple value which may be taken from the Supplementary Table 1B equals 1.

[0102] With regard to line 4 of Table 1A, which comprises an artificial compound presenting the ratio of the abundance of the natural component as comprised in line 1 of Table 1A divided by the ratio of the abundance of the natural component as comprised in line 2 of Table 1A, the abundances of the two natural components have to be recorded and, subsequently, divided. In this particular example, a value of 9.10 may have been recorded for the natural component in line 1 of Table 1A while a value of 1.40 may have been recorded for the natural component in line 2 of Table 1A. As a result, a respective ratio of 6.50 may be derived therefrom. As may be deducted from comparing this value with the cut-off level as given in line 4 of Table 1A, the ratio exceeds the cut-off level of 6.00. In addition, the direction as presented in line 4 of Table 1A indicates “up”. Consequently, the corresponding multiple value which may be taken from the Supplementary Table 1B equals 1.

TABLE-US-00003 SUPPLEMENTARY TABLE 1C Compound Multiple Scoring Compound Ref. No. Compound value factor score 478100072 ASP not derived 0 0 478100045 ASN not derived 0 0 478100010 CYS 1 2 2 999999992 ASP/ASN 1 3 3 Sample quality score 5

[0103] With regard to this example, according to step (c) of the present method, a sample quality score is subsequently derived by summing up the compound quality scores for the four compounds, whether natural compounds or artificial compounds, as comprised in both Table 1A and the Supplementary Table 10, where a value of 5 for the sample quality score is obtained. In this particular example, however, disregarding lines 1 to 2 of Table 10 or not leads to identical results, since a summing of zero addends will always provide a negligible contribution.

[0104] However, this absolute value of 5 is of little relevance until, according to step (d) of the present method, the sample quality score as acquired and presented in Supplementary Table 10 in this particular example is compared with a reference quality score as taken from the Supplementary Table 1D. By this procedure the quality of the sample may eventually be assessed. In this particular example, the acquired sample quality score of 5 does not equal or exceed the reference quality score which takes a value of 7. Consequently, the quality of the sample in question may, according to Supplementary Table 1D, here be assigned as “low”:

TABLE-US-00004 SUPPLEMENTARY TABLE 1D Sample Quality “low” “high” Reference Quality Score <7 ≧7 Corresponding colour code red green

Example 2

[0105] As a second example for step (a) of the present method for assessing a quality of a biological sample, Table 2A which comprises four separate entry lines is presented. Herein, each entry line comprises a compound reference number, an acronym of a respective compound, three parameters, i.e. a first cut-off level, a second cut-off level and a direction, related to the corresponding compound as well as a scoring factor also in relationship to the respective compound within the same entry line:

TABLE-US-00005 TABLE 2A Compound Cut-off Cut-off Scoring Ref. No. Compound level 1 level 2 Direction factor 478100072 ASP 2.00 5.00 up 1 478100045 ASN 1.50 0.50 down 1 478100010 CYS 0.50 0.30 down 2 999999992 ASP/ASN 4.00 7.00 up 3

[0106] In this particular example, the two cut-off levels may, thus, provide a range of values located between the two cut-off levels which may be of particular relevance for the quality of the sample. Herein, one of the two cut-off levels may, thus, provide a first threshold being relevant for a distinction between a contribution to a high sample quality and a medium sample quality whereas the other of the two cut-off levels may provide a second threshold being of relevance for a distinction between a contribution to the medium sample quality and to a low sample quality while the direction parameter “up” may indicate that the first sample quality may contribute to a high sample quality and the second sample quality may, accordingly, contribute to a low sample quality. In the opposite manner, the direction parameter “down” may indicate that the first sample quality may contribute to a high sample quality and the second sample quality may, accordingly, contribute to a low sample quality. The medium or intermediate quality sample may, for example, still allow for a proper analysis of some constituents whereas the proper analysis of other constituents may no longer be feasible or reliable. It may therefore depend on the respective purpose whether a sample of medium quality may further be used. In addition, the definitions and explanations made with respect to the first example apply mutatis mutandis also for the present example.

[0107] With regard to the second example, according to step (b) of the present method, a compound quality score is now determined for the four compounds as comprised within Table 2A by taking a multiple value of the scoring factor being related to the compound. Similar to the first example, the multiple value is specified by the parameters related to the compound. Within this particular example, the respective dependence of the multiple value on the parameters may be represented by an algorithm which may take the values as indicate in the following Supplementary Table 2B:

TABLE-US-00006 SUPPLEMENTARY TABLE 2B multiple Comparison direction value Value < Cut-off level 1 up 3 Value ≧ Cut-off level 1 but up 2 Value < Cut-off level 2 Value ≧ Cut-off level 2 up 1 Value ≧ Cut-off level 1 down 3 Value < Cut-off level 1 but down 2 Value ≧ Cut-off level 2 Value < Cut-off level 2 down 1

[0108] For the natural components in lines 1 to 3 of Table 2A, the same recorded values as acquired within the first example may be taken for further consideration; i.e. 9.10, 1.40, and 0.28 for the respective natural components in lines 1 to 3 of Table 2A . Consequently, by referring to the corresponding multiple value which may be taken from the Supplementary Table 2B, for each compound, whether natural compound or artificial compound, the compound score may be derived as presented in the following Supplementary Table 2C:

TABLE-US-00007 SUPPLEMENTARY TABLE 2C Compound Compound Multiple Scoring Ref. No. score value factor Compound 478100072 ASP 1 1 1 478100045 ASN 2 1 2 478100010 CYS 1 2 2 999999992 ASP/ASN 2 3 6 Sample quality score 11

[0109] With regard to this example, according to step (c) of the present method, the sample quality score is subsequently derived by summing up the compound quality scores for the four compounds, whether natural compounds or artificial compounds, as comprised in Supplementary Table 2C, where a value of 11 for the sample quality score is obtained.

[0110] However, this absolute value of 11 for the sample quality score is again of little relevance until, according to step (d) of the present method, the sample quality score as acquired and presented in Supplementary Table 2C in this particular example is compared with a reference quality score as taken from the Supplementary Table 2D. By this procedure the quality of the sample may eventually be assessed. In this particular example, the acquired sample quality score of 11 exceeds a first reference quality score of 10 for low sample quality but still remains just below a second reference quality score of 15 for high sample quality. Consequently, the quality of the sample in question may here be assigned as “medium” or “intermediate” according to Supplementary Table 2D:

TABLE-US-00008 SUPPLEMENTARY TABLE 2D Sample Quality “low” “medium” “high” Reference Quality Score <10 ≧10 but <15 ≧15 Corresponding colour code red yellow or green orange

[0111] As a result, the sample of medium or intermediate quality according to this specific example may still be feasible or reliable for a number of purposes.

[0112] In both the first and the second example, a specifically adapted kit may be used for the mentioned purpose of assessing a quality of a biological sample, wherein the kit comprises at least one detection agent for the natural compounds as used here. For this purpose, the kit may comprise a collection of the mentioned constituents provided separately or within a single container, preferably together with instructions applicable for carrying out this method. In addition, the kit may further comprise further components such as buffers or reagents, e.g. a conjugate and/or a substrate.

[0113] Further, in both the first and the second example, the results as obtained by the present method may be displayed according to a number of different arrangements. In a first kind of arrangement, a results table for a number of different samples may be provided, wherein, for each sample, an entry comprising a sample identification number, the sample quality score expressed as number and the related sample quality expressed in at least one word may be given. In a second kind of arrangement, a status report may be provided, wherein, in addition to the first kind of arrangement, the most probable matrix-type as acquired may also be presented with respect to each sample. In a third kind of arrangement, a summary table for the number of different samples may be provided, wherein, for different sample categories, the number of samples with resulting high quality, medium quality, and low quality may be given, respectively. In a fourth kind of arrangement, a chart may be provided, wherein, with respect to the sample number as abscissa, the respective sample quality score may be presented as ordinate together with the corresponding cut-off levels. In this kind of arrangement, a colour code may further be used, particularly in order to highlight the respective sample qualities with corresponding colours, preferably, as for example indicated in Supplementary Tables 1D and 2D, a green colour for the high sample quality, if applicable, yellow or orange for the medium sample quality, and red for the low sample quality. However, other colour codes may equally be used. In addition, further kinds of arrangements may be used.