AU2006200476B2 - Method for interpreting tandem mass spectrometry data for clinical diagnosis - Google Patents

Description

S&FRef: 639871D6

AUSTRALIA

PATENTS ACT 1990 COMPLETE SPECIFICATION FOR A STANDARD PATENT Name and Address of Applicant: Actual Inventor(s): Address for Service: Invention Title: Neo Gen Screening, Inc., of P.O. Box 219, Bridgeville, Pennsylvania, 15017, United States of America Donald H. Chace Spruson Ferguson St Martins Tower Level 31 Market Street Sydney NSW 2000 (CCN 3710000177) Method for interpreting tandem mass spectrometry data for clinical diagnosis The following statement is a full description of this invention, including the best method of performing it known to me/us:- 5845c TITLE OF INVENTION: METHOD FOR INTERPRETING TANDEM MASS SPECTROMETRY DATA FOR CLINICAL DIAGNOSIS TECHNICAL FIELD: Interpreting data used for clinical diagnostic purposes. In particular, a method for interpreting electro spray tandem mass spectrometry data relating to the quantification of metabolites used for diagnosing newborn babies is disclosed.

BACKGROUND ART: Automated methods for assessing a patient's condition are known. Computerized systems can be integrated to produce data that can be compared to a known result to allow for proper diagnosing. Such data might be produced by a MRI or CAT scanner, which is used to identify components within the human body.

One particular instrument used for identifying components of interest, whether they are of medicinal or chemical interest, is the mass spectrometer. In reference to U.S. Patent No. 5,453,613, compounds, when introduced to the electrospray tandem mass spectrometer, are ionized and essentially fragmented. Each fragment produces a peak having local maximums that are matched to reference spectra. A compound can be identified by its associated fragments, each having a mass to charge ratio, which is then relative to the concentrations of each'fiagment. All of the reference spectra and compound names can then be stored in a library for correlation and determination. Thus, mass/charge ratios can be used to identify components from known spectra stored in a database.

More recently, however, the use of spectrometry has been implemented in the field of clinical diagnosis. See Chace, U.S. application serial number 09/277,119.

Inborn errors of metabolism usually result from defective enzymes or cofactors.

Resulting genetic disorders can be diagnosed by the metabolic profiling of amino acids and 9-JAN-200 15:02 SPRUSON FERGUSON 92615486 NO. 4167 P. 26/46 2 O acylcamitines taken from blood spots subjected to a sampling protocol and thereafter introduced N into an electrospray tandem mass spectrometer. An electrospray tandem mass spectrometer is very sensitive and specific and can detect a broad spectrum of disorders at the genetic level. With proper standards, data produced from the spectrometer includes values for particular metabolites.

The metabolites that are of interest in detecting these disorders are, in particular, amino acids and acylcarnitines/camitines and the derivatives thereof.

1- The spectra and resulting concentration values of each metabolite, as derived from mass Sspectrometry, are then compared to thresholds as a means for evaluating the contents of the blood 0 sample. These thresholds determine the appropriate course of action necessary as a follow-up to the spectral analysis.

SAs seen in Wright et al., 5,565,895, spectrometry data is applied to a computerized search database for matching each component as a means of identification. In a clinical diagnostic setting, there must be further methods for evaluation beyond just that of the identification itself. The numbers must be quantified. Newborns can be born with metabolic disorders, which, if not treated within days, can result in death. Thus, after obtaining MS/MS (tandem mass spectrometer) data from blood samples from newborns, generally of the age of less than seven days old, there is a need for efficiently interpreting this data in relation to pre-determined metabolite concentration thresholds. This interpretation allows for proper decision-making necessary for the diagnosing and follow-up testing of newborns.

DISCLOSURE OF INVENTION: According to a first aspect of the present invention, there is provided a method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of propionyl carnitine concentration (C3) and a molar ratio of propionyl camitine and acetyl carnitine (C3/C2) or a molar ratio of propionyl caritine and palmitoyl camitine (C3/C16); comparing said values, respectively, with a C3 flag threshold and a C3/C2 flag threshold or a C3/C16 flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for propionic acidemia, provided there is no said elevation of any of said values.

According to a second aspect of the present invention, there is provided a method comprising steps of: 6MS-lhjg COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-200 15:02 SPRUSON FERGUSON 92615486 NO. 4161 P. 27/46 2a O acquiring mass spectral data from a sample that has been derived from the blood of a 4^ patient, wherein said data includes values comprised of a glutaryl camitine concentration (CSDC) and optionally a molar ratio of glutaryl camitine and palmitoyl carnitine (C5DC/C16); 0, comparing said values, respectively, with C5DC flag threshold and optionally a C5DC/C16 flag threshold; identifying whether or not there is an elevation of any said values above any of said flag thresholds; and O interpreting said sample as being normal for glutaric acidemia, provided there is no said 0 elevation of any of said values.

S1to According to a third aspect of the present invention, there is provided a method comprising 0 steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of a leucine+isoleucine concentration (leu+ile) and a valine concentration (val) and optionally one or more of a molar ratio of leucine+isoleucine s1 and phenylalanine (leu+ilelphe) and a molar ratio of leucine+isoleucine and alanine (leu+ilelala).

comparing said values, respectively, with a leu+ile flag threshold and a val flag threshold and optionally one or more of a leu+ile/phe flag threshold and a leu+ile/ala flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for maple syrup urine disease (MSUD), provided there is no said elevation of any of said values.

According to a fourth aspect of the present invention, there is provided a method comprising steps of; acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of a leucine+isoleucine concentration (leu+ile) and a molar ratio of leucine+isoleucine and alanine (leu+ilelala); and comparing said values, respectively, with a leu+ile flag threshold and a leu+ilelala flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag 3o thresholds; and interpreting said sample as being normal for maple syrup urine disease (MSUD), provided there is no said elevation of any of said values, According to a fifth aspect of the present invention, there is provided a method comprising steps of: 629591-lhg COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JA.200 15:02 SPRUSON FERGUSON 92615486 'N -4161 P 28 '46 2b t'- 0 acquiring mass spectral data from a sample that has been derived from the blood of a Spatient, wherein said data includes values comprised of a leucine+isoleucine concentration (leu+ile), a molar ratio of leucine+isoleucine and phenylalanine (leu+ilelphe), and a molar ratio of leucine+isoleucine and alanine (leu+ilelala); and S comparing said values, respectively, with a leu+ile flag threshold, a leu+ilelphe flag threshold, and a leu+ilelala flag threshold; 1 identifying whether or not there is an elevation of any of said values above any of said flag O thresholds; and interpreting said sample as being normal for maple syrup urine disease (MSUD), provided 1to there is no said elevation of any of said values.

0According to a sixth aspect of the present invention, there is provided a method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of an octanoyl camitine concentration (C8) and one or more of a molar ratio of octanoyl carnitine and palmitoyl camitine (C8C116), a hexanoyl carnitine concentration a decenoyl carnitine concentration (C10:1), and a decanoyl camitine concentration comparing said values, respectively, with a C8 flag threshold and one or more of a C8/C16 flag threshold, a C6 flag threshold, a C10:1 flag threshold, and a C10 flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for medium-chain acyl-coenzyme a dehydrogenase (MCAD) deficiency, provided there is no said elevation of any of said values.

According to a seventh aspect of the present invention, there is provided a method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of one or more of a saturated myristoyl camitine concentration (C14), an unsaturated myristoyl camitine concentration (C14:1), and a molar ratio of myristoyl camitine and palmitoyl carnitine (C14:1/C16); comparing said values, respectively, with one or more of a C14 flag threshold, a 014:1 flag threshold, and a C14:1/C16 flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for VLCAD, provided there is no said elevation of any of said values.

6293914. l COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09.

9-JAN,2007 15:03 SPRUSON FERGUSON 92615486 NO. 416 P. 29/46 2c o According to an eighth aspect of the present invention, there is provided a method Scomprising steps of: Sacquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of one or more of a hydroxyisovalerylcamitine s concentration (C50H) and a tiglylcamitine concentration (C5:1); comparing said values, respectively, with one or more of a C50H flag threshold and a C5:1 flag threshold; o identifying whether or not there is an elevation of any of said values above any of said flag cN thresholds; and interpreting said sample as being normal for crotonyl co-A carboxylase deficiency, provided 0 there is no said elevation of any of said values.

According to a ninth aspect of the present invention, there is provided a method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a is patient, wherein said data includes values comprised of an isovaleryl carnitine concentration and optionally a propionyl camitine concentration (C3); comparing said C5 to a C5 flag threshold; identifying whether or not there is an elevation of C5 above said C5 flag threshold; and interpreting said sample as being normal for said isovaleryl carnitine, provided there is no said elevation of said C5; wherein: said C5 flag threshold is at least about 0,38 pM According to a tenth aspect of the present invention, there is provided a method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of an isovaleryl camitine concentration and optionally a propionyl carnitine concentration (C3); comparing said C5 to a C5 flag threshold; identifying whether or not there is an elevation of C5 above said C5 flag threshold; interpreting said sample as being normal for said isovaleryl camitine, provided there is no o3 said elevation of said C5; and flagging the sample for re-analysis provided any of the following occur: i. said C5 is greater than about 2.0 pM; or ii. said C5 is greater than about 1,0 pM and said C3 is greater than about 2.5 pM.

According to an eleventh aspect of the present invention, there is provided a method comprising steps of: 629391-1hig COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-200 1t5:03 SPRUSON FERGUSON 92615486 NO, 4 16 P. 3 0/4 6 2d 0 acquiring mass spectral data from a sample derived from a dry blood spot on filter paper, wherein said data includes values comprised of a citrulline concentration (cit) and optionally a citrulline concentration after an mrm scan (cit[mrm]); 0 comparing said values, respectively, with a cit flag threshold and optionally a cit[mrm] flag s threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and o interpreting said sample as being normal for citrullinemia, provided there is no said elevation 0 C of any of said values; wherein: Sto said cit flag threshold and said cit (mrm) flag threshold are both at least about 19 pM.

0 According to a twelfth aspect of the present invention, there is provided a method comprising steps of: acquiring mass spectral data from a sample derived from a dry blood spot on filter paper, wherein said data includes values comprised of a citrulline concentration (cit) and optionally a citrulline concentration after an mrm scan (cit[mrm]); comparing said values, respectively, with a cit flag threshold and optionally a cit[mrm] flag threshold; identifying whether or not there, is an elevation of any of said values above any of said flag thresholds; interpreting said sample as being normal for citrullinemia, provided there is no said elevation of any of said values; and flagging the sample for re-analysis provided any of the following occur: i. said cit is greater than said cit flag threshold; or ii, said cit(mrm) is greater than said cit(mrm) flag threshold.

2s According to a thirteenth aspect of the present invention, there is provided a method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of a methionine concentration(met) and optionally a molar ratio of methionine and phenylalanine (met/phe): comparing said values, respectively, with a met flag threshold and optionally a metlphe flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; interpreting said sample as being normal for hypermethionemia, provided there is no said elevation of any of said values; and 629391-1ltls COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:03 SPRUSON FERGUSON 92615486 i\10. 4107 P. 3 1/4 6 2e 0 O flagging the sample for re-analysis provided any of the following occur: 1 i. said met is greater than said met flag threshold; or ii. said met is greater than about 50 pM and said met/phe is greater than said metlphe Sflag threshold.

The objective of the present invention is to provide a method for interpreting electrospray tandem mass spectrometry data from the steps following analysis to diagnosis. The method Sprovides the next course of action necessary in determining the deficiency or elevation of a o particular fragment directly proportional to a concentration of a metabolite that may cause a genetic C defect. In accordance with U.S. application Ser, No. 09/277,119 (US 6,250,605), when

O

629391-lbj COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 an abnormal sample is flagged after being scanned, a recommended action is to be taken.

The present method is a guideline for the necessary action following the preliminary analysis.

Internal standards are used to provide the quantitative information needed to detect specific components. Use of proper ratios of respective ions enables the detection of many metabolites at one time. Each particular metabolite is produced as a fragment yielding a concentration within the spectrometer after being quantified and derivatized from a blood ,o spot. Each metabolite concentration is compared to a flag concentration, which is a quality assurance indicator used to identify a proper sampling quantification and analysis, and which is a diagnostic limit in determining whether or not the concentration of the metabolite is significant. The flag is pre-determined based on a standard deviation from what a normal concentration of a particular metabolite should be. This concentration threshold, or flag, must be appropriated for each scan done and for each type of metabolite reviewed. The concentration values produced will be above or below this threshold flag, which allows for 2 the determination of the next course of action, whether it be a re-analysis or the interpretation that the baby is normal.

As an example, medium chain acyl-CoA dehydrogenase (MCAD) deficiency could be a result of an increased concentration of octanoylcarnitine (Chace et Deficiency in the activity of MCAD presents with a Reye-like syndrome, mild hypoglycemia, or sudden death.

The present method provides for numerical guidelines for determining just how significant the elevation is at the time of birth, and what the next step in the screening process would be, such as a follow-up and confirmatory DNA test. In this manner, decision trees for interpreting the concentrations for amino acids and acylcanitine/carnitines are presented, some of which, if properly diagnosed, can lead to treatment. Each of these potentially fatal blood elevations or deficiencies is compared against the quantified concentration thresholds to allow for immediate attention and action. The comparison with the threshold flags also is a determining factor for maintaining instrument quality and accuracy. This decision making process, coupled with the current method of screening newborns using electrospray tandem MS/MS, allows for a complete protocol for analyzing and diagnosing newborns with genetic disorders.

BRIEF DESCRIPTION OF THE DRAWINGS: FIG. 1 is a flow diagram of the overall methodology representing the major steps involved from analysis to diagnosis.

FIG. 2 is a flow diagram showing the more detailed steps and decision tree involved in the re-analysis protocol.

FIG. 3 is a flow diagram showing the more detailed steps and decision tree involved in the follow-up protocol.

FIG. 4 is the decision tree for the implementation of the method for propionyl carnitine.

FIG. 5 is the decision tree for the implementation of the method for isovaleryl carnitine.

FIG. 6 is the decision tree for the implementation of the method for methionine.

FIG. 7 is the decision tree for:the implementation of the method for glutaryl canitine.

FIG. 8 is the decision tree for the implementation of the method for phenylalanine.

2FIG. 9 is the decision tree for the implementation of the method for leucine.

FIG. 9 is the decision tree for the implementation of the method for lcitline.

FIG. 10 is the decision tree for the implementation of the method for octanoylne.

FIG. 11 is the decision tree for the implementation of the method for octanoyl 3 carnitine.

FIG. 12 is the decision tree for the implementation of the method for myristoyl carnitine.

FIG. 13 is the decision tree for the implementation of the method for BEST MODE FOR CARRYING OUT THE INVENTION: The method will now be described in detail in relation to a preferred embodiment and implementation thereof which is exemplary in nature and descriptively specific as disclosed.

As is customary, it will be understood that no limitation of the scope of the invention is thereby intended. The invention encompasses such alterations and further modifications in the illustrated device, and such further applications of the principles of the invention illustrated herein, as would normally occur to persons slilled in the art to which the invention relates.

The steps in the overall methodology are shown in FIG. 1. After the blood samples are scanned by the electrospray tandem mass spectrometer, the data is acquired 1. This data is can be presented on a monitor to allow for viewing and/or printing of the output. As part of this data acquiring 1, the first values produced from the scan of the mass spectrometer are processed and printed into spreadsheet form to further allow checking of the calculations, a means of assuring accurate number production and quality. The acquired data 1 is then examined by applying the first values obtained to the decision tree 2 particular to a metabolite. The first values to be interpreted 2 consist of mean metabolite concentrations and molar ratio concentrations produced from the fragmentation of the metabolites scanned. The concentration of the particular metabolite is read from the fragmentation of the butyl ester occurring at a specific mass to charge value upon derivatization of the metabolite. This quantified number, normally in units ofmicromolarity, is compared to the flag threshold.

The metabolites, as further described, are grouped as caritines/acylcarnitines or 3 amino acids. Each particular metabolite is derivatized to enhance the detection of the fragment of concern, and would produce a peak upon scanning corresponding to a quantified concentration number, and compared to the decision tree 2 flag threshold, which is a particular standard deviation away from a mean value for the particular metabolite fragment concentration. The flag threshold particular for that metabolite is a diagnostic limit to these first values.

When the first values for the flags and metabolite fragment concentrations or molar ratio concentrations are applied to the decision tree 2, it is identified whether or not there needs to be a subsequent re-analysis 3, or an immediate, stat re-analysis 4. A subsequent analysis 3 may be necessarily performed if the scan revealed a mean concentration that is equal to or slightly greater than the pre-determined threshold for the flag setting. Each tlueshold is unique for a particular metabolite concentration, as further described. It should be understood that a concentration is deemed relevant if it exceeds a threshold when the metabolite may cause defects if elevated, and the concentration is relevant if it is below the Sthreshold when the metabolite of question may cause defects if deficient. Because of this fact, any elevation or deficiency can be called a deviation. For the purposes of clarification, an elevation will be discussed, whereby a deficiency should be inherently understood depending on the metabolite. Both upper and lower concentration flag thresholds and molar ratio thresholds may be utilized in some cases where both an elevation and deficiency is significant in detennining what defect may be present.

A stat re-analysis 4 may be performed if an initial concentration of the metabolite Ssignificantly deviates from the flag threshold, which may be evident of a genetic disorder.

An immediate preliminary follow-up 4a would then follow. Whether or not the deviation is deemed significant depends on the amount by which the metabolite concentration deviates from the flag threshold based on the interpretation guide for each disorder. In any effect, a subsequent analysis 3 or a stat re-analysis 4 requires the data to be re-acquired 1. If the scan shows normal metabolite concentration levels as compared to the concentration flag thresholds and molar ratio thresholds, the interpretation may be that the blood component levels are normal Depending on which particular metabolite is being scanned, if the metabolite concentration is not significantly above the threshold, but still deviates in relation to the threshold, even after re-analysis, the next step would be to interpret 6 the sample as being evident of this elevation (or deficiency). In this case, a follow-up protocol 7 would be initiated, such that the detection process would be repeated arid all attention would be focused on this sample. After any subsequent repeat, a diagnostic interpretation 8 may follow if the first concentration is consistent with any subsequent evaluation.

The criteria involved for deciding whether or not to subsequently re-analyze 3, or to immediately (stat) re-analyze 4 with an immediate preliminary follow-up 4a, are further described in relation to FIG. 2. The pre-determined threshold flags for each particular metabolite are compared to the initial concentrations of the metabolites 20 after being scanned. The threshold flag settings have been developed based upon many factors such as published reports, the clinical screening of individuals who are already sick, autopsy reports, and experience through repetition of genetic data analysis. If the initial concentration of the metabolite of interest is greater than the flag threshold 21, then a determination is made as to how significant the elevation is 23. This is determined by comparing each flag threshold to the initial concentration of the metabolite and identifying whether or not the elevation (or deficiency) exceeds the flag threshold by reference to criteria for each metabolite. If this were to occur, an immediate stat re-analysis 4 and preliminary follow-up 4a would be performed. This is achieved by prioritizing the sample to allow for an immediate preliminary follow-up and re-running the sample from the same filter card to acquire a set of prioritized values. These values are then averaged as a mean with the first values to form priority mean values because they are more significant for implementation into the follow-up protocol.

If the initial concentration of the metabolite is not greater than the flag threshold 21, the molar ratio concentrations are identified and compared to their respective concentration flag thresholds and molar ratio thresholds 22. The molar ratios are important because they account for variability of the blood spot on the filter card. Because the sample is originally dry, the variability of the thickness, number of cells, and change in volume must be accounted for. Thus, as the concentration of the metabolite may go up or down, the ratio of two analytes in one sample is a more sensitive indicator because they both change relative to one another.

If the molar ratio concentrations are not greater than the concentration flag thresholds and molar ratio thresholds 22, then the sample may be labeled as normal. However, if the molar ratio concentrations are found to be greater 22 by reference to the criteria particular for that metabolite, the elevation significance is then compared as above 23. Thus, if either the initial concentration of the metabolite or the molar ratios are significantly elevated by reference to the criteria, an immediate stat re-analysis 4 with preliminary follow-up 4a is performed. And in both cases, if the elevation is present by comparison to the flag threshold 21 but not significant 23, a sub-sequent re-analysis 3 is performed. This is achieved by acquiring a new set of data to obtain second values from the sample, by re-testing the sample and averaging the results.to form mean values of the concentrations, which can then be implemented into the follow-up protocol, as follows.

A follow-up protocol is then initiated 7 following any re-analysis for determining any possible interpretation'for diagnosis' FIG. 3 lays out the criteria for broadly initiating a follow-up 7. Any mean values or priority mean values are identified from the subsequent re-analysis 3 or the immediate reanalysis 4, respectively. These values that are elevated to some degree (dependent on decision matrix) above the flag threshold are identified 30. This follow-up 7 may also follow any re-analysis. The level of elevation (or deficiency, if required) is interpreted 31 as being mild 32, moderate 33, or significant 34 based on the criteria in the interpretation guide for each metabolite, as further described. If the elevation is considered mild 32 based on the difference from the threshold, a routine repeat 35 is performed. This involves performing a less prioritized repeat of the testing without an alert to a parent or physician.

If the elevation is considered moderate 33 based on the criteria, an urgent repeat 36 is performed, which is different from a routine repeat because the elevation is reported to a physician. Accordingly, the physician can suggest to see the baby and possibly get another 1o sample or confirm the results.

If the elevation is considered significant 34 based on the criteria, an urgent repeat plus additional testing to obtain a third set of values, such as for propionic acidemia, or other organic acidemias, is performed along with a referral to a specialist particular to a disorder to ascertain an expertise for clinical evaluation.

The present method can be further understood by referencing the tables and criteria in figures 4 -10. Each figure represents the decision tree presented for each particular metabolite, which is necessary because each metabolite ionizes a butyl ester fragment at a different mass to charge value, and each metabolite concentration (in units micromolarity must be compared to a different threshold flag. The butyl ester fragment is directly proportional to the concentration of the metabolite. The preferred values of the threshold flags, or automated interpretation flag settings, are seen in tabulated form for each metabolite.

FIG. 4 is used in the method for assisting in the diagnosis of propionic acidemia after a dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer.

The method as previously discussed is applied using the flag thresholds 40 for all concentrations and molar ratios used for determining the level of elevation of propionyl carnitine. The flag thresholds 40 are preferably set at about 5.0 uM for the propionyl carnitine (C3) concentration, about 0.3 for the mrm scan of propionyl carnitine with acetyl carnitine (C3mrm/C2), and about 1.75 for the molar ratio of the propionyl camitine with palmitoyl carnitine (C3/C16).

The criteria for re-analysis 41 and criteria for an immediate, or STAT re-analysis 42 in relation to the flag thresholds 40 are also shown. A subsequent re-analysis to obtain mean values is performed provided any of the following occurs: i. C3 is equal to or greater than the C3 flag threshold; ii. C3/C16 is greater than or equal to the C3/C16 flag threshold and C3/C2 is greater than the C3/C2 flag threshold and C3 is greater than about 2.5 uM; iii. C3 is greater than about 4 uM, and either said C3/C16 is greater than said C3/C16 flag threshold or said C3/C2 is greater than said C3/C2 flag threshold.

An immediate, or STAT re-analysis with a preliminary follow-up to obtain priority mean values is performed provided any of the following occurs: i. C3 is greater than about 9.0 uM; ii. C3 is greater than about 7.0 uM and the C3/C2 is greater than the C3/C2 flag threshold, or the C3/C16 is greater than the C3/C16 flag threshold.

The procedure is repeated to get mean values for implementation into a specific follow-up protocol 43, which ultimately leads to the diagnostic assistance for propionic acidemia.

FIG. 5 is used in the method for assisting in the diagnosis ofisovaleric acidemia after a dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer.

The method as previously discussed is applied using the flag threshold 50 for the concentration used for determining the level of elevation ofisovaleryl camitine. The flag threshold 50 for isovaleryl carnitine is preferably set at about 0.8 uM.

Criteria for re-analysis 51 and criteria for an immediate, or STAT re-analysis 52 in relation to the flag threshold 50 for isovaleryl carnitine (C5) are also shown. A subsequent reanalysis 51 to obtain a mean value of C5 is performed provided the isovaleryl caritine concentration (C5) is greater than or equal to the C5 flag threshold An immediate re-analysis 52 with a preliminary follow-up to obtain a priority mean value of an isovaleryl carnitine concentration (C5) is performed provided any of the following occurs: i. the C5 is greater than about 2.0 uM; ii. the C5 is greater than about 1.0 uM and the propionyl camitine concentration (C3) [FIG. 4] is greater than about 2.5 uM.

The procedure is repeated to get mean values for implementation into a specific follow-up protocol 53, which ultimately leads to the diagnostic assistance for isovaleric acidemia.

FIG. 6 is used in the method for assisting in the diagnosis of hypermethionemia after a dry blood spot on filter paper is derivatized and scanned using a tandem miass-spectrometer.

The method as previously discussed is applied using the flag thresholds 60 for all concentrations and molar ratios used for determining the level of elevation of methionine.

The flag thresholds 60 are preferably set at 60 uM for the methionine concentration (met) and 1 for the molar ratio of methionine and phenylalanine (met/phe).

The criteria for re-analysis 61 and criteria for an immediate, or STAT re-analysis 62 in relation to the flag thresholds are also shown. A subsequent re-analysis to obtain mean values is performed provided any of the following occur: i. met is greater than the met flag threshold; ii. met is greater than about 50 uM and the met/phe is greater than the met/phe flag threshold.

An immediate re-analysis with a preliminary follow-up to obtain priority mean values is performed provided any of the following occur: i. met is greater than about 150 uM; ii. met is greater than about 125 uM and the met/phe is greater than about 1.25.

The procedure is repeated to get mean values as previously discussed for implementation into a specific follow-up protocol 63, which ultimately leads to the diagnostic assistance for hypermethionemia.

FIG. 7 is used in the method for assisting in the diagnosis of glutaric acidemia after a 1o dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer: The method as previously discussed is applied using the flag thresholds 70 for all concentrations and molar ratios used for determining the level of elevation of glutaryl carnitine. The flag thresholds 70 are preferably set at 0.17 uM for the glutaryl carnitine concentration (C5DC) and 0.12 for the molar ratio of glutaryl carnitine with palmitoyl carnitine (C5DC:C16).

Criteria for re-analysis 71 and criteria for an immediate, or STAT re-analysis 72 in relation to the flag thresholds are also shown. A subsequent re-analysis 71 to obtain mean values is performed provided any of the following occur: i. C5DC is greater than the C5DC flag threshold; ii. C5DC:C16 is greater than the C5DC:C16 flag threshold, and the C5DC is greater than about 0.14 uM.

An immediate re-analysis 72'with a preliminary follow-up to obtain priority mean values is performed provided any of the following occur: i. C5DC is greater than about 0.4 uM; ii. C5DC is greater than about 0.2 uM, and the C5DC:C16 is greater than about 0.2 uM.

The procedure is repeated to get mean values as previously discussed for implementation into a specific follow-up protocol 73, which ultimately leads to the diagnostic assistance for glutaric acidemia.

FIG. 8 is used in the method for assisting in the diagnosis of phenylketonuria

(PIKU)

after a dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer. The method as previously discussed is applied using the flag thresholds 80 for o all concentrations and molar ratios used for determining the level of elevation of phenylalanine (phe) or tyrosine (tyr). The flag thresholds 80 are preferably set at 130 uM for the phenylalanine concentration (phe), 350 uM for the tyrosine concentration (tyr), and for the molar ratio of phenylalanine with tyrosine (phe/tyr).

The criteria for re-analysis 81 and criteria for an immediate, or STAT re-analysis.82 in relation to the flag thresholds are also shown. A subsequent re-analysis 81 to obtain mean values is performed provided any of the following occur: i. phe is greater than the phe flag threshold; ii. tyr is greater than the tyr flag threshold; iii. phe/tyr is greater than the phe/tyr flag threshold and the phe is greater than about 100 uM.

An immediate re-analysis 82 with a preliminary follow-up to obtain priority mean values is performed provided any of the following occur: i. phe is greater than about 240 uM; ii. phe is greater than about 180 uM and the phe/tyr is greater than the phe/tyr flag threshold.

The procedure is repeated to get mean values as previously discussed for implementation into a specific follow-up protocol 83, which ultimately leads to the diagnostic assistance for PKU.

14 FIG. 9 is used in the method for assisting in the diagnosis of Maple. Syrup Urine Disease (MSUD) after a dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer. The method as previously discussed is applied using the flag thresholds 90 for all concentrations and molar ratios used for determining the level of elevation of leucine. The flag thresholds are preferably set at 325 uM for the concentration of a ,ombination ofleucine and isoleucine (leu+Ile); 300 uM for a concentration ofvaline (val); 8.C for the molar ratio of leucine with phenylalanine (leu/phe); and 2.25 for the molar ratio of leL :ine with alanine (leu/ala).

The criteria for re-analysis 91 and criteria for an immediate, or STAT re-analysis 92 in relation to the flag thresholds are also shown. A subsequent re-analysis 91 to obtain mean values is performed provided any of the following occur: i. leu+ile is greater than about 400 uM; ii. leu+ile is greater than about 350 uM and val is greater than the val flag threshold; iii. leu+ile is greater than the leu+ile flag threshold and the leu/ala is greater than the leu/ala flag threshold, or the leu/phe is greater than the leu/phe flag threshold and the val is greater than the val flag threshold; An immediate re-analysis 92 with a preliminary follow-up to obtain priority mean valu-s is performed provided any of the following occur: i. leu+ile is greater than about 500 uM; ii. leu+ile is greater than about 400 uM and the leu/phe is greater than the leu/phe flag threshold and the leu/ala is greater than the leu/ala flag threshold.

The procedure is repeated to get mean values as previously discussed for implementation into a specific follow-up protocol 93, which ultimately leads to the diagnostic assistance for MSUD.

FIG. 10 is used in the method for assisting in the diagnosis of citrullinemia after a dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer. The method as previously discussed is applied using the flag threshold 100 for the concentrations used for determining the level of elevation of citrulline. The flag threshold 100 is preferably set at 55 uM for a concentration of citrulline determined after a full scan (cit), and 55 uM for a concentration of citrulline determined after an mrm scan (cit[mrm]).

The criteria for re-analysis 101 and criteria for an immediate, or STAT re-analysis 102 in relation to the flag thresholds are also shown. A subsequent re-analysis 101 to obtain mean values is performed provided the following occurs: i. cit or cit(mrm) is greater than the cit flag threshold or the cit(mrm) flag threshold.

An immediate re-analysis 102 with a preliminary follow-up to obtain priority mean values is performed provided the following occurs: i. cit is greater than about 100 uM.

The procedure is repeated to get mean values as previously discussed for implementation into a specific follow-up protocol 103, which ultimately leads to the diagnostic assistance for citrullinemia.

FIG. 11 is used in the method for assisting in the diagnosis of medium-chain acylcoenzyme A dehydrogenase (MCAD) deficiency after a diy blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer. The method as previously discussed is applied using the flag thresholds 110 for all concentrations and molar ratios used for determining the level of elevation of octanoyl camitine. The flag thresholds 110 are preferably set at 0.35 uM for an octanoyl carnitine concentration 0.28 for a molar ratio of octanoyl camitine with pahnitoyl carnitine; 0.16 uM for a hexanoyl carnitine concentration 0.32 uM for a decenoyl camitine concentration (C10:1); and 0.42 uM for a decanoyl carnitine concentration (C The criteria for re-analysis 111 and criteria for an immediate, or STAT re-analysis 112 in relation to the flag thresholds 110 are also shown. A subsequent re-analysis 111 to obtain mean values is performed provided any of the following occur: i. C8 is greater than or equal to about 0.4 uM; ii. C8 is greater than about 0.3 uM and the C8/C16 is greater than about 0.15; iii. C8 is greater than about 0.3 uM and the C6 is greater than about 0.2 uM, or the C10:1 is greater than about 0.2 uM and the C0 Ois greater than about 0.3 uM with a low acetyl flag; An immediate re-analysis 112 with a preliminary follow-up to obtain priority mean values is performed provided any of the following occur: i. CS is greater than about 1.0 uM; ii. C8 is greater than about 0.5 uM and the C8/C16 is greater than about 0.35, or the C6 is greater than about 0.3 uM and the C10:1 is greater than about 0.3 uM.

The piocedure is repeated to get mean values as previously discussed for implementation into a specific follow-up protocol 113, which ultimately leads to the diagnostic assistance for MCAD deficiency.

FIG. 12 is used in the method for assisting in the diagnosis of very long chain acylCoA dehydrogenase (VLCAD) deficiency after a dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer. The method as previously discussed is applied using the flag thresholds 120 for all concentrations and molar ratios used for determining the level of elevation of the myristoylcamitines. The flag thresholds 120 are 3preferably set at 0.85 uM for a saturated myristoyl carnitine concentration (C14); 0.70 for an unsaturated myristoyl carnitine concentration (C14:1); and 0.24 for a molar ratio of the unsaturated (C 14:1) with palmitoyl carnitine.

The criteria for re-analysis 121 and criteria for an immediate, or STAT re-analysis 122 in relation to the flag thresholds are also shown. A subsequent re-analysis 121 to obtain mean values is performed provided any of the following occur: i. C14 is greater than the C14 flag threshold, or said C14:1 is greater than the C14:1 flag threshold; ii. C14 is greater than about 0.75 uM, or the C14:1 is greater than about 0.65 uM and ,o the C14:1/C16 is greater than about 0.24.

An immediate re-analysis 122 with a preliminary follow-up to obtain priority mean values is performed provided any of the following occur: i. C14 is greater than about 2.0 uM, or the C14:1 is greater than about 1.5 uM; Sii. C14 is greater than about 1.5 uM, and the C14:1 is greater than about 1.0 uM, and the C14:1/C16 is greater than about 0.3.

The procedure is repeated to get mean values as previously discussed for 2o implementation into a specific follow-up protocol 123, which ultimately leads to the diagnostic assistance for VLCAD deficiency.

FIG. 13 is used in the method for assisting in the diagnosis of crotonyl co-A carboxylase deficiency after a dry blood spot on filter paper is derivatized and scanned using a tandem mass spectrometer. The method as previously discussed is applied using the flag thresholds 130 for all concentrations used for determining the level of elevation of the hydroxy C5. The flag thresholds 130 are preferably set at 0.85 uM for a concentration (C50H), and 0.35 for a C5:1 concentration.

The criteria for re-analysis 131 and criteria for an immediate, or STAT re-analysis 132 in relation to the flag thresholds are also shown. A subsequent re-analysis 131 to obtain mean values is performed provided any of the following occur: 3s i. C50H is greater than or equal to the C50H flag threshold; ii. C5:1 is greater than or equal to the C5:1 flag threshold; An immediate re-analysis 132 with a preliminary follow-up to obtain priority mean values is performed provided any of the following occur: i. C50H is greater than about 3.0 uM; ii. C5:1 is greater than about 1.0 uM.

The procedure is repeated to get mean values as previously discussed for implementation into a specific follow-up protocol 133, which ultimately leads to the diagnostic assistance for crotonyl coA carboxylase deficiency.

represents a hydroxy-C5, which is an abbreviated form for hydroxyisovalerylcarnitine and/or hydroyxlmethylbutylcamitine. The C5:1 is the unsaturated form known as tiglylcamitine.

In conclusion, according to each decision tree, or interpretation guide particular for each metabolite, the present method allows the data that is acquired to be quantified and reported to a physician to assist in a diagnosis of a genetic disease resulting from the 2deviation (elevation or deficiency) of a blood metabolite. The method allows one to provide information to a physician that additional tests and/or clinical assessments (check up, examination, etc) are necessary because of the resulting elevation or deficiency of the metabolite, which then results in the confirmed final diagnosis. The values of the flag thresholds for a particuilar concentration and the molar ratio flag thresholds must be quantified for a consistent and accurate interpretation of acylcarnitine and amino acid data.

TERMS

It should be understood that "about" as used in relation to Figs 4 13 means 15% of the value shown in the criteria for each figure, which values are dependent upon the flag threshold. Any change in the value of the flag threshold, which might result from filter paper characteristics, new insights into disease characterisitics, new diseases found, methods of sample collection, changes in methodology, or corrections from quality assurance programs, would necessitate the relative change of each value in the criteria for all follow-ups. Thus, all values shown in the drawings are the preferred values, which might fluctuate then by no more than INDUSTRIAL APPLICABILITY: The present method quantifies measurements for detecting inborn errors of S metabolism usually resulting from defective enzymes or cofactors. Genetic disorders can ultimately be diagnosed by the metabolic profiling of the amino acids and acylcarnitines taken from the blood spots. Newborn babies born with certain metabolic disorders can die if not treated within days. Thus, after obtaining MS/MS (tandem mass spectrometer) data from 5 blood samples from newborns, there is a need for efficiently interpreting this data in relation to a variety of pre-determined metabolite concentration thresholds. This interpretation allows for proper decision-making necessary for the diagnosing and follow-up testing of newborns over a wide range of genetic disorders.

Claims (2)

1. 9-JAN-200 15:04 SPRUSON FERGUSON 92615486 'NO. 4167 F. 32/46 0 The claims defining the invention are as follows: 1. A method comprising steps of: Sacquiring mass spectral data from a sample that has been derived from the blood of a N patient, wherein said data includes values comprised of propionyl carnitine concentration (C3) and a molar ratio of propionyl carnitine and acety! caritine (C3/C2) or a molar ratio of propionyl carnitine and palmitoyl carnitine (C31016); comparing said values, respectively, with a C3 flag threshold and a C3/C2 flag threshold or a OC3/C16 flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag Sto thresholds; and O interpreting said sample as being normal for propionic acidemia, provided there is no said elevation of any of said values. 2. The method of claim 1, wherein: in the acquiring step, said data includes values comprised of a propionyl camitine s1 concentration (C3) and a molar ratio of propionyl carnitine and acetyl carnitine (C3/C2); and in the comparing step, said C3 and C3/C2 are compared with a C3 flag threshold and a C3/C2 flag threshold, respectively. 3. The method of claim 1 or 2, wherein: in the acquiring step, said data includes values comprised of a propionyl carnitine concentration (C3) and a molar ratio of propionyl camitine and acetyl carnitine (C3/C16); and in the comparing step, said C3 and 03/C16 are compared with a C3 flag threshold and a C3/C16 flag threshold, respectively. 4. The method of any one of claims 1 to 3, wherein: in the acquiring step, said data includes values comprised of a propionyl carnitine concentration (C3) and a molar ratio of propionyl camitine and acetyl carnitine (C3/C2) and a molar ratio of propionyl camitine and acetyl camitine (C3C16); and in the comparing step, said C3, C3/C2 and C3/ C16 are compared with a C3 flag threshold, a C3/C2 flag threshold and a C3/C6I flag threshold, respectively. The method of any one of claims 1 to 4 further comprising: 3o flagging the sample for re-analysis provided any of the following occur: i. said C3 is equal to or greater than said C3 flag threshold; ii. said C3/C16 is greater than or equal to said C3/C16 flag threshold and said C3/C2 is greater than said C3/C2 flag threshold and said C3 is greater than 2.5 p M; or iii. said C3 is greater than 4 pM, and either said C3/C16 is greater than said C3/C16 flag threshold or said C3/C2 is greater than said C3/C2 flag threshold.
2. 629391.Ihj COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:04 SPRUSON FERGUSON 92615486 10, 416 P. 3 3/4 6 21 0 O 6 The method of claim 5 further comprising: Sperforming a re-analysis of said sample or a new sample from the same patient to obtain mean values. 7. The method of claim 6 further comprising: 0 s initiating a follow-up protocol based on follow-up criteria utilizing said mean values. 8. The method of any one of claims 1 to 7 further comprising: 1- flagging the sample for re-analysis provided any of the following occur. Si. said C3 is greater than about 9.0 pM; or Sii. said C3 is greater than about 7.0 pM and said C31C2 is greater than said C3/C2 flag threshold or said C3/C16 is greater than said 03/016 flag threshold. o 9, The method of claim 8 further comprising; performing a re-analysis of said sample or a new sample from the same patient to obtain priority mean values. The method of claim 9 further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said priority mean values. 11. The method of any one of claims 1 to 10, wherein said C3 flag threshold, said C3/C2 flag threshold, and said C3/016 flag threshold are, respectively, at least about 3.4 pM, 0.21, and 1.12, 12. The method of any one of claims 1 to 10, wherein said C3 flag threshold, said C31C2 flag threshold, and said C3/C16 flag threshold are, respectively at least about 4.6 pM, 0.29, and 1.54. 13. The method of any one of claims 1 to 10, wherein said C3 flag threshold, said C3IC2 flag threshold, and said C3/016 flag threshold are, respectively about 5.0 pM, 0.30, and 1,75. 14. The method of any one of claims 1 to 13, wherein the sample was derived from a dry blood spot on filter paper. The method of claim 14, wherein the sample was derivatized. 16. The method of any one of claims 1 to 15, wherein: in the acquiring step, said data was acquired using a tandem mass spectrometer. 17. A method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patent, wherein said data includes values comprised of a glutaryl camitine concentration and optionally a molar ratio of glutaryl camitine and palmitoyl camitine (C5DC/C16); comparing said values, respectively, with C5DC flag threshold and optionally a C5DC/C16 flag threshold; 0t29t-lhj 6 COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2001 15:04 SPRUSON FERGUSON 92615486 NO, 416 P. 3 4/4 6 22 0 identifying whether or not there is an elevation of any said values above any of said flag cil Sthresholds; and interpreting said sample as being normal for glutaric acidemia, provided there is no said C elevation of any of said values. S 18. The method of claim 17, wherein: in the acquiring step, said data includes values comprised of a glutaryl camitine concentration (C5DC) and a molar ratio of glutaryl camitine and palmitoyl carnitine (C5DC/C16); O and C in the comparing step, said C5DC and C5DC/C16 are compared with a C5DC flag threshold S1to and a C5DC/C16 flag threshold, respectively. S19. The method of claim 17 or 18 further comprising: flagging the sample for re-analysis provided any of the following occur: i. said C5DC is greater than said C5DC flag threshold; or ii. said C5DCIC16 is greater than said C5DC flag threshold and said C5DC is greater than about 0.14 pM. The method of claim 19 further comprising: performing a re-analysis of said sample or a new sample from the same patient to obtain mean values. 21. The method of claim 20 further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said mean values. 22. The method of any one of claims 17 to 21 further comprising: flagging the sample for re-analysis provided any of the following occur: i. said C5DC is greater than about 0.4 pM; or ii, said C5DC is greater than about 0.2 pM and said C5DC/C16 is greater than about 0.2 pM. 23. The method of claim 22 further comprising: performing a re-analysis of said sample or a new sample from the same patient to obtain mean values. 24. The method of claim 23 further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said mean values. The method of any one of claims 17 to 24, wherein said C5DC flag threshold and said C5DCIC16 flag threshold are, respectively, at least about 0.13 pM and 0.04. 26. The method of any one of claims 17 to 24, wherein said C5DC flag threshold and said C5DC/C16 flag threshold are, respectively, at least about 0.18 pM and 0.06. z29391-hlli COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:04 SPRUSON FERGUSON 92615486 NO. 4167 P. 3 5/4 6 23 o 27. The method of any one of claims 17 to 24, wherein said CSDC flag threshold and said N C5DC/C16 flag threshold are, respectively, about 0.17 pM and 0.12. 28. The method of any one of claims 17 to 27, wherein the sample was derived from a dry Sblood spot on filter paper. 29. The method of claim 28, wherein the sample was derivatized. The method of any one of claims 17 to 29, wherein: Sin the acquiring step, said data was acquired using a tandem mass spectrometer. S31. A method comprising steps of: Sacquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of a leucine+isoleucine concentration (leu+ile) 0 and a valine concentration (vai) and optionally one or more of a molar ratio of leucine+isoleucine and phenylalanine (leutilelphe) and a molar ratio of leucine+isoleucine and alanine (leu+ileiala). comparing said values, respectively, with a leu+ile flag threshold and a val flag threshold and optionally one or more of a leu+ile/phe flag threshold and a leu+ile/ala flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for maple syrup urine disease (MSUD), provided there is no said elevation of any of said values. 32. The method of claim 31, wherein: in the acquiring step, said data includes values comprised of a leucine+isoleucine concentration (leu+ile), a molar ratio of leucine+isoleucine and phenylalanine (leu+ile/phe), and a valine concentration (val); and in the comparing step, said leu+ile, leu+ile/phe, and val are compared with a leu+ile flag threshold, a leu+ilelphe flag threshold, and a val flag threshold, respectively, 33. A method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of a leucinetisoleucine concentration (leu+ile) and a molar ratio of leucine+isoleucine and alanine (leu+ile/ala); and comparing said values, respectively, with a leu+ile flag threshold and a leu+ile/ala flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for maple syrup urine disease (MSUD), provided there is no said elevation of any of said values. 34, A method comprising steps of: 619391-thj5 COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:05 SPRUSON FERGUSON 92615486 MUO 416 P. 36/46 24 o acquiring mass spectral data from a sample that has been derived from the blood of a Spatient, wherein said data includes values comprised of a leucine+isoleucine concentration (leutile), a molar ratio of leucine+isoleucine and phenylalanine (leu+ile/phe), and a molar ratio of 0\ leucine+isoleucine and alanine (leu+ile/ala); and s comparing said values, respectively, with a leu+ile flag threshold, a leu+ile/phe flag threshold, and a leu+ile/ala flag threshold; Sidentifying whether or not there is an elevation of any of said values above any of said flag O thresholds; and N interpreting said sample as being normal for maple syrup urine disease (MSUD), provided there is no said elevation of any of said values. 0 35. The method of any one of claims 31 to 34 further comprising: flagging the sample for re-analysis provided any of the following occur: i. said leu+ile is greater than about 400 pM; ii. said leu+ile is greater than about 350 pM and said val is greater than said val flag is threshold; iii. said leu+ile is greater than said leu+ile flag threshold and said leu+ilelala is greater than said leu+ilelala flag threshold; or iv. said leu+ilelphe is greater than said leu+ile/phe flag threshold and said val is greater than said val flag threshold. 36, The method of any one of claims 31 to 34 further comprising: flagging the sample for re-analysis provided any of the following occur: i. said leu+ile is greater than about 500 pM; or ii. said leu+ile is greater than about 400 pM and said leu+ilelphe is greater than said leu+ilelphe flag threshold and said leu+ile/ala is greater than said leu+ilelala flag threshold. 37. The method of claim 35 or 36 further comprising: performing a re-analysis of said sample or a new sample from the same patient to obtain mean values. 38. The method of claim 37 further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said mean values. 39. The method of any one of claims 31 to 38, wherein said leu+ile flag threshold, said val flag threshold, said leu+ilelphe flag threshold, and said leu+ile/ala flag threshold are, respectively, at least about 229 pM, 215 pM, 4.36, and 1.19. The method of any one of claims 31 to 38, wherein said leu+ile flag threshold, said val flag threshold, said leu+ile/phe flag threshold, and said leu+ile/ala flag threshold are, respectively, at least about 291 pM, 288 pM, 5.53, and 1,54. 29391-lhjs COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2001 15:05 SPRUSON FERGUSON 92615486 NO. 4167 P. 37/46 o 41. The method of any one of claims 31 to 38, wherein said leu+ile flag threshold, said val flag threshold, said leu+ilelphe flag threshold, and said leu+ile/ala flag threshold are, respectively, about 325 pM, 300 pM, 8.0, and 2.25. S42. The method of any one of claims 31 to 41, wherein the sample was derived from a dry 0 s blood spot on filter paper, 43, The method of claim 42, wherein the sample was derivatized. 44. The method of any one of claims 31 to 43, wherein: O in the acquiring step, said data was acquired using a tandem mass spectrometer. C 45. A method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a Spatient, wherein said data includes values comprised of an octanoyl camitine concentration (C8) and one or more of a molar ratio of octanoyl camitine and palmitoyl carnitine (C8/C16), a hexanoyl carnitine concentration a decenoyl carnitine concentration (C10:1), and a decanoyl camitine concentration comparing said values, respectively, with a C8 flag threshold and one or more of a C8/C16 flag threshold, a C6 flag threshold, a C10:1 flag threshold, and a C10 flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency, provided there is no said elevation of any of said values. 46. The method of claim 45, wherein: in the acquiring step, said data includes values comprised of an octanoyl carnitine concentration (C8) and a molar ratio of octanoyl camitine and palmitoyl camitine (C8/C16); and in the comparing step, said C8 and C8/C16 are compared with a C8 flag threshold and a C8/C16 flag threshold, respectively. 47. The method of claim 45 or 46, wherein: in the acquiring step, said data includes values comprised of an octanoyl carnitine concentration (C8) and a hexanoyl camitine concentration and in the comparing step, said C8 and C6 are compared with a C8 flag threshold and a C6 flag o threshold, respectively. 48. The method of any one of claims 45 to 47, wherein: in the acquiring step, said data includes values comprised of an octanoyl camitine concentration a decanoyl camitine concentration (C10), and a decenoyl carnitine concentration (C10:1); and b629391-Thji COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:05 SPRUSON FERGUSON 92615486 NO. 4107 P. 3 8/4 6 26 Sin the comparing step, said C8, C10, and C10:1 are compared with a C8 flag threshold, a flag threshold, and a C10:1 flag threshold, respectively. 49. The method of any one of claims 45 to 48, wherein: S in the acquiring step, said data includes values comprised of an octanoyl camitine concentration a hexanoyl camitine concentration and a decenoyl carnitine concentration (C10:1); and in the comparing step, said C8, C6, and C10:1 are compared with a C8 flag threshold, a C6 Sflag threshold, and a C10:1 flag threshold, respectively. 50. The method of any one of claims 45 to 49 further comprising: Sto flagging the sample for re-analysis provided any of the following occur. S. said C8 is greater than or equal to about 0.4 pM; ii. said C8 is greater than about 0.3 pM and said C8/C16 is greater than about 0.15; iii, said C8 is greater than about 0.3 pM and said C6 is greater than about 0.2 pM; or iv. said C10:1 is greater than about 0.2 pM and said C10 is greater than about 0.3 pM 1s 51. The method of any one of claims 45 to 49 further comprising: flagging the sample for re-analysis provided any of the following occur: i. said C8 is greater than about 1,0 pM; ii. said C8 is greater than about 0.5 pM and said C8/C16 is greater than about 0.35; or iii. said C6 is greater than about 0,3 pM and said C10:1 is greater than about 0.3 pM. 52. The method of claim 50 or 51 further comprising: performing a re-analysis of said sample or a new sample from the same patient to obtain mean values, 53. The method of claim 52 further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said mean values. 54. The method of any one of claims 45 to 53, wherein said C8 flag threshold, said C8/C16 flag threshold, said C6 flag threshold, said C10:1 flag threshold, and said C10 flag threshold are, respectively, at least about 0.19 pM, 0,08, 0.16 pM, 0,18 pM, and 0,31 pM. The method of any one of claims 45 to 53, wherein said C8 flag threshold, said C8/C16 flag threshold, said C6 flag threshold, said C10:1 flag threshold, and said C10 flag threshold are, respectively, at least about 0.26 pM, 0.12, 0.22 pM, 0.24 pM, and 0.42 pM. 56. The method of any one of claims 45 to 53, wherein said C8 flag threshold, said C8/C16 flag threshold, said C6 flag threshold, said C10:1 flag threshold, and said C10 flag threshold are, respectively, about 0.35 pM, 0,28, 0.16 pM, 0.32 pM, and 0.42 pM. 57. The method of any one of claims 45 to 56, wherein the sample was derived from a dry blood spot on filter paper. Ge-uM-lhjg COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9,JAN-200) 15:06 SPRUSON FERGUSON 92615486 'NO.416) P 391/46 27 0 O 58. The method of claim 57 wherein the sample was derivatized. S59. The method of any one of claims 45 to 58, wherein: Sin the acquiring step, said data was acquired using a tandem mass spectrometer. 060. A method comprising steps of: 3 acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of one or more of a saturated myristoyl carnitine concentration (C14), an unsaturated myristoyl camitine concentration (C14:1), and a Smolar ratio of myristoyl carnitine and palmitoyl carnitine (C14:1/C16); N comparing said values, respectively, with one or more of a C14 flag threshold, a C14:1 flag threshold, and a C14:1/C16 flag threshold; 0identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for VLCAD, provided there is no said elevation of any of said values, 61. The method of claim 60, wherein: in the acquiring step, said data includes a saturated myristoyl camitine concentration (C14); and in the comparing step, said C14 is compared with a C14 flag threshold. 62. The method of claim 60 or 61, wherein: in the acquiring step, said data includes an unsaturated myristoyl carnitine concentration (C14:1); and in the comparing step, said C14:1 is compared with a C14:1 flag threshold. 63. The method of any one of claims 60 to 62, wherein: in the acquiring step, said data includes a molar ratio of myristoyl carnitine and palmitoyl camitine (014:1/C16); and in the comparing step, said C14:1/C16 is compared with a C14:11C16 flag threshold. 64. The method of any one of claims 60 to 63, wherein: in the acquiring step, said data includes values comprised of a saturated myristoyl camitine concentration (C14) and a molar ratio of myristoyl carnitine and palmitoyl carnitine (C14:1/C16); and in the comparing step, said C14 and C14:1/C16 are compared with a C14 flag threshold and a C14:1/C16 flag threshold, respectively. The method of any one of claims 60 to 64, wherein: 629391-ie COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:06 SPRUSON FERGUSON 92615486 NO. 4107 P. 40/46 28 Sin the acquiring step, said data includes values comprised of an unsaturated myristoyl carnitine concentration (C14:1) and a molar ratio of myristoyl camitine and palmitoyl carnitine (C14:1/C16); and 0" in the comparing step, said C14:1 and C14:1/C16 are compared with a C14:1 flag threshold s and a C14:1/C16 flag threshold, respectively, 66. The method of any one of claims 60 to 65, wherein: 1- in the acquiring step, said data includes values comprised of a saturated myristoyl camitine O concentration (014), an unsaturated myristoyl carnitine concentration (014:1) and a molar ratio of Smyristoyl carnitine and palmitoyl carnitine (014:1/C16); and S0o in the comparing step, said C14, C14:1, and C14:1/C16 are compared with a C14 flag 0 threshold, a C14;1 flag threshold, and a C14:1/C16 flag threshold, respectively. 67. The method of any one of claims 60 to 66 further comprising: flagging the sample for re-analysis provided any of the following occur: i, said C14 is greater than said C14 flag threshold; ii. said C14:1 is greater than said C14:1 flag threshold; or iii. said C14 is greater than about 0.75 pM or said C14:1 is greater than about 0.65 pM and said C14:1/C16 is greater than about 0.24. 68. The method of any one of claims 60 to 66 further comprising: flagging the sample for re-analysis provided any of the following occur. i. said C14 is greater than about 2.0 pM ii. said C14:1 is greater than about 1.5 pM; or iii. said C14 is greater than about 1.5 pM and said C14;1 is greater than about 1.0 pM and said C14:1/C16 is greater than about 0.3. 69. The method of claim 67 or 68 further comprising: performing a re-analysis of said sample or a new sample from the same patient to obtain mean values. The method of claim 69 further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said mean values, 71. The method of any one of claims 60 to 70, wherein said C14 flag threshold, said C14:1 flag threshold, and said C14:1/C16 flag threshold are, respectively, at least about 0.45 pM, 0.28 pM, and 0.11. 72. The method of any one of claims 60 to 70, wherein said C14 flag threshold, said C14:1 flag threshold, and said C14:1/016 flag threshold are, respectively, at least about 0.56 pM, 0.38 pM, and 0.17. 6M 9t-hjS COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-20P7 15:06 SPRUSON FERGUSON 92615486 M .416 7 P 41/146 29 0 73. The method of any one of claims 60 to 70, wherein said C14 flag threshold, said C14:1 N flag threshold, and said C14:10C16 flag threshold are, respectively, about 0.85 pM, 0.70 pM, and 0.24. 74. The method of any one of claims 60 to 73 wherein the sample was derived from a dry 0 s blood spot on filter paper. The method of claim 74 wherein the sample was derivatized. 76. The method of any one of claims 60 to 75, wherein: O in the acquiring step, said data was acquired using a tandem mass spectrometer, N 77. A method comprising steps of: O 1o acquiring mass spectral data from a sample that has been derived from the blood of a 0patient, wherein said data includes values comprised of one or more of a hydroxyisovalerylcamitine concentration (C50H) and a tiglylcarnitine concentration (C5:1); comparing said values, respectively, with one or more of a C50H flag threshold and a C5:1 flag threshold; is identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and interpreting said sample as being normal for crotonyl co-A carboxylase deficiency, provided there is no said elevation of any of said values. 78. The method of claim 77, wherein: in the acquiring step, said data includes a hydroxyisovalerylcamitine concentration and in the comparing step, said C50H is compared with a C50H flag threshold. 79. The method of claim 77 or 78, wherein: in the acquiring step, said data includes a tiglylcarnitine concentration and in the comparing step, said C5:1 is compared with a C5:1 flag threshold. The method of any one of claims 77 to 79 further comprising: flagging the sample for re-analysis provided any of the following occur i. said C50H is greater than or equal to said C50H flag threshold; or ii. said C5:1 is greater than or equal to said C5:1 flag threshold. 81. The method of any one of claims 77 to 79 further comprising: flagging the sample for re-analysis provided any of the following occur: i. said C50H is greater than about 3.0 pM; or ii. said C5:1 is greater than about 1.0 pM. 82. The method of claim 80 or 81 further comprising: 629391.1ws COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:06 SPRUSON FERGUSON 92615486 NO, 4107 P. 42/146 0 O performing a re-analysis of said sample or a new sample from the same patient to obtain mean values. t 83, The method of claim 82 further comprising: a initiating a follow-up protocol based on follow-up criteria utilizing said mean values, 84. The method of any one of claims 77 to 83, wherein said C50H flag threshold and said C5:1 flag threshold are, respectively, at least about 0.42 pM and 0.09 pM. 85, The method of any one of claims 77 to 83, wherein said C50H flag threshold and said o C5:1 flag threshold are, respectively, at least about 0.57 pM and 0.13 pM. 0 86. The method of any one of claims 77 to 83, wherein said C50H flag threshold and said o io C5:1 flag threshold are, respectively, about 0.85 pM and 0.35 pM. O 87. The method of any one of claims 77 to 86, wherein the sample was derived from a dry blood spot on filter paper 88. The method of claim 87 wherein the sample was derivatized. 89. The method of any one of claims 77 to 88, wherein: in the acquiring step, said data was acquired using a tandem mass spectrometer. A method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of an isovaleryl camitine concentration and optionally a propionyl camitine concentration (C3); comparing said C5 to a C5 flag threshold; identifying whether or not there is an elevation of C5 above said C5 flag threshold; and interpreting said sample as being normal for said isovaleryl carnitine, provided there is no said elevation of said C5; wherein: said C5 flag threshold is at least about 0,38 pM 91. A method comprising steps of: acquiring mass spectral data from a sample that has been derived from the blood of a patient, wherein said data includes values comprised of an isovaleryl camitine concentration and optionally a propionyl carnitine concentration (C3); comparing said C5 to a C5 flag threshold; identifying whether or not there is an elevation of C5 above said C5 flag threshold; interpreting said sample as being normal for said isovaleryl camitine, provided there is no said elevation of said C5; and flagging the sample for re-analysis provided any of the following occur: i. said C5 is greater than about 2.0 pM; or ii. said C5 is greater than about 1.0 pM and said C3 is greater than about 2.5 pM. 629301-lljig COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:07 SPRUSON FERGUSON 92615486 NO. 16 P. 4 3/4 6 31 0 O 92. The method of claim 90 further comprising: Sflagging the sample for re-analysis provided said C5 is greater than or equal to said C5 flag threshold. 93. The method of claim 90 further comprising: flagging the sample for re-analysis provided any of the following occur: i. said C5 is greater than about 2.0 pM; or ii. said C5 is greater than about 1.0 pM and said C3 is greater than about 2,5 pM. S94. The method of any one of claims 91 to 93 further comprising: C0 performing a re-analysis of said sample or a new sample from the same patient to obtain a O 10o mean value of said 0 95. The method of claim 94 further comprising: initializing a follow-up protocol based on follow-up criteria utilizing said mean value. 96, The method of any one of claims 90 to 95, wherein said C5 flag threshold is at least about 0.51 pM. 97. The method of any one of claims 90 to 95, wherein said C5 flag threshold is about 0.8 pM. 98. The method of any one of claims 90 to 97, wherein the sample was derived from a dry blood spot on filter paper. 99. The method of claim 98, wherein the sample was derivatzed. 100. The method of any one of claims 90 to 99 wherein: in the acquiring step, said data was acquired using a tandem mass spectrometer. 101, A method comprising steps of: acquiring mass spectral data from a sample derived from a dry blood spot on filter paper, wherein said data includes values comprised of a citrulline concentration (cit) and optionally a citrulline concentration after an mrm scan (cit[mrm]); comparing said values, respectively, with a cit flag threshold and optionally a cit[mrm] flag threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; and so interpreting said sample as being normal for citrullinemia, provided there is no said elevation of any of said values; wherein: said cit flag threshold and said cit (mrm) flag threshold are both at least about 19 pM. 102. A method comprising steps of: C.trL4i- COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-2007 15:07 SPRUSON FERGUSON 92615486 NO. 416) P. 44 '46 32 0 0 acquiring mass spectral data from a sample derived from a dry blood spot on filter paper, Swherein said data includes values comprised of a citrulline concentration (cit) and optionally a citrulline concentration after an mrm scan (cit[mrml); Scomparing said values, respectively, with a cit flag threshold and optionally a cit[mrm] flag s threshold; O identifying whether or not there is an elevation of any of said values above any of said flag thresholds; Sinterpreting said sample as being normal for citrullinemia, provided there is no said elevation Ci of any of said values; and Va 0 to flagging the sample for re-analysis provided any of the following occur: O i. said cit is greater than said cit flag threshold; or ii, said cit(mrm) is greater than said cit(mrm) flag threshold. 103. The method of claim 101 or 102, wherein: in the acquiring step, said data includes values comprised of a citrulline concentration (cit) and a citrulline concentration after an mrm scan (cit[mrm]); and in the comparing step, said cit and cit[mrm] are compared with a cit flag threshold and a cit[mrm] flag threshold, respectively. 104. The method of any one of claims 101 or 103 further comprising: flagging the sample for re-analysis provided said cit is greater than about 100 PM. 105. The method of claim 102 or 104 further comprising: performing a re-analysis of said sample or a new sample from the same patient to obtain mean values. 106. The method of claim 105further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said mean values. 107. The method of any one of claims 101 to 106, wherein said cit flag threshold and said cit(mrm) flag threshold are both at least about 19 pM. 108. The method of any one of claims 101 to 106, wherein said cit flag threshold and said cit(mrm) flag threshold are both at least about 26 pM, 109. The method of any one of claims 101 to 106, wherein said cit flag threshold and said cit(mrm) flag threshold are both about 55 pM. 110. The method of any one of claims 101 to 109, wherein the sample was derivatized. 111. The method of any one of claims 101 to 110, wherein: in the acquiring step, said data was acquired using a tandem mass spectrometer. 112. A method comprising steps of: s93I-Ihja COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9-JAN-207 15:07 SPRUSCN FERGUSON 92615486 NO. 4107 P 45/46 33 0 0 acquiring mass spectral data from a sample that has been derived from the blood of a Spatient, wherein said data includes values comprised of a methionine concentration(met) and optionally a molar ratio of methionine and phenylalanine (met/phe): 0" comparing said values, respectively, with a met flag threshold and optionally a met/phe flag 0 s threshold; identifying whether or not there is an elevation of any of said values above any of said flag thresholds; O interpreting said sample as being normal for hypermethionemia, provided there is no said C elevation of any of said values; and o 10 flagging the sample for re-analysis provided any of the following occur: Si. said met is greater than said met flag threshold; or ii. said met is greater than about 50 pM and said met/phe is greater than said met/phe flag threshold, 113. The method of claim 112, wherein: in the acquiring step, said data includes values comprised of a methionine concentration (met) and a molar ratio of methionine and phenylalanine (met/phe); and in the comparing step, said met and met/phe are compared with a met flag threshold and a met/phe flag threshold, respectively. 114. The method of any one of claims 112 or 113 further comprising: flagging the sample for re-analysis provided any of the following occur; i. said met is greater than about 150 pM; or ii said met is greater than about 125 pM and said met/phe is greater than about 1.25. 115. The method of any one of claims 112 to 114 further comprising: performing a re-analysis of said sample or a new sample from the same patient to obtain mean values. 116, The method of claim 115 further comprising: initiating a follow-up protocol based on follow-up criteria utilizing said mean values. 117. The method of any one of claims 112 to 116, wherein said met flag threshold and said met/phe flag threshold are, respectively at least about 31 pM and 0.54. 118. The method of any one of claims 112 to 116, wherein said met flag threshold and said met/phe flag threshold are, respectively at least about 41 pM and 0,69. 119. The method of any one of claims 112 to 116, wherein said met flag threshold and said met/phe flag threshold are, respectively, about 60 pM and 120. The method of any one of claims 112 to 119, wherein the sample was derived from a 3s dry blood spot on filter paper, 629i91-lhjg COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09 9. JAN. 2007 15:08 SPRUSON FERGUSON 92615486 NO, 4167 P. 46/46 34 0 S121. The method of claim 120, wherein the sample was derivatized, 122. The method of any one of claims 112 to 121, wherein: in the acquiring step, said data was acquired using a tandem mass spectrometer. 0> 123. The method of any one of claims 1, 17, 31, 33, 34, 45, 60, 77, 84, 90, 91, 101 or 112, 0 s substantially as hereinbefore described with reference to any one of the accompanying drawings. Dated 9 January, 2007 0 Neo Gen Screening, Inc. 0 O No Patent Attorneys for the Applicant/Nominated Person SSPRUSON FERGUSON COMS ID No: SBMI-05854612 Received by IP Australia: Time 15:07 Date 2007-01-09