1. A method comprising:
bringing a fluid into contact with the surface of a surface acoustic wave sensor;
propagating input waves through the surface acoustic wave sensor to produce transmitted waves;
determining a phase frequency response of the transmitted waves; identifying a segment of phase frequency response by determining first and second phase inflection frequencies, at +180 and \u2212180 degree phase points, proximate to a running frequency associated with the surface acoustic wave sensor;
estimating a time delay associated with wave propagation through the surface acoustic wave sensor based on the identified segment of phase frequency response;
identifying a material in the fluid as a function of an estimated propagation velocity, the estimated propagation velocity being estimated based on the estimated time delay.
2. The method of claim 1, wherein the surface acoustic wave sensor comprises a Love mode shear-horizontal surface acoustic wave sensor.
3. The method of claim 1, wherein determining phase inflection frequencies comprises:
sampling a plurality of phase responses at frequencies proximate to the running frequency and initially estimating phase inflection frequencies as a function of the plurality of phase responses at frequencies proximate to the running frequency;
sampling a plurality of phase responses at frequencies proximate to the initially estimated phase inflection frequencies; and
more accurately estimating the phase inflection frequencies as a function of the plurality of phase responses at frequencies proximate to the initially estimated phase inflection frequencies.
4. The method of claim 1, wherein the first and second phase inflection frequencies define edges of a monotonically changing subset of a graph of phase versus frequency of the surface acoustic wave sensor.
5. The method of claim 1 further comprising:
estimating the time delay associated with wave propagation through the surface acoustic wave sensor based on the identified segment of phase frequency response according to approximately the following equation:
\u03c4
^
\u2061
(
f
0
)
=
f
1
f
0
\u2062
1
f
2
–
f
1
–
1
360
\u2062
\u03d5
\u2061
(
f
0
)
f
0
+
0.5
f
0
where {circumflex over (\u03c4)}(f0) is the time delay at frequency f0, f0 is the running frequency, f1 is the first phase inflection frequency, f2, is the second phase inflection frequency, and \u03c6(f0) is a measured phase response of the surface acoustic wave sensor at frequency f0.
6. The method of claim 1, further comprising estimating the time delay according to approximately the following equation:
\u03c4
^
\u2061
(
f
0
)
=
–
1
360
\u2062
f
*
f
0
\u2062
\u03d5
.
\u2061
(
f
*
)
–
1
360
\u2062
1
f
0
\u2062
\u03d5
\u2061
(
f
0
)
+
1
360
\u2062
1
f
0
\u2062
\u03d5
\u2061
(
f
*
)
where {circumflex over (\u03c4)}(f0) is the time delay, f0 is the running frequency, \u03c6(f0) is a measured phase response of the surface acoustic wave sensor, f* is any frequency between a first phase inflection frequency and a second phase inflection frequency, \u03c6(f*) is a measured phase frequency response at the frequency f*, and {dot over (\u03c6)}(f*) is a first order of derivative of the measured phase response at the frequency f*.
7. The method of claim 1, further comprising estimating the time delay according to approximately the following equation:
\u03c4
^
=
(
f
0
)
=
–
1
360
\u2062
\u03d5
.
\u2061
(
f
0
)
where {circumflex over (\u03c4)}(f0) is the time delay, and {dot over (\u03c6)}(f0) is a first order of derivative of a measured phase response at a frequency f0.
8. The method of claim 1, further comprising estimating the time delay according to approximately the following equation:
\u03c4
^
\u2061
(
f
0
)
=
\u2062
1
f
0
\u2062
f
1
f
2
–
f
1
–
1
360
\u2062
1
f
0
\u2062
\u03d5
\u2061
(
f
0
)
+
\u2062
0.5
f
0
+
1
180
\u2062
1
f
0
\u2062
1
f
2
–
f
1
\u2062
\u222b
f
1
f
2
\u2062
\u03d5
\u2061
(
f
00
)
\u2062
\u2062
\u2146
f
00
where {circumflex over (\u03c4)}(f0) is the time delay, f0 is the running frequency, f1 is the first phase inflection frequency, f2 is the second phase inflection frequency, and \u03c6(f0) is a measured phase response of the surface acoustic wave sensor, integral
\u222b
f
1
f
2
\u2062
\u03d5
\u2062
(
f
00
)
\u2062
\u2062
\u2146
f
00
is equal to integral
\u222b
f
1
f
2
\u2062
\u03d5
\u2061
(
f
)
\u2062
\u2062
\u2146
f
,
where \u03c6(f) is a measured phase response at frequency f and f varies from f1 to f2.
9. The method of claim 1, further comprising estimating the propagation velocity of a surface acoustic wave through the surface acoustic wave sensor from the estimated time delay according to the following equation:
v
^
\u2061
(
f
)
=
L
\u03c4
^
\u2061
(
f
)
,
where {circumflex over (v)}(f) is the estimated propagation velocity of the surface acoustic wave at frequency f, {circumflex over (\u03c4)}(f) is the estimated time delay at the frequency f, and L is a distance between centers of an input inter-digitized transducer (IDT) and an output IDT which are part of the surface acoustic wave sensor.
10. A computer-readable medium comprising instructions that when executed in a processor:
determine phase frequency response of transmitted waves of a surface acoustic wave sensor;
identify a segment of phase frequency response of the surface acoustic wave sensor by determining first and second phase inflection frequencies proximate to a running frequency associated with the surface acoustic wave sensor;
estimate a time delay associated with wave propagation through the surface acoustic wave sensor based on the identified frequency response according to approximately the following equation:
\u03c4
^
\u2061
(
f
0
)
=
f
1
f
0
\u2062
1
f
2
–
f
1
–
1
360
\u2062
\u03d5
\u2061
(
f
0
)
f
0
+
0.5
f
0
where {circumflex over (\u03c4)}(f0) is the time delay at frequency f0, f0 is the running frequency, f1 is the first phase inflection frequency, f2 is the second phase inflection frequency, and \u03c6(f0) is a measured phase response of the surface acoustic wave sensor at the running frequency f0; and
identify a concentration of a material in a fluid as a function of an estimated propagation velocity that is based on the estimated time delay.
11. The computer-readable medium of claim 10, further comprising instructions that when executed determine phase inflection frequencies for a discrete phase frequency response by:
sampling a plurality of phase responses at frequencies proximate to the running frequency and initially estimating phase inflection frequencies as a function of the plurality of phase responses at frequencies proximate to the running frequency; sampling a plurality of phase responses at frequencies proximate to the initially estimated phase inflection frequencies; and
more accurately estimating phase inflection frequencies as a function of the plurality of phase responses at frequencies proximate to the initially estimated phase inflection frequencies.
12. The computer-readable medium of claim 10, wherein the first and second phase inflection frequencies define edges of a monotonically changing subset of a graph of phase versus frequency of the surface acoustic wave sensor.
13. The computer-readable medium of claim 10, further comprising instructions that when executed estimate a propagation velocity of the surface acoustic wave from the estimated time delay according to the following equation:
v
^
\u2061
(
f
)
=
L
\u03c4
^
\u2061
(
f
)
,
where {circumflex over (v)}(f) is the estimated propagation velocity of the surface acoustic wave at frequency f, {circumflex over (\u03c4)}(f) is the estimated time delay at frequency f, and L is a distance between centers of an input inter-digitized transducer IDT and an output IDT which are part of the surface acoustic wave sensor.
14. The computer-readable medium of claim 10, wherein the surface acoustic wave sensor comprises a Love mode shear-horizontal surface acoustic wave sensor.
15. A system comprising:
a surface acoustic wave sensor;
a sensor analyzer to receive output of the surface acoustic wave sensor and determine a phase frequency response from the output; and
a processor to receive input from the sensor analyzer, identify a segment of phase frequency response of the surface acoustic wave sensor by determining first and second phase inflection frequencies proximate to a running frequency associated with the surface acoustic wave sensor, estimate a time delay associated with wave propagation through the surface acoustic wave sensor based on the identified segment of phase frequency response according to approximately the following equation:
\u03c4
^
\u2061
(
f
0
)
=
f
1
f
0
\u2062
1
f
2
–
f
1
–
1
360
\u2062
\u03d5
\u2061
(
f
0
)
f
0
+
0.5
f
0
where {circumflex over (\u03c4)}(f0) is the time delay at frequency f0, f0 is the running frequency, f1 is the first phase inflection frequency, f2 is the second phase inflection frequency, and \u03c6(f0) is a measured phase response of the surface acoustic wave sensor at the running frequency f0, estimate a propagation velocity of the surface acoustic wave based on the estimated time delay, and identify a concentration of a material in a fluid as a function of the estimated propagation velocity.
16. The system of claim 15 wherein the processor determines the phase inflection frequencies by:
sampling a plurality of phase responses at frequencies proximate to the running frequency and initially estimating the phase inflection frequencies as a function of the plurality of phase responses at frequencies proximate to the running frequency;
sampling a plurality of phase responses at frequencies proximate to the initially estimated phase inflection frequencies; and
more accurately estimating the phase inflection frequencies as a function of the plurality of phase responses at frequencies proximate to the initially estimated phase inflection frequencies.
17. The system of claim 15 wherein the first and second phase inflection frequencies define edges of a monotonically changing subset of a graph of phase versus frequency of the surface acoustic wave sensor.
18. The system of claim 15, wherein the processor estimates propagation velocity of the surface acoustic wave based on the estimated time delay according to the following equation:
v
^
\u2061
(
f
)
=
L
\u03c4
^
\u2061
(
f
)
,
where {circumflex over (v)}(f) is an estimated propagation velocity of the surface acoustic wave at a frequency f, {circumflex over (\u03c4)}(f) is the estimated time delay at the frequency f, and L is a distance between centers of an input inter-digitized transducer IDT and an output IDT which are part of the surface acoustic wave sensor.
19. The system of claim 15, wherein the surface acoustic wave sensor comprises a Love mode shear-horizontal surface acoustic wave sensor.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A method for identifying a segregating single point mutation at a genetic locus that modifies an index phenotype in a non-human index inbred strain, the segregating mutation causing an outlying phenotype relative to the index phenotype, the method comprising the steps of:
outcrossing at least one male animal of a non-human founder inbred strain to at least one female animal of a non-human index inbred strain to obtain F1 progeny, the founder inbred strain carrying random point mutations relative to a wild-type animal of the founder inbred strain, the index inbred strain carrying a congenic dominant allele at a locus known to confer the index phenotype and being genetically distinguishable from the founder inbred strain,
identifying one or more F1 individuals displaying an outlying phenotype relative to the index phenotype displayed by the index inbred strain, thereby indicating that at least one F1 individual possesses an index phenotype-modifying mutation;
backcrossing gametes from male F1 progeny to at least one female of the index inbred strain, with or without the index allele, to obtain N2 backcross progeny, wherein at least one of the N2 backcross progeny that carry the dominant allele also exhibit the outlying phenotype; and
verifying that the outlying phenotype is caused by a segregating single point mutation.
2. A method as claimed in claim 1 wherein any of the crosses employ preserved gametes.
3. A method as claimed in claim 1 wherein the segregating mutation is a heterozygous modifier of the index phenotype selected from a group consisting of an enhancing modifier and a suppressing modifier.
4. A method as claimed in claim 1 wherein the dominant allele is a Min allele at an Apc locus in a mouse.
5. A method as claimed in claim 1 wherein the index inbred strain and the founder inbred strain share an isogenic genetic background.
6. A method as claimed in claims further comprising the step of mapping the segregating mutation using a mapping partner strain, the mapping partner strain being produced by the steps of:
treating an animal of the founder strain with a mutagenic agent to induce point mutations in the treated animal,
crossing the treated animal to an animal of the founder strain to produce F1 progeny; and
sib-mating F1 and subsequent generation progeny until detrimental and lethal mutations are eliminated.
7. A method as claimed in claim 5 wherein the method identifies a segregating mutation at a genetic locus that modifies tumor multiplicity in a C57BL6 mouse congenic for the Min allele at the Apc locus, the method comprising the steps of:
outcrossing at least one male C57BL6 mouse carrying random point mutations to a female C57BL6 mouse congenic for the Min allele at the Apc locus to obtain F1 progeny;
identifying one or more F1 individuals displaying an outlying tumor multiplicity phenotype relative to the tumor multiplicity phenotype in a C57BL6 mouse congenic for the Min allele at the Apc locus, thereby indicating that at least one F1 individual possesses a segregating mutation that modifies tumor multiplicity; and
backcrossing gametes from male F1 progeny to at least one female C57BL6 mouse congenic for the Min allele at the Apc locus to obtain N2 backcross progeny, wherein at least one of the N2 backcross progeny carries the Min allele and has a tumor multiplicity that is modified relative to tumor multiplicity in a C57BLJ6 mouse congenic for the Min allele at the Apc locus, the modified tumor multiplicity being characteristic of the segregating mutation thereby identified.
8. A method as claimed in claim 7 the modified tumor multiplicity is evaluated according to a method comprising the steps of:
repeatedly applying for random permutations of mice among N2 backcross subkindreds a likelihood ratio test of the null hypothesis that no multiplicity modifier is segregating to obtain a p-value, wherein a p-value of less than 0.05 indicates a potential carrier of the segregating mutation;
when the p-value is less than 0.05, calculating, for each potential carrier that has offspring with information about tumor multiplicity, a LOD score for presence of the segregating mutation, wherein the LOD score is log10 of a ratio of a first probability of offspring phenotype data if the potential carrier mouse carries a multiplicity modifier to a second probability of offspring phenotype data if the potential carrier mouse does not carry a multiplicity modifier, and wherein the second probabilities are calculated from an estimated background distribution and the first probabilities are calculated from a mixture of the estimated background distribution and an estimated modified distribution, where the estimated distributions are obtained by a maximum likelihood method, and
ranking the LOD scores of potential carriers, whereby animals having the highest LOD scores are likely carriers of the segregating mutation.
9. A method as claimed in claim 7, further comprising the step of mapping the segregating mutation in the N2 backcross progeny using a mapping partner strain having a C57BL6 genetic background.
10. A method as claimed in claim 9 wherein the mapping partner strain is produced by the steps of:
treating a C57BL6 mouse with a mutagen to introduce random point mutations; crossing the treated mouse to a C57BL6 mouse to produce F1 progeny; and sib-mating F1 and subsequent generation progeny until detrimental and lethal mutations are eliminated.
11. A method as claimed in claim 1 wherein the founder inbred mouse strain is produced by a method comprising the step of treating a wild-type inbred mouse with a mutagenic agent to induce point mutations.
12. A method as claimed in claim 11 wherein the mutagenic agent is ethylnitrosourea.
13. A method for identifying a human genetic sequence that corresponds to a segregating mutation at a genetic locus in a non-human animal, the segregating mutation causing an outlying phenotype relative to an index phenotype in an index inbred mouse strain, the method comprising the steps of:
outcrossing a founder inbred non-human strain to an index inbred non-human strain to obtain F1 progeny, the founder inbred strain carrying random point mutations relative to a wild-type animal of the founder inbred strain, the index inbred strain carrying a dominant allele at a locus known to confer the index phenotype and being genetically distinguishable from the founder inbred strain, wherein some of the F1 progeny that carry the dominant allele also carry at least one random mutation;
backcrossing the F1 progeny to the index inbred strain, with or without the index allele, to obtain N2 backcross progeny, wherein at least some of the N2 backcross progeny that carry the dominant allele also exhibit the outlying phenotype;
verifying that the outlying phenotype is caused by a segregating mutation;
identifying genetic markers linked to the segregating mutation;
identifying a gene on a contig that encodes the segregating mutation; and
recovering human genetic sequences that correspond to the mutation-encoding gene.
14. A method for identifying a segregating mutation at a genetic locus that modifies an index phenotype in a non-human index inbred strain, the segregating mutation causing an outlying phenotype relative to the index phenotype, the method comprising the steps of:
crossing a non-human founder inbred strain with a non-human index inbred strain to obtain Gen1 progeny, the founder inbred strain carrying random point mutations relative to a wild-type animal of the founder inbred strain, the index inbred strain carrying a congenic dominant allele at a locus known to confer the index phenotype, the founder strain and the index strain sharing an isogenic genetic background, wherein some of the Gen1 progeny that carry the dominant allele also exhibit a modified index phenotype; and
verifying that Gen1 progeny that carry the dominant allele and exhibit a modified index phenotype carry a segregating mutation.
15. A method as claimed in claim 14 wherein the genetic background has no modifying effect upon the index phenotype.
16. A method as claimed in claim 14 the genetic background has a modifying effect upon the index phenotype.
17. A method as claimed in claim 16 wherein the genetic background has an enhancing effect upon the index phenotype, and wherein the Gen1 animals exhibit a suppressed phenotype relative to the index inbred strain.
18. A method as claimed in claim 4 further comprising the steps of:
mapping the segregating mutation by crossing Gen1 animals that have the dominant allele and a modified index phenotype to a genetically distinguishable inbred strain; and
evaluating the progeny of the mapping cross.
19. A method as claimed an claim 18 wherein the genetically distinguishable inbred strain shares an isogenic genetic background with the founder and index strains and further comprises single nucleotide polymorphisms relative to the founder inbred strain.
20. A method for identifying a segregating mutation at a genetic locus that modifies an index phenotype in a non-human index inbred strain, the segregating mutation causing an outlying phenotype relative to the index phenotype, the method comprising the steps of:
outcrossing a non-human founder inbred strain with the non-human index inbred strain to obtain Gen1F1 progeny, the founder strain being heterozygous only for random point mutations relative to a wild-type animal of the founder inbred strain, the index inbred strain carrying a dominant allele at a locus known to confer the index phenotype, where at least some of the Gen1F1 progeny carry both the dominant allele and at least one random mutation;
crossing a founder animal of the founder inbred strain to an animal of the founder strain that lacks the mutations to obtain Gen2 offspring, where the founder animal has at least one outcrossed F1 progeny that displays the outlying phenotype relative to the index phenotype,
outcrossing Gen2 offspring to the index strain to obtain Gen2F1 backcross progeny, half of which, on average, carry the dominant allele that confers the index phenotype; and
verifying that a subset of the Gen2F1 progeny shows the outlying phenotype.
21. A method for identifying a segregating single point mutation at a genetic locus that modifies an index phenotype in a mouse index inbred strain, the segregating mutation causing an outlying phenotype relative to the index phenotype, the method comprising the steps of:
outcrossing at least one male animal of a mouse founder inbred strain to at least one female animal of a mouse index inbred strain to obtain F1 progeny, the founder inbred strain carrying random point mutations relative to a wild-type animal of the founder inbred strain, the index inbred strain carrying a congenic dominant allele at a locus known to confer the index phenotype and being genetically distinguishable from the founder inbred strain,
identifying one or more F1 individuals displaying an outlying phenotype relative to the index phenotype displayed by the index inbred strain, thereby indicating that at least one F1 individual possesses an index phenotype-modifying mutation;
backcrossing gametes from male F1 progeny to at least one female of the index inbred strain, with or without the index allele, to obtain N2 backcross progeny, wherein at least one of the N2 backcross progeny that carry the dominant allele also exhibit the outlying phenotype, and
verifying that the outlying phenotype is caused by a segregating single point mutation.
22. A method as claimed in claim 21 wherein any of the crosses employ preserved gametes.
23. A method as claimed in claim 21 wherein the dominant allele is a Min allele at an Apc locus in a mouse.
24. A method as claimed in claim 21 wherein the index inbred strain and the founder inbred strain share an isogenic genetic background.
25. A method as claimed in claim 24 further comprising the step of mapping the segregating mutation using a mapping partner strain produced by the steps of:
treating an animal of the founder strain with a mutagenic agent to induce point mutations in the treated animal;
crossing the treated animal to an animal of the founder strain to produce F1 progeny; and
sib-mating F1 and subsequent generation progeny until detrimental and lethal mutations are eliminated.
26. A method as claimed in claim 24 wherein the method identities a segregating mutation at a genetic locus that modifies tumor multiplicity in a C57BL6 mouse congenic for the Min allele at the Apc locus, the method comprising the steps of:
outcrossing at least one male C57BL6 mouse carrying random point mutations to a female C57BL6 mouse congenic for the Min allele at the Apc locus to obtain F1 progeny, wherein at least one of the F1 progeny carries both the Min allele and a random point mutation; and
backcrossing gametes from male F1 progeny to at least one female C57BL6 mouse congenic for the Min allele at the Apc locus to obtain N2 backcross progeny, wherein at least one of the N2 backcross progeny carries the Min allele and has a tumor multiplicity that is modified relative to tumor multiplicity in a C57BL6 mouse congenic for the Min allele at the Ape locus, the modified tumor multiplicity being characteristic of the segregating mutation.
27. A method as claimed in claim 26 wherein the modified tumor multiplicity is evaluated according to a method comprising the steps of:
repeatedly applying for random permutations of mice among N2 backcross subkindreds a likelihood ratio test of the null hypothesis that no multiplicity modifier is segregating to obtain a p-value, wherein a p-value of less than 0.05 indicates a potential carrier of the segregating mutation;
when the p-value is less than 0.05, calculating, for each potential carrier that has offspring with information about tumor multiplicity, a LOD score for presence of the segregating mutation, wherein the LOD score is log10 of a ratio of a first probability of offspring phenotype data if the potential carrier mouse carries a multiplicity modifier to a second probability of offspring phenotype data if the potential carrier mouse does not carry a multiplicity modifier, and wherein the second probabilities are calculated from an estimated background distribution and the first probabilities are calculated from a mixture of the estimated background distribution and an estimated modified distribution, where the estimated distributions are obtained by a maximum likelihood method; and
ranking the LOD scores of the potential carriers, whereby animals having the highest LOD scores are likely carriers of the segregating mutation.
28. A method as claimed in claim 26, further comprising the step of mapping the segregating mutation in the N2 backcross progeny using a mapping partner strain.
29. A method as claimed in claim 28 wherein the mapping partner strain is produced by the steps of:
treating a C57BL6 mouse with a mutagen to introduce random point mutations;
crossing the treated mouse to a C57BL6 mouse to produce F1 progeny; and
sib-mating F1 and subsequent generation progeny until detrimental and lethal mutations are eliminated.
30. A method as claimed in claim 21 wherein the founder inbred mouse strain is produced by a method comprising the step of treating a wild-type inbred mouse with a mutagenic agent to induce point mutations.
31. A method as claimed in claim 30 wherein the mutagenic agent is ethylnitrosourea.