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1
Department of Clinical Biology, Division of Pharmacology, University of Bergen, N-5021 Haukeland Hospital, Norway.
2
Department of Pediatrics, University Hospital
Nijmegen, 6500 HB Nijmegen, The Netherlands.
a Author for correspondence. Fax +47-55-974605; e-mail arve.ulvik{at}ikb.uib.no
| Abstract |
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Key Words: indexing terms: restriction enzyme analysis genotyping homocysteine hyperhomocysteinemia risk factors premature atherosclerosis cardiovascular disease heritable disorders folate deficiency
| Introduction |
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Determination of the MTHFR genotype will probably become valuable for assessment of cardiovascular risk in large populations. Its effects will be investigated in future epidemiological studies of total homocysteine and cardiovascular disease, including prospective studies based on stored serum/plasma samples. Determination of genotype in large populations or in routine laboratories demands high assay throughput, and genotyping in residual blood cells in plasma/serum requires extensive amplification or sensitive detection systems.
The C677T mutation in MTHFR creates a HinfI restriction site that is detected by digestion of a polymerase chain reaction (PCR)-amplified fragment analyzed by conventional agarose gel electrophoresis (3). Electrophoretic separation of DNA fragments by dynamic sieving in coated capillaries filled with entangled polymers (e.g., linear polyacrylamide or cellulose derivatives) has recently become an attractive alternative, characterized by short analysis time, automation, high resolution, and unsurpassed separation efficiency (8). High sensitivity of detection can be obtained by staining the DNA with fluorescent dyes or fluorescent intercalators present in the sieving medium, combined with laser-induced fluorescence (LIF) detection (8). We have recently demonstrated the applicability of the novel monomeric dyes, SYBR Green I, YO-PRO-1, and Thiazole Orange, for the analysis of DNA fragments by capillary electrophoresis (CE) and LIF detection (CE-LIF) (9).
Here, we demonstrate a method for analyzing the C677T mutation in the MTHFR gene, in which the technique based on PCR amplification and HinfI restriction cleavage (3) has been modified and adapted to a CE-LIF format. The modifications include addition of a truncated fragment, which serves as a digestion control and time marker, and use of a nested PCR protocol, required when plasma or serum samples are the sources of DNA. Because commercial CE systems usually are equipped with a single capillary, we devised a multiple-injection mode that allows simultaneous separation of as many as eight samples, thereby increasing the sample throughput of the assay.
| Materials and Methods |
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The microtiter plate filtration unit MADV N65 was from Millipore (Bedford, MA). Hydroxypropylmethylcellulose (4000 cP at 25 °C, 20 g/L aqueous solution) and other chemicals (analytical- or molecular biology-grade) were obtained from E. Merck (Darmstadt, Germany) and Sigma Chemical Co. (St. Louis, MO). Solutions containing hydroxypropylmethylcellulose were prepared as described elsewhere (10). Water, doubly distilled and purified with a MilliQ Plus Water Purification System (Millipore), was used to prepare all aqueous solutions.
ce instrumentation
CE was performed on a Prince CE system from Prince Technologies
(Emmen, The Netherlands), equipped with an in-house-built LIF detector.
Laser excitation was at 488 nm (produced with a 20-mW argon laser from
Uniphase, Herts, UK), and the light was focused 30 µm below the end
of the capillary that was placed in a rectangular sheath-flow cuvette.
A sheath flow of electrophoresis buffer (without entangled polymer) was
delivered at a rate of 30 µL/h. The emitted light was collected
through a 535-nm band-pass filter (no. 535DF35; Omega Optical,
Brattleboro, VT).
We used a 50 µm (i.d.)/192 µm (o.d.) silica capillary (Polymicro Technologies, Phoenix, AZ) coated according to Hjertén (11). Total capillary length, and the distance between the column inlet and detector window, was 42 cm.
Caesar software (Version 4.1) from Prince Technologies was used for data collection and processing. Electropherograms used to prepare the illustrations were transferred as text files to an Apple Macintosh computer and redrawn by Sigma Plot (Version 5.0; Jandel Scientific, Erkrath, Germany).
dna extraction
Three different methods for DNA extraction were used, involving
magnetic particles, filtration, or adsorption to silica.
Magnetic particle method.
DNA was extracted
from whole blood by using the DNA Direct kit and following the
instructions provided by the manufacturer. Briefly, 5 µL of
whole-blood sample was mixed with 200 µL of magnetic particles
suspended in a buffer; this lysed the blood cells and allowed the DNA
to adhere to the magnetic particles. The particles were washed twice
and thereafter resuspended in 40 µL of Tris-EDTA buffer (10 mmol/L
Tris-HCl, 1 mmol/L EDTA, pH 8.0); 5 µL of the particle suspension was
used for PCR.
Filtration.
Serum or plasma samples (100 µL) were
loaded on a microtiter plate filtration unit (MADV N65), and cell
debris was trapped on the filters by centrifugation at 500g
for 5 min. DNA was released from the filters by adding 40 µL of
ion-exchange purified water and heating at 95 °C for 2 min. We used
15 µL of the crude DNA preparation for the first PCR reaction in the
seminested protocol.
Adsorption to silica.
Serum or plasma samples were
purified with the QIAamp Blood Kit, according to the instructions of
the manufacturer. Briefly, 200 µL of plasma was treated with a lysis
buffer containing proteinase K. Isopropanol was added to the solution,
and the mixture was applied to a column containing an integrated silica
membrane and centrifuged. The DNA adhered to the membrane, and
impurities were removed by a washing step. Captured DNA was eluted in
50 µL of 10 mmol/L Tris buffer, pH 9.0, and 15 µL of the effluent
was used for PCR.
pcr
The PCR reaction mixture contained 10 mmol/L Tris-HCl (pH 9.0), 50
mmol/L KCl, 1.5 mmol/L MgCl2, 0.1 g/L gelatin, 1 mL/L
Triton X-100, 125 µmol/L of each dNTP, 0.2 µmol/L of each primer,
0.2 U of Taq polymerase, and template DNA in a total volume of 100
µL. A Perkin-Elmer 480 thermocycler was used for a two-step
thermocycling profile: denaturation at 94 °C for 15 s and
annealing at 55 °C for 30 s, the temperature cycles being
preceded by 2 min at 94 °C and concluded with 5 min at 72 °C.
A seminested protocol and a single-step protocol were constructed. The seminested protocol included the OF and R primers in the first reaction of 25 cycles; 1 µL of the first reaction was then transferred to the second reaction, which consisted of 40 cycles with the F and R primers. The single-step protocol was identical to the second reaction of the seminested protocol, except the template was 5 µL of purified DNA.
restriction enzyme cleavage
The C677T substitution creates a HinfI recognition
sequence. A solution containing HinfI, reaction buffer, and
a 183-bp control fragment was pipetted in 15-µL aliquots, and 10 µL
of PCR product was added. The final mixture contained 2 U of
HinfI in 1x Gibco buffer II (50 mmol/L Tris-HCl, pH 8.0, 10
mmol/L MgCl2, and 50 mmol/L NaCl) and a 2:5 dilution of the
PCR reaction buffer (see preceding section) in a total volume of 25
µL. Incubation was at 37 °C for 90 min.
capillary electrophoresis
Electrophoresis buffer was 89 mmol/L Tris-borate, pH 8.3,
containing 1 mmol/L EDTA. Separation buffer was electrophoresis buffer
containing 6 g/L hydroxypropylmethylcellulose as sieving matrix.
The separation buffer was passed through the Acrodisc filters before
use. SYBR Green I (1:20 000 final dilution of stock solution) was
added to the separation buffer after filtration (to avoid adsorption of
dye to the filter matrix).
Before each series of injections, the capillary was flushed with the electrophoresis buffer for 30 s and then filled with separation buffer by applying a pressure of 200 kPa for 150 s. Samples were diluted 1:50 in distilled water and injected electrokinetically. Separation field strength was between 500 and 700 V/cm, and temperature was set at 20 °C.
| Results and Discussion |
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single-injection analysis
DNA samples were PCR-amplified, digested with HinfI
after addition of the control fragment, and then subjected to CE-LIF. A
sample from a heterozygous subject showed four major peaks: the
primers, the digested control fragment, the fragment of the mutated
allele (T), and the fragment of the normal allele (C) (Fig. 2
).
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The control fragment (f) provided a reference for the migration of C
and T, and the combinations of fT, fC, or fTC peaks formed
characteristic patterns for each of the three possible genotypes (TT,
CC, and CT, respectively). The digestion control was built into the
pattern recognition design, in that an incomplete cleavage was revealed
by the appearance of the intact control fragment at a position between
the mutated (T) and the normal (C) fragment. Remnants of uncleaved
control fragment are indicated with arrows in Fig. 3
. A further function of the control fragment was to
differentiate between a failed PCR amplification (only control fragment
was detected after amplification) and inadequate sample injection (no
fragments were detected).
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multiple-injection analysis
When adapting the single-injection analysis to a
multiple-injection mode, the essential requirements were (a)
to avoid coelution of primers from one sample with the digested PCR
fragments from another sample, and (b) to avoid injection
during the time interval when the PCR fragments pass the detector. The
analytical parameters used for designing an optimized injection
protocol that would meet these requirements are defined in Fig. 2
: the
analysis window Wa; the time interval W, which spans
Wa and the primers; and
tf, the time at which the control
fragment elutes at the detector.
The injections were performed with alternating time intervals
s (small interval) and
L (long
interval). Two injections separated by
s defined a
group.
s had to be >Wa to avoid overlap
between analysis windows, and maximal separation was obtained when
s = W/2. Thus, an optimal
s (balancing
analysis throughput and separation) would be within the interval
Wa <
s < W/2.
To fulfill the second requirement above (b), g groups
were distributed in the capillary (by means of varying
L) so that elution of a group at the detector was
followed by injection of a group at the capillary inlet, and vice
versa. This put some limitations on
L, which were
determined by Wa, tf,
s, and g as shown by the expression:
![]() | (1) |
L had to be larger than one group, that is
L >
s + Wa. To avoid
coelution between PCR fragments and primers (requirement a),
a stronger restriction was
L > W. By substituting W for
L in expression 1, we obtained the following expression
for gmax: gmax < (tf +
W)/(
s + W).
Using the values of tf, W, and Wa
from Fig. 2
, we determined a gmax of 4 (i.e., 4 x 2
samples migrating simultaneously). Fig. 4
depicts schematically the distribution of eight injections
(g = 4) in the capillary at the boundary conditions for
L (A and B). Expression 1 and the expression for
gmax can be derived from this Fig. 4
.
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Reduction of g from its maximal value increases the separation between
the peaks of successive injections, thereby allowing for some
variability in system performance that affects parameters
Wa, W, and tf. Thus, we
routinely used g = 3 for calculating the appropriate
L. Fig. 3
shows the last six injections in a run with 10
injections (g = 3). Mean analysis time was 1.5 min per sample.
The above discussion is based on grouping two injections together,
separated by a single
s. Conceivably, each group
could comprise more than two injections. The grouping of the injections
depends on the analytical parameters (e.g., Wa, W, and
tf), the relative values of which can be
modified by changing the position of the PCR primers that determine the
sizes of the analysis products and control fragment(s). In practice,
the difference between the cut and uncut fragments should be as small
as possible. This would decrease Wa and make the small part
of the cut fragment elute close to the primers, which would allow
several injections to be grouped within the time period W. The
parameters also reflect the resolution properties of the system, which
in turn are related to type and concentration of the sieving matrix and
fluorescent dye, temperature, and field strength (8).
durability of the separation matrix
One multiple-injection run was usually programmed to have 10 or 20
injections, but as many as 30 injections could be performed without
replacing the separation matrix. There were minor changes in plate
number and resolution during the course of 1020 multiple injections,
but a progressive decrease in W was observed (i.e., the primers eluted
closer to the PCR fragments).
With low concentration of SYBR Green I (dilution 1:100 000) in the sieving medium, we observed a decrease in resolution and migration time after the separation of several samples with high DNA content. Based on previous observations (9), this can probably be explained by extraction of dye by the DNA. The electrophoretic performance was stabilized by increasing the SYBR Green I concentration to dilution 1:20 000 in the present protocol.
dna purification, amplification, and validation of ce-lif assay
The CE-LIF assay described here was developed to analyze the MTHFR
C677T mutation in the clinical setting but also to genotype large
populations as part of prospective studies based on stored samples. In
the routine laboratory, DNA is obtained from whole blood, whereas
stored sample collections often contain only serum or plasma.
We used the DNA Direct Kit for extraction of DNA from whole blood. This method is based on capture of the DNA in lysed blood onto magnetic beads. The extraction is carried out manually, but we are currently automating it, using the BioMek 2000 robot from Beckman Instruments (Fullerton, CA). Using this technique in combination with single-step PCR, we could determine the genotype of ~100% of the whole-blood samples. For plasma/serum samples, however, this DNA extraction procedure was inadequate. Moreover, combining this extraction approach with the seminested PCR technique described in Materials and Methods correctly identified the genotype of <10% of the serum/plasma samples.
Methods for the extraction of DNA from serum (12)(13) and plasma (13) have been reported before. In the present work, we established and demonstrated the applicability of two alternative methods. Collecting cell debris by filtration in a multiwell unit in combination with the seminested PCR protocol was successful with serum samples (29 of 30 were genotyped) but not with plasmas (5 of 30 were genotyped).
The silica adsorption method (QIAamp) was used to extract DNA remaining
in 30 plasma samples that had been stored at -20 °C for 20 years.
Fig. 5
shows the genotypes and the relative amounts of PCR products.
Signals from 15 of the 30 samples could be detected by CE-LIF after the
single-step PCR protocol (Fig. 5A
), whereas 29 of 30 were positive
after PCR amplification with the seminested protocol (Fig. 5B
). We also
compared the sensitivity of CE-LIF (Fig. 5B
) and a conventional agarose
gel stained with ethidium bromide (Fig. 5C
) for determining the
genotypes of the samples amplified by seminested PCR. Some (57)
of the samples genotyped by CE-LIF could not be determined by
conventional agarose gel electrophoresis.
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The versatility of the CE-LIF method is demonstrated by reliable
genotyping based on highly variable amounts of PCR products. In the
experiments depicted in Fig. 5
, the ratio of the largest to the
smallest amount was 117.
In conclusion, this work demonstrates a high-throughput method for analyzing the MTHFR C677T mutation based on CE-LIF. The method can be used with either rich sources of DNA (e.g., whole blood) or, coupled with a seminested PCR protocol, poor sources of DNA (e.g., serum or plasma). The built-in control features of the method make the genotyping reliable and robust. The principles of multiple injection and digestion control by inclusion of a control fragment should be widely applicable to mutation analyses based on restriction enzyme cleavage.
| Acknowledgments |
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| Footnotes |
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| References |
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The following articles in journals at HighWire Press have cited this article:
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R. Meleady, P. M Ueland, H. Blom, A. S Whitehead, H. Refsum, L. E Daly, S. E. Vollset, C. Donohue, B. Giesendorf, I. M Graham, et al. Thermolabile methylenetetrahydrofolate reductase, homocysteine, and cardiovascular disease risk: the European Concerted Action Project Am. J. Clinical Nutrition, January 1, 2003; 77(1): 63 - 70. [Abstract] [Full Text] [PDF] |
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H. Refsum, C. S Yajnik, M. Gadkari, J. Schneede, S. E Vollset, L. Orning, A. B Guttormsen, A. Joglekar, M. G Sayyad, A. Ulvik, et al. Hyperhomocysteinemia and elevated methylmalonic acid indicate a high prevalence of cobalamin deficiency in Asian Indians Am. J. Clinical Nutrition, August 1, 2001; 74(2): 233 - 241. [Abstract] [Full Text] [PDF] |
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A. Ulvik, J. Ren, H. Refsum, and P. M. Ueland Simultaneous determination of methylenetetrahydrofolate reductase C677T and factor V G1691A genotypes by mutagenically separated PCR and multiple-injection capillary electrophoresis Clin. Chem., February 1, 1998; 44(2): 264 - 269. [Abstract] [Full Text] [PDF] |
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R. Clarke, P. Woodhouse, A. Ulvik, C. Frost, P. Sherliker, H. Refsum, P. M. Ueland, and K.-T. Khaw Variability and determinants of total homocysteine concentrations in plasma in an elderly population Clin. Chem., January 1, 1998; 44(1): 102 - 107. [Abstract] [Full Text] [PDF] |
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