0095-1137/92/040987-06$02.00/0
Copyright ©)1992, AmericanSociety for Microbiology
Comparison of
a
One-Step and
a
Two-Step
Polymerase Chain
Reaction with Degenerate General Primers in
a
Population-Based
Study of Human Papillomavirus Infection in
Young
Swedish
Women
MAGNUS EVANDER,1* KARIN EDLUND,' ELISABETH BODEN,2AKE
GUSTAFSSON,l
MONICAJONSSON,3 ROGER KARLSSON,3 EVA RYLANDER,2ANDGORANWADELL'Departmentsof Virology,1Obstetrics and Gynecology,2andFamily Medicine,3 University of Umeac, S-901 85 Umea, Sweden
Received 15 July 1991/Accepted 26 December 1991
The prevalence ofhuman papillomavirus (HPV) infection in cervical cell scrapesfrom young women was
determined by polymerase chain reaction (PCR) by using generalprimer pairs localized within the Li region. With aone-stepgeneral PCR, 5.9%Yo (35 of 590) ofyoung women in apopulation-based studywerefoundto contain HPV DNA. Theproportion of HPV-positivewomen increased withage, from 1.4% (1 of 69) among
womenaged19yearsto9.2% (13 of 142)among womenaged25years.Among the cervicalscrapesfromwomen
with normal cytology, 5.6% (30 of 539) harbored HPVDNA.A total of 5 of 19 (26.3%) ofthewomen with pathological signswerepositive forHPVDNA.Byatwo-stepPCR, using nested general primers, 20.3% (118 of581)of allwomenwereshowntocontainHPVDNA. The proportion of HPV-positivewomenalso increased
withage,from 17.4% (12 of 69)among womenaged 19yearsto31.9%o(43 of 135)among womenaged25years, when thetwo-step PCRwas used. Some 19.2% (102 of 530) of cervical scrapes from women with normal cytologycontained HPVDNA. Among thewomenwith pathologicalsigns, 16 of19(84.2%)werepositive for HPV DNA. The HPV DNA-positive specimensweredemonstratedtocontain HPVtype6, 11, 16, 18, 31, 33,
35, 39, 40, 45, 55,or56.ThemostprevalentHPVtypeswere6(2.0%o)and 16(2.7%).Morethanonetypewas
found in16 specimens. SixtyHPV-positive samplescould notbe typed. Human papillomaviruses (HPVs) are double-stranded
DNAviruses thatcausevariousproliferative diseases in the infected epithelium (18). Over 60differenttypes have been isolated from human tissue. Different types of HPV are
associated with specific lesions. Several types, HPVtypes 6, 11, 16, 18, 31, 33 to 35, 39, 40, 42 to 45, and51 to 59, infect thegenitaltract (4). HPVtypes16, 18, 31,and 33 are mainlyassociated withmalignantlesions of the cervix(2, 6, 12, 14), while HPVtypes 6 and 11 are generally limited to low-grade lesions which rarely progress to malignancy (3, 14).
In large cancer-screening programs, about 2 to 3% of Papanicolaou (Pap) smears from essentially asymptomatic
womenshow abnormalcytologies (16). Nearlyallsquamous
cell abnormalities in thePap smears (koilocytosis, cervical intraepithelial neoplasiatypeI, higher-grade lesions)appear
to be associated with HPV infections (24). Koutsky et al. (11) have estimated that genital tract HPV infections are prevalent in approximately 10% of the men and women in the 15-to 49-yearage groupin theUnited States and thata majority of these infections are subclinical. They further suggestthat thetrue prevalencemaybesignificantly higher
because of the lowersensitivityofthecommonlyused HPV detection methods(dot blot,Southernblot, and filter in situ hybridization).
During the last few years, studies based on polymerase
chain reaction (PCR) technology have been performed in which type-specific as well as general HPV primers have been used. HPV DNA was demonstrated in 5 to 49% of
cytologically normal women (1, 17, 25-28). HPV DNA
sequences were present in 80 to 100% of patients with
* Correspondingauthor.
cervicalcancersand in 60to90% ofpatientswithhigh-grade cervicalintraepithelial neoplasia.HPVtype16wasthemost
frequently present type, but unknown HPVs have been detectedbyPCR inaportion (maximumof 10to15%)of the
cases(24).
We determined the prevalence of HPV infection in a population-based studyofyoung Swedishwomenbyuseof
ageneral primer-based PCR. We also compared the sensi-tivityofaone-stepgeneral primer-based PCR with that ofa
two-stepgeneral primer-basedPCR.
MATERLALS AND METHODS
Populationandspecimencollection. Allwomenaged 19, 21,
23, and 25 yearswhowere inhabitants ofa primary health
care areainUmea, Sweden, accordingtothepublic record,
were asked to participate in the study during the period September 1989 to September 1990. Among the women
asked to participate, 70 could not be reached. Cervical
scrapesfrom 602womenweretakenbythesameregistered
midwife; 590 of the scrapes were analyzed for presence of HPVDNA. At thesametime,asecond cellsmear wastaken from558 of thewomen forcytologicalevaluation.
Cytology. A total of 558 Pap smears were taken for cytological evaluation. Theywere evaluated at the
Depart-mentofCytology, University HospitalofUmea,and abnor-mal results were categorized according to the Bethesda system.
DNApreparation. Cervical cellswerecollectedby scrap-ingacotton-tippedswaboverthe entire surface of theportio vaginalis. Subsequently,the swabwassuspendedinaplastic
tubewith 1.5 ml of STE(0.1MNaCl, 10mMTris-HCl [pH 8.0], 1 mM EDTA) and centrifuged to pelletthe cells. The
987
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DNAwas
prepared
asdescribedpreviously (8).
Forampli-fication,
20RI
of thesolutionwasuseddirectly.PCR.
Amplification
of HPV DNAwascarriedoutin threeways. First, a consensus primer pair, MY11-MY09, which spans nucleotides 6722 to 7170 in HPV type 6 and the
corresponding regions
of the othergenital
HPVs (15), was used inaone-stepamplification
of the DNAprepared from the cervical scrapes(40 cycles) (Fig.
1 and 2A). Second,another
general primer pair,
GP5-GP6, which spans nucleo-tides 6764 to 6902 in HPV type 6 and thecorresponding
regions
of othergenital
HPVs(23),
was used in combination with theMY11-MY09primer
pairinanestedgeneral primertwo-step
amplification
of the HPV DNA(20 cycles
forMY11-MY09,
30cycles
forGP5-GP6) (Fig.
1and2B). Third,
the GP5-GP6
primer pair
was used ina one-stepamplifica-tion of the HPV DNA
(40 cycles).
Allprimers
weresynthe-sizedon aBeckman DNA SM automated DNA
synthesizer.
For a
typical
one-stepamplification
reaction, 20 ,ul of DNA prepared from cervical cells was mixed with PCR buffer[16.6
mM(NH4)2SO4,
67 mM Tris-HCl (pH 8.8) at25°C,
6.7 mM MgCl2, 10 mM1-mercaptoethanol];
the fourdeoxynucleotides
dATP, dlTP, dCTP, and dGTP at finalconcentrations of 50
puM
each; 12pmolof either theMY11-MY09 or the GP5-GP6
primer pair;
and 2 U of Taq DNApolymerase (Amplitaq;
Cetus, Berkeley, Calif.) to a final volume of 50plI.
This mixturewasoverlaid with 2to3 dropsof mineral oil. Thermal
cycling
of theamplification
mixture(denaturation, annealing,
andextension)
wasperformed
in aprogrammable
heatblock(Techne
PHC-2;TecheLtd.,Cam-bridge,
UnitedKingdom)
for a total of 40cycles.
Denatur-ation wasperformed
at94°C
for 30 s,annealing
was per-formedat45°C
for 30 s, and extensionwasperformedat72°Cfor 30sfor all
amplifications.
For a
typical
two-step amplification, 0.2 pmol of theMY11-MY09
primer pair
wasmixed with thePCRbuffer,
the fourdeoxynucleotides
at a final concentration of 100puM
each,
2U ofTaq
DNApolymerase,
and 20pul
ofthe DNAprepared
from the cervical scrapes. The mixture was over-laid with mineraloil,
andatotalof 20cycles
wasperformed
as described above. A total of 20
pmol
of the GP5-GP6primer pair
wasthenadded, together
with 2 U ofTaqDNApolymerase,
tothe reactionmixture,
and 30 additionalcycles
were
performed.
All clinical
specimens
were alsoamplified
with theP-globin
primers
PCO3 and PCO4(19)
to excludefalse-negative
results.Samples
that werenegative
for3-globin
amplification
were extracted withphenol
andprecipitated
with
ethanol,
andasecond13-globin
PCRwasperformed.All 3-globin-positive samples (590 of 602 samples) wereampli-fied with the HPV
general primers.
All PCRswere
performed
sothat every thirdsample
wasa
negative
control. All such controls werenegative.
Tominimizethe riskofcontamination,strict precautionswere taken
during sample collection, preparation
ofDNA,
and PCR.Detection and hybridization. For
detection,
40% of theamplified
DNA(20
p.l)
wasseparated
on a 2.0% NuSieveGTG
plus
1.0% SeaKemMEagarosegel
(FMC Bioproducts,
Rockland, Maine)
by electrophoresisandstained with ethid-ium bromide. Two32P-end-labeled
internaloligonucleotideprobes,
MY1019andMY18(15),wereused forhybridizationof theMY11-MY09one-step
amplification
productsfrom223 ofthesamples.
For HPV typing, 10% of the amplified DNA (5
p.l)
was boundtoanylon
filterbyslotblotting by usingaMinifold IISlot-Blotter
(Schleicher
& SchuellGmbH, Dassel,
Germa-ny). The entire genomes ofHPVtypes6, 11, 16, 18, 31, 33, 35, 39, 40, 45, 54, 55, 56, and 58 (kindly provided by E.-M. de Villiers, A. Irincz, T. Matsukura, G. Orth, K. Shah, and H. zurHausen) were radioactively labeled and usedas probes for hybridization. The nylon filters were prehybrid-ized andhybridized in a solution containing 5 x SSC (0.75 M NaCl plus 0.075 M sodium citrate), 5x Denhardt solution (0.1% bovine serum albumin, 0.1% Ficoll, 0.1%
polyvi-nylpyrrolidone), 1mMEDTA,0.1%sodium dodecyl sulfate
(SDS), sonicated salmon sperm DNA(100
p,g/ml),
and 50% formamideat 42°C. The filters were then washed at 20°C in 2x SSC-0.1% SDS for 30 min, two times for 15 min each time with 2x SSC-0.1% SDS at65°C, and finally, two times for15 min each time with 0.5x SSC-0.1% SDS at 65°C. The filterswereexposedtoCronex 4 film(DuPont) for 1to3 daysby using intensifyingscreens. RESULTS
Cytology. The cytological evaluation of the cell samples revealed that of 558 cell samples, 539 (96.6%) showed normal cytology and 19 (3.4%) had pathological signs. Of
these, 12 (2.2%) had cytological patterns of condyloma, 3
(0.5%)had patterns of dysplasia, and 4 (0.7%)hadsigns of inflammation.
One-stepPCR withthe outerprimer pair.To determinethe
prevalence of HPV infection in the cell samples, we first usedaone-step PCRprocedure with the MY11-MY09 con-sensusprimers(Fig. 1 and 2A). Among cervical scrapes from womenwith normalcytology, 30 of 539 (5.6%) were shown to contain HPV DNA. Of the women with pathological
signs,5 of 19(26.3%)werepositive for HPV DNA (Table 1). In total, samples from 590 women were tested by the MY11-MY09 one-step PCR. We detected HPV DNA in 35
(5.9%)of the cervical scrapes (Table 2). Theproportion of
HPV-positivewomen increased with age, from 1.4% HPV
positive among the women aged 19 years to 9.2% HPV
positiveamongthewomenaged 25 years(Table 2).The SiHa cell line(which containsone totwocopiesof HPV type16) was usedto determine thesensitivity of the one-step PCR.
BydilutingSiHa cellDNA,whichwaspreparedin thesame wayasthecervical scrapes were,wedetected100copies of
the HPV type 16 genomebyethidium bromidestaining. Two-step PCR. We then assembled a nested PCR with
general primerstobe abletoincrease thesensitivityof HPV DNAdetection(Fig.1and2B).The two-step PCRwasused foranalysisof allsamplesexceptfor ninesamplesthatwere notavailable foranalysis, thatwere negative by the MY11-MY09 one-step PCR.Among cervical scrapes fromwomen with normalcytology, 102 of 530 (19.2%)werepositivefor HPVDNAafterthe two-step PCR.Amongthewomenwith
pathological signs, specimensfrom 16 of 19(84.2%)of them had HPV DNA (Table 1). In addition to the 35 HPV
DNA-positive specimens from the MY11-MY09 one-step
PCR, we detected 83 HPV-containing specimens by the two-step PCR,givingatotal HPVprevalenceof 118 of 581
(20.3%) (Table 3). The proportion ofHPV-positive women increased with age, also when the two-step PCRwasused, from17.4% amongwomenaged 19 yearsto31.9%amongthe women aged 25 years (Table 3). The two-step PCR was showntodetect1 to10copiesof theHPVtype 16 genomeby usingthe SiHa cell lineasdescribed above.
Hybridization. Afteramplification,223 of theMY11-MY09 one-step PCRamplimerswerehybridizedtothe
oligonucle-otideprobesMY1019 andMY18(15).All samplesthatwere
negative after ethidium bromide staining (209 of 223) were
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6722 6764 6904
MYll GP5 GP6
_ -b -04
7170
MY09
El
FIG. 1. Locations of the MY11-MYO9consensusprimers(15)and theGP5-GP6general primers (23)in the Li regionof the HPVgenome.
alsonegative after hybridization. Of the ethidium
bromide-positive samples, 9 of 14were also hybridization positive. Detection by ethidium bromide staining revealed 83 speci-mensthatwere negative bytheMY11-MY09 one-step PCR
A- 1 2
-.142bp
FIG. 2. DNA fromcervicalscrapes wasanalyzedby the
MY11-MY09 one-stepPCR(A) and the two-stepPCR (B). Lanes 1to 6,
DNAfrom cervicalscrapes. +,cloned HPVtype16 DNAamplified
as a positive control; -, negative control containing all PCR
reagents except DNA; m, DNAmolecular mass standard. In the
one-stepPCR,allsamplesweresubjectedto40cyclesof
amplifica-tion withtheMY11-MY09 primer pair (15).Inthetwo-stepPCR, all samples were subjected to 20 cycles of amplification with the
MY11-MY09 primer pair; thiswasfollowedby30cyclesof
ampli-fication with theGP5-GP6primer pair (23).
but that were positive by the two-step PCR. Ofthese, 36 specimens were hybridized to the oligonucleotide probes. None of thesampleswas positiveafterhybridization.
One-step PCR with the inner primer pair. We also
per-formedaone-step PCR with the innerprimer pairGP5-GP6. Weanalyzed 62 of the 83specimensearlier scored asHPV positive by the two-step PCR but HPV negative by the MY11-MY09 one-step PCR. After ethidium bromide stain-ing, 35 specimenswere foundto be HPVpositive. We also analyzed 90HPV-negative specimens bythe two-step PCR with the GP5-GP6primer pair. Allof these specimenswere negative. The number of HPV-positive specimens in the GP5-GP6one-step PCRcorresponds toabout 14% of HPV-positive specimens in the total population. The GP5-GP6 one-step PCR was shown to detect 10 copies of the HPV
type 16 genome by using the SiHa cell line as described
above.
HPVtyping.The HPVtypesweredeterminedbyslot blot hybridizationof the HPV DNA-positive amplification prod-ucts to 14 different genital HPV types. Themost prevalent types were HPV type 6, 12 of590 (2.0%) specimens, and HPVtype 16,16 of 590(2.7%) specimens (Table 4).We also
TABLE 1. PrevalenceofHPVinfection comparedwith cytologicalevaluation ofPapsmearsdetermined
byMY11-MY09one- ortwo-stepPCR'
Cytologyand PCR No.(%)HPV:
method(no.ofpatients) Positive Negative
Normalcytology
One-stepPCR(539) 30(5.6) 509(94.4)
Two-step PCR(530) 102(19.2) 428(80.8) Pathological signsb
One-stepPCR(19) 5(26.3) 14(73.7)
Two-stepPCR(19) 16(84.2) 3(15.8)
aAll the HPV DNA-positive specimens from the MY11-MYO9 one-step
PCRareincludedastwo-stepPCRpositives.
bCytological patterns of condyloma (n = 12), dysplasia (n = 3), or
inflammation(n =4).
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TABLE 2. MY11-MYO9 one-stepamplification for determination
of theprevalence of HPVinfection in comparison withage
Patientage No. (%) HPV:
(yr [no.ofpatients]) Positive Negative
19(69) 1 (1.4) 68(98.6)
21(158) 6(3.8) 152 (96.2)
23(221) 15(6.8) 206(93.2)
25(142) 13(9.2) 129(90.8)
Total(590) 35(5.9) 555(94.1)
detected HPVtypes11, 18, 31, 33, 35, 39, 40, 45, 55, and 56. Sixty HPV-positive samples could not be typed. Infection with more than one typewasfound in 16 specimens (Table 4).
DISCUSSION
Several approaches have been tested to determine the prevalence of HPV in the population. Southern blot, dot blot, and filter in situ hybridization have been used for the detection of HPV DNA in women attending clinics for routine gynecologic screening (5, 13) or large
population-based studies(10). Morerecently, PCR has beenapplied for the demonstration of HPV DNA in clinical specimens. Several selections oftype-specific primers for HPV detec-tionareavailable(7, 17, 21, 30).Primers for thedetection of a broad spectrum of HPV types, consensus or general primers, have been presented (8, 9, 15, 23). Degenerate primers for HPV DNA detection, arranged in a nested fashion, have alsobeen developed (29).
We chose to use the MY11-MY09consensus primer pair (15)for detection of HPVDNA, toallowcomparison ofour
results with thoseof other studies. TheMY11-MY09 primer pair is localized within the Li region of the HPVgenome.
The Li regioncanbe lostatlatestagesofneoplasia (22),but this is hardly relevant in HPV infections in very young women.
By using the MY11-MY09 consensus primer pair in a
one-stepPCRdirectly oncytological scrapesfroma nonse-lected, young female population, we demonstrated HPV
DNA in5.9%ofthewomen.Among thewomenwithnormal cytology, 5.6%were shownto beHPV DNApositive.
To check the sensitivity of the one-stepPCR directlyon cytological scrapes,weassembledatwo-stepPCR. We took advantageof thefact that the GP5-GP6 general primers (23) werepositionedwithin theMY11-MY09 consensusprimers
and used thesetwo primerpairs to setup a two-step PCR with theprimers arranged in a nestedfashion. Anew PCR system should beevaluated inaclinicalsettingbefore itcan
TABLE 3. Two-stepPCR amplification for determination of the prevalenceof HPVinfection incomparisonwithagea
Patientage No. (%)HPV:
(yr [no.ofpatients]) Positive Negative
19(69) 12(17.4) 57(82.6)
21(158) 24(15.2) 134(84.8)
23(218) 39(17.9) 179(82.1)
25(135) 43(31.9) 92(68.1)
Total(581) 118(20.3) 463(79.7)
aAll the HPV DNA-positive specimens from the MY11-MYO9 one-step
PCRareincludedastwo-stepPCRpositives.
TABLE 4. Determination of the HPV type in the HPV-containing specimens by slot blothybridizationa
HPV type No.positive
6... 12
11... 2
16... 16
18... 7
31... 8
33... 8
35... 4
39... 3
40... 4
45... 4
54... 0
55... 1
56... 4
58... 0
Unknown... 60
a Sixteenspecimenswere demonstratedtocontaintwo or moretypes: 4
contained HPVtypes6 and16;twocontainedHPV types 16 and33;andthe
10remaining specimenscontained HPV types 6 and 31, HPV types 6 and 39,
HPVtypes 11 and16,HPV types 16 and18,HPV types 16 and 56, HPVtypes
18and45,HPVtypes31 and33,HPVtypes 33 and 40, HPV types 35 and 56,
andHPVtypes6, 39, and 45, respectively.
be regardedasanapplicable system(20). The nested primer-based PCRwas evaluated on samples from the same non-selectedfemalepopulation thatwereanalyzed by the MY11-MY09 one-step PCR. The total detection rate of HPVDNA increased from 5.9 to20.3%. Among the women with normal cytology, the detection rate of HPV increased from 5.6 to
19.2%.Itwasclear from theMY11-MY09 one-step PCR that HPVprevalence increases withage(Table2). The frequency of HPV-positive women also increased with age in the
samples analyzed bythe two-step PCR(Table 3).
Demonstration by the two-step PCR of 83 HPV-positive specimens thatwerenegative bytheMY11-MY09 one-step PCR may indicate variationsin the HPV copy number in the lesions. The two-step PCR was more sensitive than the one-stepPCR; i.e.,fewercopies of the HPV genome could be detected. Theinnerprimer pair GP5-GP6was also used foramplificationof some of thespecimens,which increased thesensitivityof the one-step PCR. However, the two-step PCRwasthemostsensitivetechnique.TheGP5-GP6primer pairspansaregionof about 140bp compared with450bp for
the MY11-MY09 primer pair. The shorter amplification product may increase the efficiency of the PCR.
Further-more, the GP5-GP6 primersdo notcontain anydegenerate bases, which may result in increased amplification
effi-ciency.
The HPV type 6 genomewas detected in 10 of 35
HPV-positive sampleswhen the MY11-MY09 one-step PCRwas used, but only 2additional HPV type 6-containing cervical scrapeswerefoundbythe two-step PCR(datanotshown).
This could reflect the fact that HPV type 6was present at
high copy numbers in the lesions, while other types may havehad alower genome copy number. It is alsopossible
thatsometypes(unknowntypes)couldnotbeamplifiedtoa detectable level by using ethidiumbromide-stained gels in the one-step PCR. Inthe two-step system, theamplification
products can be visualized on an agarose gel when the second amplification round is performed with the inner
primer pair. Theconditions foramplification can also vary
considerably between different specimens, since the PCR was performed directly on the DNA prepared from cell
scrapings.However, allsamplesthatwereanalyzedwith the
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HPV-specific primers were positive for the
P-globin
geneby a one-stepPCR.HPV types 6and 16 werethe most commonly found HPV types amongthewomenin this study. In total,wedetected 12 different types. We were not able to determine the HPV type amonga largeproportion of the two-step PCR-positive specimens incomparisonwith theproportion we determined amongthe one-step PCR-positive specimens. A higher pro-portion of unknown HPV types was amplified with the nestedprimer-based PCR system, andit is also possible that thetypingwaseasiertoperform on the larger amplimer (450 bp) from the MY11-MY09 one-step PCR.
The increase in the unknown HPV types among the positive specimens after the two-step PCR may indicate nonspecific amplification. However, the ethidium bromide-stained amplification product was always of the predicted size. Furthermore, women with antichlamydial antibodies
displayed a statistically significant higher presence of HPV than other women did (P < 0.001; data not shown). This correlateswith the increase in the number of HPV-positive women with age determined by the two-step PCR. We also analyzed DNA prepared from the HPV-negative cell line A549originating from a human lung carcinoma. No amplifi-cation product of the predicted HPV amplimer size was
detected(datanotshown).Thenatureof theamplimers from theunknown HPV types can beverifiedby sequencing.
By use ofthe two-step general PCR, we determined the HPVprevalencetobe 19.2% among young (age range, 19 to 25 years) Swedish women with normal cytology in a popu-lation-based study. Some 20.3% of all women were HPV
positive, and the prevalence of HPV 16 was 2.7%. In Holland, HPV DNA was found by using the GP6-GP6 general primer pair in 14 to 25% of cervical scrapes from womenwith normalcytologyattending gynecological clinics
forawide range ofgynecological complaints (agerange, 16 to60years) (26, 27).Amongfemale university students from
Berkeley, Calif., who underwent a routine gynecological
examination, 31% had normalcytology and 46% were HPV
positive when the consensus primer pair MY11-MY09was used(1). Theirmean age was22.9 years.
The one-step PCR consensusprimer system
from
theLiregion (15) was, in our hands, not sufficiently robust to detect all the HPV DNA-positive cytological scrapes that werepositive by use of a two-step general PCRfromthe
Li
region. By
using
the two-stepPCR,wefound that even in a population-based study of young women, HPV infection of theuterine cervix is common.ACKNOWLEDGMENTS
We aregrateful to T.
Angstrom
of the Department of Cytology, UniversityofUmea, forcytological analysis.This work was supported by a grant from the Labor Market Insurance Company, grant 1547-B90 from the Swedish Cancer Society, and grants from the Research Foundation of the Depart-mentofOncology, University ofUmeg.
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