reply to gyorkos, joseph and carabin

1
Techniques Parasitology Today, vol. 15, no. 11, 1999 465 12 Hovig, E. et al. (1991) Constant denaturant gel electrophoresis, a modification of denaturing gradient gel electrophoresis, in mutation detection. Mutat. Res. 262, 63–71 13 Hecker, R. et al. (1988) Analysis of RNA structure by tempera- ture-gradient gel electrophoresis: viroid replication and pro- cessing. Gene 72, 59–74 14 Orita, M. et al. (1989) Rapid and sensitive detection of point mu- tations and DNA polymorphisms using the polymerase chain reaction. Genomics 5, 874–879 15 Zhu, X.Q. and Gasser, R.B. (1998) SSCP-based mutation scanning approaches to fingerprint sequence variation in ribosomal DNA of ascaridoid nematodes. Electrophoresis 19, 1366–1373 16 Gasser, R.B. et al. (1998) A mutation scanning approach for the identification of hookworm species and analysis of population variation. Mol. Biochem. Parasitol. 92, 303–312 17 Bøgh, H.O. et al. (1999) Scanning for nucleotide variations in mitochondrial DNA fragments of Schistosoma japonicum by single-strand conformation polymorphism. Parasitology 118, 73–82 18 Liang, P. and Pardee, A. (1992) Differential display of eu- karyotic messenger RNA by means of the polymerase chain reaction. Science 257, 967–971 19 Reed, M.B. et al. (1998) Fasciola hepatica: stage-specific expres- sion of novel gene sequences as identified by differential dis- play. Exp. Parasitol. 89, 169–179 20 Hetsko, M.L. et al. (1998) Cellular and transcriptional changes during excystation of Giardia lamblia in vitro. Exp. Parasitol. 88, 172–183 21 Miele, G. et al. (1998) Elimination of false positives generated through PCR re-amplification of differential display cDNA. BioTechniques 25, 138–144 22 Mathieu-Daude, F. et al. (1998) Differentially expressed genes in the Trypanosoma brucei life cycle identified by RNA finger- printing. Mol. Biochem. Parasitol. 92, 15–28 23 Sarkar, G. et al. (1992) Dideoxy fingerprinting: a rapid and efficient screen for the presence of mutations. Genomics 13, 441–443 24 Liu, Q. and Sommer, S.S. (1995) Restriction endonuclease fingerprinting (REF): a sensitive method for screening mutations in long contiguous segments of DNA. BioTechniques 18, 470–477 25 Sanger, F. et al. (1977) DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. U. S. A. 74, 5463–5467 26 Liu, Q. and Sommer, S.S. (1994) Parameters affecting the sensi- tivities of dideoxy fingerprinting and SSCP. PCR Methods Appl. 4, 97–108 27 Gasser, R.B. et al. (1998) Dideoxy fingerprinting: application to the genotyping of Echinococcus. Int. J. Parasitol. 28, 1775–1779 28 Børresen, A-L. (1996) in Technologies for Detection of DNA Damage and Mutations (Pfeifer, G.P., ed.), pp 267–278, Plenum Press Letters The article by Booth 1 in the December 1998 issue of Parasitology Today makes an important contribution to the field, because parasitologists can see how specific epi- demiological methodology can be adapted into a familiar context, in this instance, to enhance data analysis and interpretation. To avoid any possible confusion in such adaptations, it becomes essential to ensure that correct epidemiological terminology is used. In this regard, it might be helpful to point out some inconsistencies with epi- demiological terminology. The definitions presented in Box 2 of Ref. 1, for example, are not strictly the definitions presented in Last’s Dictionary 2 and have been adapted considerably for the very specific applica- tion presented. The term ’randomized cross-sectional data’ is incorrect; cross-sec- tional data might be obtained from a ran- dom sample of a population, but they are not randomized. ‘Risk’ and its estimation is most appropriately obtained from cohort studies and not from cross-sectional studies. The denominator of PR w should be c i e i / N i and not a i e i / N i . These examples highlight the challenge facing us all when we incorporate a new, or unfamiliar, specialized vocabulary into our work (see Ref. 3). Authors, editors and reviewers share the responsibility of provid- ing the readership with a vocabulary that is correct and current. References 1 Booth, M. (1998) Parasitol. Today 14, 497–500 2 Last, J.M. (1988) A Dictionary of Epidemiology (2nd edn), Oxford University Press 3 Rothman, K.J. and Greenland, S. (1998) Mod- ern Epidemiology (2nd edn), Lippincott-Raven Publishers Theresa W. Gyorkos Lawrence Joseph Department of Epidemiology and Biostatistics McGill University, Montreal, Quebec, Canada H3A 1A2 Helene Carabin Wellcome Trust Centre for the Epidemiology of Infectious Disease Oxford University, Oxford, UK OX1 3PS Reply Theresa Gyorkos and colleagues make several valid points in their letter, and I thank them for correcting the typographical error in the equation of PR w . In addition, they criticize the use of the term ‘risk’, and correctly point out that the terminology was heavily adapted for the situation. In doing so, they highlight a general problem associated with terminology of cross- sectional data. The issue is whether concepts and terms of risk analysis should only be used with incidence data (which record the number of cases over a given period of time), or if they can also be used when discussing prevalence data (which record the number of cases at a particular point in time). There is often no distinction in the literature, which is not surprising since analytical methods for prevalence data are essentially a special application of methods developed for cohort studies 1 . Even Last’s Dictionary offers no special terminology for prevalence data – for example, the term ‘attributable fraction’ is defined only for incidence data 2 . Thus, the problem lies in having to use methods in a situation where there is no suitable terminology, rather than introducing unfamiliar terminology into a particular field of research. References 1 Rothman, K.J. and Greenland, S. (1998) Modern Epidemiology (2nd edn), Lippincott– Raven Publishers 2 Last, J.M. (1995) A Dictionary of Epidemiology (3rd edn), Oxford University Press Mark Booth Department of Public Health and Epidemiology Swiss Tropical Institute Socinstrasse 57 CH4051 Basel, Switzerland Further Analysis of Attributable Risk in Helminth Epidemiology

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Techniques

Parasitology Today, vol. 15, no. 11, 1999 465

12 Hovig, E. et al. (1991) Constant denaturant gel electrophoresis, amodification of denaturing gradient gel electrophoresis, in mutation detection. Mutat. Res. 262, 63–71

13 Hecker, R. et al. (1988) Analysis of RNA structure by tempera-ture-gradient gel electrophoresis: viroid replication and pro-cessing. Gene 72, 59–74

14 Orita, M. et al. (1989) Rapid and sensitive detection of point mu-tations and DNA polymorphisms using the polymerase chainreaction. Genomics 5, 874–879

15 Zhu, X.Q. and Gasser, R.B. (1998) SSCP-based mutation scanning approaches to fingerprint sequence variation in ribosomal DNA of ascaridoid nematodes. Electrophoresis 19,1366–1373

16 Gasser, R.B. et al. (1998) A mutation scanning approach for theidentification of hookworm species and analysis of populationvariation. Mol. Biochem. Parasitol. 92, 303–312

17 Bøgh, H.O. et al. (1999) Scanning for nucleotide variations inmitochondrial DNA fragments of Schistosoma japonicum bysingle-strand conformation polymorphism. Parasitology 118,73–82

18 Liang, P. and Pardee, A. (1992) Differential display of eu-karyotic messenger RNA by means of the polymerase chain reaction. Science 257, 967–971

19 Reed, M.B. et al. (1998) Fasciola hepatica: stage-specific expres-sion of novel gene sequences as identified by differential dis-play. Exp. Parasitol. 89, 169–179

20 Hetsko, M.L. et al. (1998) Cellular and transcriptional changesduring excystation of Giardia lamblia in vitro. Exp. Parasitol. 88,172–183

21 Miele, G. et al. (1998) Elimination of false positives generatedthrough PCR re-amplification of differential display cDNA.BioTechniques 25, 138–144

22 Mathieu-Daude, F. et al. (1998) Differentially expressed genes inthe Trypanosoma brucei life cycle identified by RNA finger-printing. Mol. Biochem. Parasitol. 92, 15–28

23 Sarkar, G. et al. (1992) Dideoxy fingerprinting: a rapid and efficient screen for the presence of mutations. Genomics 13,441–443

24 Liu, Q. and Sommer, S.S. (1995) Restriction endonuclease fingerprinting (REF): a sensitive method for screening mutations in long contiguous segments of DNA. BioTechniques18, 470–477

25 Sanger, F. et al. (1977) DNA sequencing with chain terminatinginhibitors. Proc. Natl. Acad. Sci. U. S. A. 74, 5463–5467

26 Liu, Q. and Sommer, S.S. (1994) Parameters affecting the sensi-tivities of dideoxy fingerprinting and SSCP. PCR Methods Appl.4, 97–108

27 Gasser, R.B. et al. (1998) Dideoxy fingerprinting: application to the genotyping of Echinococcus. Int. J. Parasitol. 28, 1775–1779

28 Børresen, A-L. (1996) in Technologies for Detection of DNA Damageand Mutations (Pfeifer, G.P., ed.), pp 267–278, Plenum Press

Letters

The article by Booth1 in the December1998 issue of Parasitology Today makes animportant contribution to the field, becauseparasitologists can see how specific epi-demiological methodology can be adaptedinto a familiar context, in this instance, toenhance data analysis and interpretation.To avoid any possible confusion in suchadaptations, it becomes essential to ensurethat correct epidemiological terminology isused. In this regard, it might be helpful topoint out some inconsistencies with epi-demiological terminology. The definitionspresented in Box 2 of Ref. 1, for example,are not strictly the definitions presented in

Last’s Dictionary2 and have been adaptedconsiderably for the very specific applica-tion presented. The term ’randomizedcross-sectional data’ is incorrect; cross-sec-tional data might be obtained from a ran-dom sample of a population, but they arenot randomized. ‘Risk’ and its estimation ismost appropriately obtained from cohortstudies and not from cross-sectional studies.The denominator of PRw should be ∑ ci ei / Niand not ∑ ai ei / Ni.

These examples highlight the challengefacing us all when we incorporate a new, orunfamiliar, specialized vocabulary into ourwork (see Ref. 3). Authors, editors and

reviewers share the responsibility of provid-ing the readership with a vocabulary that iscorrect and current.

References1 Booth, M. (1998) Parasitol. Today 14,

497–5002 Last, J.M. (1988) A Dictionary of Epidemiology

(2nd edn), Oxford University Press3 Rothman, K.J. and Greenland, S. (1998) Mod-

ern Epidemiology (2nd edn), Lippincott-RavenPublishers

Theresa W. GyorkosLawrence JosephDepartment of Epidemiology and BiostatisticsMcGill University, Montreal, Quebec, CanadaH3A 1A2

Helene CarabinWellcome Trust Centre for the Epidemiology ofInfectious DiseaseOxford University, Oxford, UK OX1 3PS

Reply

Theresa Gyorkos and colleagues makeseveral valid points in their letter, and Ithank them for correcting the typographicalerror in the equation of PRw. In addition,they criticize the use of the term ‘risk’, andcorrectly point out that the terminologywas heavily adapted for the situation. Indoing so, they highlight a general problemassociated with terminology of cross-sectional data.

The issue is whether concepts and termsof risk analysis should only be used with

incidence data (which record the numberof cases over a given period of time), or ifthey can also be used when discussingprevalence data (which record the numberof cases at a particular point in time). Thereis often no distinction in the literature,which is not surprising since analyticalmethods for prevalence data are essentiallya special application of methods developedfor cohort studies1. Even Last’s Dictionaryoffers no special terminology for prevalencedata – for example, the term ‘attributablefraction’ is defined only for incidence data2.Thus, the problem lies in having to usemethods in a situation where there is no

suitable terminology, rather thanintroducing unfamiliar terminology into aparticular field of research.

References1 Rothman, K.J. and Greenland, S. (1998)

Modern Epidemiology (2nd edn), Lippincott–Raven Publishers

2 Last, J.M. (1995) A Dictionary of Epidemiology(3rd edn), Oxford University Press

Mark BoothDepartment of Public Health and EpidemiologySwiss Tropical InstituteSocinstrasse 57CH4051 Basel, Switzerland

Further Analysis of Attributable Risk in

Helminth Epidemiology