Skip to main content
SpringerLink
Log in

Modifier gene study of meconium ileus in cystic fibrosis: statistical considerations and gene mapping results

  • Original Investigation
  • Published:
Human Genetics Aims and scope Submit manuscript

Abstract

Cystic fibrosis (CF) is a monogenic disease due to mutations in the CFTR gene. Yet, variability in CF disease presentation is presumed to be affected by modifier genes, such as those recently demonstrated for the pulmonary aspect. Here, we conduct a modifier gene study for meconium ileus (MI), an intestinal obstruction that occurs in 16–20% of CF newborns, providing linkage and association results from large family and case–control samples. Linkage analysis of modifier traits is different than linkage analysis of primary traits on which a sample was ascertained. Here, we articulate a source of confounding unique to modifier gene studies and provide an example of how one might overcome the confounding in the context of linkage studies. Our linkage analysis provided evidence of a MI locus on chromosome 12p13.3, which was segregating in up to 80% of MI families with at least one affected offspring (HLOD = 2.9). Fine mapping of the 12p13.3 region in a large case–control sample of pancreatic insufficient Canadian CF patients with and without MI pointed to the involvement of ADIPOR2 in MI (p = 0.002). This marker was substantially out of Hardy–Weinberg equilibrium in the cases only, and provided evidence of a cohort effect. The association with rs9300298 in the ADIPOR2 gene at the 12p13.3 locus was replicated in an independent sample of CF families. A protective locus, using the phenotype of no-MI, mapped to 4q13.3 (HLOD = 3.19), with substantial heterogeneity. A candidate gene in the region, SLC4A4, provided preliminary evidence of association (p = 0.002), warranting further follow-up studies. Our linkage approach was used to direct our fine-mapping studies, which uncovered two potential modifier genes worthy of follow-up.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Abreu PC, Hodge SE, Greenberg DA (2002) Quantification of type I error probabilities for heterogeneity LOD scores. Genet Epidemiol 22:156–169

    Article  PubMed  Google Scholar 

  • Ahmed N, Corey M, Forstner G, Zielenski J, Tsui LC, Ellis L, Tullis E, Durie P (2003) Molecular consequences of cystic fibrosis transmembrane regulator (CFTR) gene mutations in the exocrine pancreas. Gut 52:1159–1164

    Article  CAS  PubMed  Google Scholar 

  • Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263–265

    Article  CAS  PubMed  Google Scholar 

  • Blackman SM, Deering-Brose R, McWilliams R, Naughton K, Coleman B, Lai T, Algire M, Beck S, Hoover-Fong J, Hamosh A, Fallin MD, West K, Arking DE, Chakravarti A, Cutler DJ, Cutting GR, the CF Twin and Sibling Study (2006) Relative contribution of genetic and nongenetic modifiers to intestinal obstruction in cystic fibrosis. Gastroenterology 131:1030–1039

    Article  PubMed  Google Scholar 

  • Blackwelder WC, Elston RC (1985) A comparison of sib-pair linkage tests for disease susceptibility loci. Genet Epidemiol 2:85–97

    Article  CAS  PubMed  Google Scholar 

  • Clayton D, Chapman J, Cooper J (2004) Use of unphased multilocus genotype data in indirect association studies. Genet Epidemiol 27:415–428

    Article  PubMed  Google Scholar 

  • Clerget-Darpoux F, Bonaïti-Pellié C, Hochez J (1986) Effects of misspecifying genetic parameters in LOD score analysis. Biometrics 42:393–399

    Article  CAS  PubMed  Google Scholar 

  • Cottingham RW Jr, Idury RM, Schaffer AA (1993) Faster sequential genetic linkage computations. Am J Hum Genet 53:252–263

    PubMed  Google Scholar 

  • Cutting GR, Antonarakis SE, Buetow KH, Kasch LM, Rosenstein BJ, Kazazian HH Jr (1989) Analysis of DNA polymorphism haplotypes linked to the cystic fibrosis locus in North American black and Caucasian families supports the existence of multiple mutations of the cystic fibrosis gene. Am J Hum Genet 44:307–318

    CAS  PubMed  Google Scholar 

  • Daw EW, Lu Y, Marian AJ, Shete S (2008) Identifying modifier loci in existing genome scan data. Ann Hum Genet 72:670–675

    Article  CAS  PubMed  Google Scholar 

  • Dizier MH, Babron M-C, Clerget-Darpoux F (1996) Conclusion of LOD-score analysis for family data generated under two-locus models. Am J Hum Genet 58:1338–1346

    CAS  PubMed  Google Scholar 

  • Durner M, Vieland VJ, Greenberg DA (1999) Further evidence for the increased power of LOD scores compared with nonparametric methods. Am J Hum Genet 64:281–289

    Article  CAS  PubMed  Google Scholar 

  • Elston RC (1989) Man bites dog? The validity of maximizing LOD scores to determine mode of inheritance. Am J Med Genet 34:487–488

    Article  CAS  PubMed  Google Scholar 

  • Forrest WF, Feingold E (2000) Composite statistics for QTL mapping with moderately discordant sibling pairs. Am J Hum Genet 66:1642–1660

    Article  CAS  PubMed  Google Scholar 

  • Greenberg DA (1990) Linkage analysis assuming a single-locus mode of inheritance for traits determined by two loci: inferring mode of inheritance and estimating penetrance. Genet Epidemiol 7:467–479

    Article  CAS  PubMed  Google Scholar 

  • Greenberg DA, Abreu PC (2001) Determining trait locus position from multipoint analysis: accuracy and power of three different statistics. Genet Epidemiol 21:299–314

    Article  CAS  PubMed  Google Scholar 

  • Greenberg DA, Hodge SE (1989) Linkage analysis under “random” and “genetic” reduced penetrance. Genet Epidemiol 6:259–264

    Article  CAS  PubMed  Google Scholar 

  • Greenberg DA, Abreu P, Hodge SE (1998) The power to detect linkage in complex disease by means of simple LOD-score analyses. Am J Hum Genet 63:870–879

    Article  CAS  PubMed  Google Scholar 

  • Guo X, Elston RC (2000) Two-stage global search designs for linkage analysis II: including discordant relative pairs in the study. Genet Epidemiol 18:111–127

    Article  CAS  PubMed  Google Scholar 

  • Haston CK, Tsui LC (2003) Loci of intestinal distress in cystic fibrosis knockout mice. Physiol Genom 12:79–84

    CAS  Google Scholar 

  • Hodge SE, Elston RC (1994) Lods, wrods, and mods: the interpretation of LOD scores calculated under different models. Genet Epidemiol 11:329–342

    Article  CAS  PubMed  Google Scholar 

  • Hodge SE, Abreu PC, Greenberg DA (1997) Magnitude of type I error when single-locus linkage analysis is maximized over models: a simulation study. Am J Hum Genet 60:217–227

    CAS  PubMed  Google Scholar 

  • Houlston RS, Tomlinson IPM (1998) Modifier genes in humans: strategies for identification. Eur J Hum Genet 6:80–88

    Article  CAS  PubMed  Google Scholar 

  • Kadowaki T, Yamauchi T (2005) Adiponectin and adiponectin receptors. Endocr Rev 26:439–451

    Article  CAS  PubMed  Google Scholar 

  • Kristidis P, Bozon D, Corey M, Markiewicz D, Rommens J, Tsui LC, Durie P (1992) Genetic determination of exocrine pancreatic function in cystic fibrosis. Am J Hum Genet 50:1178–1184

    CAS  PubMed  Google Scholar 

  • Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996) Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 58:1347–1363

    CAS  PubMed  Google Scholar 

  • Laird NM, Horvath S, Xu X (2000) Implementing a unified approach to family-based tests of association. Genet Epidemiol 19(Suppl 1):S36–S42

    Article  PubMed  Google Scholar 

  • Lee MG, Ahn W, Lee JA, Kim JY, Choi JY, Moe OW, Milgram SL, Muallem S, Kim KH (2001) Coordination of pancreatic HCO3-secretion by protein–protein interaction between membrane transporters. JOP 2:203–206

    CAS  PubMed  Google Scholar 

  • Li W, Zou F, Lee S, Corey M, Sun L, Wright F, Strug LJ (2009) Analysis of population stratification in North American CF patients. In: North American CF conference, Minneapolis

  • Norkina O, De Lisle RC (2005) Potential genetic modifiers of the cystic fibrosis intestinal inflammatory phenotype on mouse chromosomes 1, 9, and 10. BMC Genet 6:29

    Article  PubMed  Google Scholar 

  • Oh DK, Ciaraldi T, Henry RR (2007) Adiponectin in health and disease. Diabetes Obes Metab 9:282–289

    Article  CAS  PubMed  Google Scholar 

  • Ott J (1999) Analysis of human genetic linkage, 3rd edn. The Johns Hopkins University Press, Baltimore

    Google Scholar 

  • Ouchi N, Walsh K (2007) Adiponectin as an anti-inflammatory factor. Clin Chim Acta 380:24–30

    Article  CAS  PubMed  Google Scholar 

  • Pal DK, Durner M, Greenberg DA (2001) Effect of misspecification of gene frequency on the two-point LOD score. Eur J Hum Genet 9:855–859

    Article  CAS  PubMed  Google Scholar 

  • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575

    Article  CAS  PubMed  Google Scholar 

  • Quinton PM (2008) Cystic fibrosis: impaired bicarbonate secretion and mucoviscidosis. Lancet 372:415–417

    Article  CAS  PubMed  Google Scholar 

  • Risch N, Zhang H (1995) Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science 268:1584–1589

    Article  CAS  PubMed  Google Scholar 

  • Rogus JJ, Poznik GD, Pezzolesi MG, Smiles AM, Dunn J, Walker W, Wanic K, Moczulski D, Canani L, Araki S, Makita Y, Warram JH, Krolewski AS (2008) High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach. Diabetes 57:2519–2526

    Article  CAS  PubMed  Google Scholar 

  • Romero MF (2005) Molecular pathophysiology of SLC4 bicarbonate transporters. Curr Opin Nephrol Hypertens 14:495–501

    Article  CAS  PubMed  Google Scholar 

  • Rovner AJ, Stallings VA, Schall JI, Leonard MB, Zemel BS (2007) Vitamin D insufficiency in children, adolescents, and young adults with cystic fibrosis despite routine oral supplementation. Am J Clin Nutr 86:1694–1699

    CAS  PubMed  Google Scholar 

  • Rozmahel R, Wilschanski M, Matin A, Plyte S, Oliver M, Auerbach W, Moore A, Forstner J, Durie P, Nadeau J, Bear C, Tsui LC (1996) Modulation of disease severity in cystic fibrosis transmembrane conductance regulator deficient mice by a secondary genetic factor. Nat Genet 12:280–287

    Article  CAS  PubMed  Google Scholar 

  • Schaffer AA, Gupta SK, Shriram K, Cottingham RW Jr (1994) Avoiding recomputation in linkage analysis. Hum Hered 44:225–237

    Article  CAS  PubMed  Google Scholar 

  • Shumaker H, Soleimani M (1999) CFTR upregulates the expression of the basolateral Na(+)–K(+)–2Cl(−) cotransporter in cultured pancreatic duct cells. Am J Physiol 277:C1100–C1110

    CAS  PubMed  Google Scholar 

  • Shumaker H, Amlal H, Frizzell R, Ulrich CDII, Soleimani M (1999) CFTR drives Na+–nHCO3 − cotransport in pancreatic duct cells: a basis for defective HCO3 − secretion in CF. Am J Physiol 276:C16–C25

    CAS  PubMed  Google Scholar 

  • Soleimani M (2001) Impaired pancreatic ductal bicarbonate secretion in cystic fibrosis. JOP 2:237–242

    CAS  PubMed  Google Scholar 

  • Soleimani M, Burnham CE (2001) Na+:HCO(3 −) cotransporters (NBC): cloning and characterization. J Membr Biol 183:71–84

    Article  CAS  PubMed  Google Scholar 

  • Speeckaert MM, Wehlou C, Vandewalle S, Taes YE, Robberecht E, Delanghe JR (2008) Vitamin D binding protein, a new nutritional marker in cystic fibrosis patients. Clin Chem Lab Med 46:365–370

    Article  CAS  PubMed  Google Scholar 

  • Stephens M, Donnelly P (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162–1169

    Article  CAS  PubMed  Google Scholar 

  • Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978–989

    Article  CAS  PubMed  Google Scholar 

  • Taylor C, Webel A, Cutting GR, Knowles MR, Corey M (2009) A new cf lung disease severity phenotype for genetic modifier studies. In: North American CF conference, Minneapolis

  • Vanscoy LL, Blackman SM, Collaco JM, Bowers A, Lai T, Naughton K, Algire M, McWilliams R, Beck S, Hoover-Fong J, Hamosh A, Cutler D, Cutting GR (2007) Heritability of lung disease severity in cystic fibrosis. Am J Respir Crit Care Med 175:1036–1043

    Article  CAS  PubMed  Google Scholar 

  • Vieland V, Greenberg DA, Hodge SE, Ott J (1992a) Linkage analysis of two-locus diseases under single-locus and two-locus analysis models. Cytogenet Cell Genet 59:145–146

    Article  CAS  PubMed  Google Scholar 

  • Vieland VJ, Hodge SE, Greenberg DA (1992b) Adequacy of single-locus approximations for linkage analyses of oligogenic traits. Genet Epidemiol 9:45–59

    Article  CAS  PubMed  Google Scholar 

  • Vieland VJ, Greenberg DA, Hodge SE (1993) Adequacy of single-locus approximations for linkage analyses of oligogenic traits: extension to multigenerational pedigree structures. Hum Hered 43:329–336

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Shete S (2008) A test for genetic association that incorporates information about deviation from Hardy–Weinberg proportions in cases. Am J Hum Genet 83:53–63

    Article  CAS  PubMed  Google Scholar 

  • Wood SD, Adams S, Dunn J, Baler J, Xu A, Pace RG, Kohl A, Yeatts J, Stonebreaker JR, Konstan MW, Drumm ML, Knowles MR (2007) Inaccuracy of reporting of meconeum ileus on case report forms of the gene modifier study. Pediatr Pulmonol S30:272

    Google Scholar 

  • Zielenski J, Corey M, Rozmahel R, Markiewicz D, Aznarez I, Casals T, Larriba S, Mercier B, Cutting GR, Krebsova A, Macek M Jr, Langfelder-Schwind E, Marshall BC, DeCelie-Germana J, Claustres M, Palacio A, Bal J, Nowakowska A, Ferec C, Estivill X, Durie P, Tsui LC (1999) Detection of a cystic fibrosis modifier locus for meconium ileus on human chromosome 19q13. Nat Genet 22:128–129

    Article  CAS  PubMed  Google Scholar 

  • Zielenski J, Dorfman R, Markeiwiz D, Corey M, Ng P, Mak W, Durie P, Tsui LC (2005) Tagging SNP analyses of the CFM1 locus in CF patients with and without meconium ileus. Pediatric Pulmonol S28

Download references

Acknowledgments

This project was supported by Genome Canada through the Ontario Genomics Institute per research agreement 2004-OGI-3-05, by the Canadian Cystic Fibrosis Foundation, by the Ontario Research Fund—Research Excellence Program. L.J. Strug is supported by the NIH (HG-0004314) and the Natural Sciences and Engineering Research Council. R. Dorfman was supported by the joint Fellowship of Canadian Institutes of Health Research and Ontario Women’s Health Council. Support by VZFNM00064203 to Milan Macek. The authors express gratitude to all CF patients and their families for participating in this study. The authors thank Nicole Anderson, Jennifer Breaton, Mary Cristofi, Roxanne Rousseau, and Michael Van Spall for their exceptional effort in recruiting and ascertaining Canadian CF families for the study, as well Drs. Miroslava Balascakova, Vera Vavrova and Dana Zemkova for provision of patients with MI. The authors are indebted to the following individuals from member institutions of the Canadian Consortium for CF Genetic Studies for ascertaining patient data and blood samples from CF patients and their families: S. Aaron, P. Barrett, B. Beaurivage, Y. Berthiaume, P. Bigonesse, M. Boland, L. Boucher, J. Boucher, S. Bourgh, F. Brosseau, N.E. Brown, C. Brunoro, N. Bureau, A. Cantin, L. Charette, G. Cote, A. Dale, G. Davidson, K. Devesceri, R. Dicaire, V. Fauvel, A. Freitag, D.N. Garey, M. Gaul, W. Gervais, J. Gjevre, F. Gosse, A. Gravelle, B. Habbick, R. Hennessey, S.B. Holmes, J. Hopkins, D. Hughes, M. Jackson, J. Jacob, A. Jeanneret, P. Kean, W. Kepron, T. Kovesi, V.J. Kumar, L. Lands, M. LaPerriere, J. Leong, R. Levesque, D. Lougheed, M. Lowe, B. Lyttle, K. Malhotra, J.E. Marcotte, S. Marsolais, C. Martineau, E. Matouk, D. McCulloch, R.T. Michael, M. Montgomery, R. Morris, E.M. Nakielna, F. Paquet, H. Pasterkamp, N. Patterson, L. Pedder, L. Peterson, N. Petit, C. Piche, M. Plante, H.R. Rabin, K. Ramlall, F. Raymong, L. Rivard, G. Rivard, M. Roussin, M. Ruel, J. Salgado, L. Semple, E. Sheppard, F. Simard, A. Smith, M. Solomon, R. Stackhouse, J. Tabak, L. Taylor, A. Tsang, E. Tullis, C. Turtle, K. Vandamheen, M. van Spall, R. van Wylick, I. Waters, T. Wells, S. Wiltse, and P. Zuberbuhler.

Author information

Authors and Affiliations

  1. Child Health Evaluative Sciences Program, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada

    Weili Li, Mary Corey & Lisa J. Strug

  2. Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada

    Ruslan Dorfman, Lei Sun, Fan Lin, Yongqian Wang, Lap-Chee Tsui & Julian Zielenski

  3. Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada

    Lei Sun, Mary Corey & Lisa J. Strug

  4. The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, University of British Columbia, Vancouver, Canada

    Andrew Sandford & Peter D. Paré

  5. Department of Respiratory Medicine, The Children’s Hospital at Westmead, Westmead, NSW, Australia

    Karen McKay

  6. Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovak Republic

    Hana Kayserova

  7. Department of Biology and Medical Genetics, University Hospital Motol, 2nd School of Medicine, Charles University Prague, Prague, Czech Republic

    Tereza Piskackova & Milan Macek

  8. Institute of Mother and Child, Warsaw, Poland

    Kamila Czerska & Dorota Sands

  9. Erasmus Medical Centre Rotterdam, Sophia Children’s Hospital, Rotterdam, The Netherlands

    Harm Tiddens

  10. Human Genetics Center, Clínica Alemana, Universidad del Desarrollo de Santiago, Santiago, Chile

    Sonia Margarit & Gabriela Repetto

  11. Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA

    Marci K. Sontag

  12. Department of Pediatrics, Mike McMorris Cystic Fibrosis Care and Research Center, Children’s Hospital, University of Colorado Denver, Aurora, CO, 80045, USA

    Frank J. Accurso

  13. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Scott Blackman & Garry R. Cutting

  14. University of Hong Kong, Hong Kong, China

    Lap-Chee Tsui

  15. Program in Physiology and Experimental Medicine, Hospital for Sick Children, Toronto, ON, Canada

    Peter Durie

Authors
  1. Ruslan Dorfman
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Weili Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lei Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fan Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yongqian Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Andrew Sandford
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Peter D. Paré
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Karen McKay
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Hana Kayserova
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Tereza Piskackova
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Milan Macek
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Kamila Czerska
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Dorota Sands
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Harm Tiddens
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Sonia Margarit
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Gabriela Repetto
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Marci K. Sontag
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Frank J. Accurso
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Scott Blackman
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Garry R. Cutting
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Lap-Chee Tsui
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Mary Corey
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Peter Durie
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Julian Zielenski
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. Lisa J. Strug
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lisa J. Strug.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 385 kb)

Web resources

Web resources

Mendelian inheritance in man listed in online http://www.ncbi.nlm.gov/entrez. The Haploview application can be downloaded at http://www.broad.mit.edu/mpg/haploview. Information about marker location can be found at UniSTS at the NCBI website above, and through the Ensembl genome browser at http://www.ensembl.org/Homo_sapiens/index.html. SNP frequencies were accessed at dbSNP: http://www.ncbi.nlm.nih.gov/projects/SNP. TCAG Copy Number Variation database http://projects.tcag.ca/variation/.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dorfman, R., Li, W., Sun, L. et al. Modifier gene study of meconium ileus in cystic fibrosis: statistical considerations and gene mapping results. Hum Genet 126, 763–778 (2009). https://doi.org/10.1007/s00439-009-0724-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00439-009-0724-8

Keywords

Search

Navigation