Targeted mutation screening panels expose systematic population bias in detection of cystic fibrosis risk

Genetics in Medicine

Volumn 18, Issue 2, 2016, Pages 174-179

  Lim, Regine M ^a   Silver, Ari J ^a,b   Silver, Maxwell J ^a   Borroto, Carlos ^a   Spurrier, Brett ^a   Petrossian, Tanya C ^a   Larson, Jessica L ^b   Silver, Lee M ^a,b,c,d  

^a GenePeeks Inc   (United States)

^b GenePeeks Inc   (United States)

^c PRINCETON UNIVERSITY   (United States)

^d PRINCETON UNIVERSITY   (United States)

Author keywords

carrier screening; cystic fibrosis; ExAC; exome sequencing; genetic testing; next generation sequencing

Indexed keywords

AFRICA; ARTICLE; CFTR GENE; COHORT ANALYSIS; CYSTIC FIBROSIS; EAST ASIAN; EUROPEAN; FINLAND; GENE; GENE FREQUENCY; GENETIC RISK; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; HETEROZYGOTE; HUMAN; MUTATIONAL ANALYSIS; PHENOTYPE; POPULATION GENETICS; SOUTH ASIAN; WESTERN HEMISPHERE; EVALUATION STUDY; GENETICS; HETEROZYGOTE DETECTION; MASS SCREENING; MUTATION; RISK FACTOR;

CFTR PROTEIN, HUMAN; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR;

CYSTIC FIBROSIS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; GENETIC TESTING; HETEROZYGOTE DETECTION; HUMANS; MASS SCREENING; MUTATION; RISK FACTORS;

EID: 84957695350     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2015.52     Document Type: Article

References (29)

1. Cutting GR. Cystic fibrosis genetics: from molecular understanding to clinical application. Nat Rev Genet 2015; 16: 45-56
2. De Boeck K, Wilschanski M, Castellani C., et al.; Diagnostic Working Group. Cystic fibrosis: terminology and diagnostic algorithms. Thorax 2006; 61: 627-635
3. Noone PG, Knowles MR. 'CFTR-opathies': disease phenotypes associated with cystic fibrosis transmembrane regulator gene mutations. Respir Res 2001; 2: 328-332
4. Ngiam NS, Chong SS, Shek LP., et al. Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in Asians with chronic pulmonary disease: a pilot study. J Cyst Fibros 2006; 5: 159-164
5. Sakamoto H, Yajima T, Suzuki K, Ogawa Y. Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation associated with a congenital bilateral absence of vas deferens. Int J Urol 2008; 15: 270-271
6. Grody W, Cutting GR, Klinger KW., et al. Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Genet Med 2001; 3: 149
7. Watson MS, Cutting GR, Desnick RJ., et al. Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Genet Med 2004; 6: 387-391
8. Lazarin GA, Haque IS, Nazareth S., et al. An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23, 453 individuals. Genet Med 2012; 15: 178-186
9. Rohlfs EM, Zhou Z, Heim RA., et al. Cystic fibrosis carrier testing in an ethnically diverse US population. Clin Chem 2011; 57: 841-848
10. Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132: 1077-1130
11. Sosnay PR, Siklosi KR, Van Goor F., et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet 2013; 45: 1160-1167
12. Castellani C; CFTR2 team. CFTR2: How will it help care?. Paediatr Respir Rev 2013; 14 Suppl 1: 2-5
13. Reppell M, Koch E, Peter BM, Novembre J. Surfing waves of data in San Diego: sophisticated analyses provide a broad view of human genetic diversity. Genome Biol 2014; 15: 562
14. Landrum MJ, Lee JM, Riley GR., et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 2014; 42(Database issue): D980-D985
15. Goldstein DB, Allen A, Keebler J., et al. Sequencing studies in human genetics: design and interpretation. Nat Rev Genet 2013; 14: 460-470
16. Adzhubei IA, Schmidt S, Peshkin L., et al. A method and server for predicting damaging missense mutations. Nat Methods 2010; 7: 248-249
17. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS One 2012; 7: e46688
18. den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 2000; 15: 7-12
19. Taschner PE, den Dunnen JT. Describing structural changes by extending HGVS sequence variation nomenclature. Hum Mutat 2011; 32: 507-511
20. Palo JU, Ulmanen I, Lukka M, Ellonen P, Sajantila A. Genetic markers and population history: Finland revisited. Eur J Hum Genet 2009; 17: 1336-1346
21. Nevanlinna HR. The Finnish population structure. A genetic and genealogical study. Hereditas 1972; 71: 195-236
22. Krasnov KV, Tzetis M, Cheng J, Guggino WB, Cutting GR. Localization studies of rare missense mutations in cystic fibrosis transmembrane conductance regulator (CFTR) facilitate interpretation of genotype-phenotype relationships. Hum Mutat 2008; 29: 1364-1372
23. Schneider A, Larusch J, Sun X., et al. Combined bicarbonate conductanceimpairing variants in CFTR and SPINK1 variants are associated with chronic pancreatitis in patients without cystic fibrosis. Gastroenterology 2011; 140: 162-171
24. Strom CM, Redman JB, Peng M. The dangers of including nonclassical cystic fibrosis variants in population-based screening panels: p.L997F, further genotype/phenotype correlation data. Genet Med 2011; 13: 1042-1044
25. Oka H, Ishii H, Kishi K., et al. A Japanese adult case of forme fruste cystic fibrosis. Intern Med 2010; 49: 1251-1252
26. Dequeker E, Stuhrmann M, Morris MA., et al. Best practice guidelines for molecular genetic diagnosis of cystic fibrosis and CFTR-related disorders-updated European recommendations. Eur J Hum Genet 2009; 17: 51-65
27. Lee JH, Choi JH, Namkung W., et al. A haplotype-based molecular analysis of CFTR mutations associated with respiratory and pancreatic diseases. Hum Mol Genet 2003; 12: 2321-2332
28. Chang MC, Chang YT, Wei SC., et al. Spectrum of mutations and variants/haplotypes of CFTR and genotype-phenotype correlation in idiopathic chronic pancreatitis and controls in Chinese by complete analysis. Clin Genet 2007; 71: 530-539
29. Prasad R, Sharma H, Kaur G. Molecular basis of cystic fibrosis disease: an Indian perspective. Indian J Clin Biochem 2010; 25: 335-341