Erratum: Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis (The American Journal of Human Genetics (2017) 101(2) (227–238), (S000292971730277X), (10.1016/j.ajhg.2017.06.014));Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis

American Journal of Human Genetics

Volumn 101, Issue 2, 2017, Pages 227-238

  Manousaki, Despoina ^a,b   Dudding, Tom ^c   Haworth, Simon ^c   Hsu, Yi Hsiang ^d,e,f   Liu, Ching Ti ^g   Medina Gómez, Carolina ^h   Voortman, Trudy ^h   van der Velde, Nathalie ^h,i   Melhus, Håkan ^j   Robinson Cohen, Cassianne ^k   Cousminer, Diana L ^l,m   Nethander, Maria ⁿ   Vandenput, Liesbeth ⁿ   Noordam, Raymond ^o   Forgetta, Vincenzo ^a,b   Greenwood, Celia M T ^a,b   Biggs, Mary L ^k   Psaty, Bruce M ^k,p   Rotter, Jerome I ^q,r   Zemel, Babette S ^l,m   Mitchell, Jonathan A ^l,m   Taylor, Bruce ^s   Lorentzon, Mattias ^n,t   Karlsson, Magnus ^u,v   Jaddoe, Vincent V W ^h   Tiemeier, Henning ^h   Campos Obando, Natalia ^h   Franco, Oscar H ^h   Utterlinden, Andre G ^h   Broer, Linda ^h   van Schoor, Natasja M ^w   Ham, Annelies C ^h   Ikram, M Arfan ^h   Karasik, David ^d   de Mutsert, Renée ^o   Rosendaal, Frits R ^o   den Heijer, Martin ^w   Wang, Thomas J ^x   Lind, Lars ^j   Orwoll, Eric S ^y   Mook Kanamori, Dennis O ^o   Michaëlsson, Karl ^j   Kestenbaum, Bryan ^k   Ohlsson, Claes ⁿ   Mellström, Dan ⁿ   de Groot, Lisette C P G M ^z   Grant, Struan F A ^l,m   Kiel, Douglas P ^d,e,f,aa   Zillikens, M Carola ^h   Rivadeneira, Fernando ^h   Sawcer, Stephen ^ab   Timpson, Nicholas J ^c   Richards, J Brent ^a,b,ac   more..

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c UNIVERSITY OF BRISTOL   (United Kingdom)

^d Hebrew Senior Life   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^g BOSTON UNIVERSITY SCHOOL OF PUBLIC HEALTH   (United States)

^h ERASMUS MEDICAL CENTER   (Netherlands)

ⁱ ACADEMIC MEDICAL CENTER   (Netherlands)

^j UPPSALA UNIVERSITY   (Sweden)

^k UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^l CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^m UNIVERSITY OF PENNSYLVANIA   (United States)

ⁿ UNIVERSITY OF GOTHENBURG   (Sweden)

^o LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^p KAISER PERMANENTE   (United States)

^q LOS ANGELES BIOMEDICAL RESEARCH INSTITUTE   (United States)

^r HARBOR UCLA MEDICAL CENTER   (United States)

^s UNIVERSITY OF TASMANIA   (Australia)

^t SAHLGRENSKA UNIVERSITY HOSPITAL   (Sweden)

^u LUND UNIVERSITY   (Sweden)

^v LUND UNIVERSITY HOSPITAL   (Sweden)

^w VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^x VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^y OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^z WAGENINGEN UNIVERSITY   (Netherlands)

^aa BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^ab UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^ac KING'S COLLEGE LONDON   (United Kingdom)

more..

Author keywords

GWAS; low frequency genetic variants; multiple sclerosis; vitamin D

Indexed keywords

25 HYDROXYVITAMIN D; ADENINE; ASPARTIC ACID; GUANINE; 25-HYDROXYVITAMIN D; CHOLESTANETRIOL 26 MONOOXYGENASE; CYP2R1 PROTEIN, HUMAN; CYTOCHROME P450 FAMILY 2; VITAMIN D;

ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; CYP2R1 GENE; GENE; GENE FREQUENCY; GENETIC VARIATION; GENOTYPE; HETEROZYGOTE; HUMAN; MULTIPLE SCLEROSIS; PATHOGENESIS; PRIORITY JOURNAL; VITAMIN D DEFICIENCY; WHOLE GENOME SEQUENCING; ANALOGS AND DERIVATIVES; BLOOD; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME; META ANALYSIS; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM;

CHOLESTANETRIOL 26-MONOOXYGENASE; CYTOCHROME P450 FAMILY 2; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MULTIPLE SCLEROSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; VITAMIN D; VITAMIN D DEFICIENCY;

EID: 85026218390     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2018.11.010     Document Type: Erratum

References (36)

1. Forrest, K.Y., Stuhldreher, W.L., Prevalence and correlates of vitamin D deficiency in US adults. Nutr. Res. 31 (2011), 48–54.
2. Rosen, C.J., Adams, J.S., Bikle, D.D., Black, D.M., Demay, M.B., Manson, J.E., Murad, M.H., Kovacs, C.S., The nonskeletal effects of vitamin D: an Endocrine Society scientific statement. Endocr. Rev. 33 (2012), 456–492.
3. Shea, M.K., Benjamin, E.J., Dupuis, J., Massaro, J.M., Jacques, P.F., D'Agostino, R.B. Sr., Ordovas, J.M., O'Donnell, C.J., Dawson-Hughes, B., Vasan, R.S., Booth, S.L., Genetic and non-genetic correlates of vitamins K and D. Eur. J. Clin. Nutr. 63 (2009), 458–464.
4. Livshits, G., Karasik, D., Seibel, M.J., Statistical genetic analysis of plasma levels of vitamin D: familial study. Ann. Hum. Genet. 63 (1999), 429–439.
5. Wang, T.J., Zhang, F., Richards, J.B., Kestenbaum, B., van Meurs, J.B., Berry, D., Kiel, D.P., Streeten, E.A., Ohlsson, C., Koller, D.L., et al. Common genetic determinants of vitamin D insufficiency: a genome-wide association study. Lancet 376 (2010), 180–188.
6. Sidore, C., Busonero, F., Maschio, A., Porcu, E., Naitza, S., Zoledziewska, M., Mulas, A., Pistis, G., Steri, M., Danjou, F., et al. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat. Genet. 47 (2015), 1272–1281.
7. Zheng, H.F., Forgetta, V., Hsu, Y.H., Estrada, K., Rosello-Diez, A., Leo, P.J., Dahia, C.L., Park-Min, K.H., Tobias, J.H., Kooperberg, C., et al. AOGC Consortium, UK10K Consortium. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. Nature 526 (2015), 112–117.
8. Cohen, J.C., Kiss, R.S., Pertsemlidis, A., Marcel, Y.L., McPherson, R., Hobbs, H.H., Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305 (2004), 869–872.
9. Huang, J., Howie, B., McCarthy, S., Memari, Y., Walter, K., Min, J.L., Danecek, P., Malerba, G., Trabetti, E., Zheng, H.F., et al., UK10K Consortium. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nat. Commun., 6, 2015, 8111.
10. Mokry, L.E., Ross, S., Ahmad, O.S., Forgetta, V., Smith, G.D., Goltzman, D., Leong, A., Greenwood, C.M., Thanassoulis, G., Richards, J.B., Vitamin D and Risk of Multiple Sclerosis: A Mendelian Randomization Study. PLoS Med., 12, 2015, e1001866.
11. Walter, K., Min, J.L., Huang, J., Crooks, L., Memari, Y., McCarthy, S., Perry, J.R., Xu, C., Futema, M., Lawson, D., et al., UK10K Consortium. The UK10K project identifies rare variants in health and disease. Nature 526 (2015), 82–90.
12. Li, H., A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27 (2011), 2987–2993.
13. Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al., 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics 27 (2011), 2156–2158.
14. DePristo, M.A., Banks, E., Poplin, R., Garimella, K.V., Maguire, J.R., Hartl, C., Philippakis, A.A., del Angel, G., Rivas, M.A., Hanna, M., et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43 (2011), 491–498.
15. McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A.R., Teumer, A., Kang, H.M., Fuchsberger, C., Danecek, P., Sharp, K., et al., Haplotype Reference Consortium. A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48 (2016), 1279–1283.
16. Mägi, R., Morris, A.P., GWAMA: software for genome-wide association meta-analysis. BMC Bioinformatics, 11, 2010, 288.
17. Xu, C., Tachmazidou, I., Walter, K., Ciampi, A., Zeggini, E., Greenwood, C.M., UK10K Consortium. Estimating genome-wide significance for whole-genome sequencing studies. Genet. Epidemiol. 38 (2014), 281–290.
18. Yang, J., Lee, S.H., Goddard, M.E., Visscher, P.M., GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88 (2011), 76–82.
19. Team, R.C., R: A language and environment for statistical computing. 2013, R Foundation for Statistical Computing.
20. Aragon, T.J., Wollschlaeger, D., and Omidpanah, A. (2017). epitools: Epidemiology Tools. https://cran.r-project.org/package=epitools.
21. Viechtbauer, W., Conducting meta-analyses in R with the metafor package. J. Stat. Softw. 36 (2010), 1–48.
22. Sudlow, C., Gallacher, J., Allen, N., Beral, V., Burton, P., Danesh, J., Downey, P., Elliott, P., Green, J., Landray, M., et al. UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med., 12, 2015, e1001779.
23. Hafler, D.A., Compston, A., Sawcer, S., Lander, E.S., Daly, M.J., De Jager, P.L., de Bakker, P.I., Gabriel, S.B., Mirel, D.B., Ivinson, A.J., et al., International Multiple Sclerosis Genetics Consortium. Risk alleles for multiple sclerosis identified by a genomewide study. N. Engl. J. Med. 357 (2007), 851–862.
24. Australia and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene). Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20. Nat. Genet. 41 (2009), 824–828.
25. Anderson, C.A., Pettersson, F.H., Clarke, G.M., Cardon, L.R., Morris, A.P., Zondervan, K.T., Data quality control in genetic case-control association studies. Nat. Protoc. 5 (2010), 1564–1573.
26. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., Reich, D., Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38 (2006), 904–909.
27. Patterson, N., Price, A.L., Reich, D., Population structure and eigenanalysis. PLoS Genet., 2, 2006, e190.
28. Auton, A., Brooks, L.D., Durbin, R.M., Garrison, E.P., Kang, H.M., Korbel, J.O., Marchini, J.L., McCarthy, S., McVean, G.A., Abecasis, G.R., 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526 (2015), 68–74.
29. Loh, P.R., Danecek, P., Palamara, P.F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G.R., et al. Reference-based phasing using the Haplotype Reference Consortium panel. Nat. Genet. 48 (2016), 1443–1448.
30. Durbin, R., Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). Bioinformatics 30 (2014), 1266–1272.
31. Marchini, J., Howie, B., Myers, S., McVean, G., Donnelly, P., A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39 (2007), 906–913.
32. Cheng, J.B., Levine, M.A., Bell, N.H., Mangelsdorf, D.J., Russell, D.W., Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase. Proc. Natl. Acad. Sci. USA 101 (2004), 7711–7715.
33. Beecham, A.H., Patsopoulos, N.A., Xifara, D.K., Davis, M.F., Kemppinen, A., Cotsapas, C., Shah, T.S., Spencer, C., Booth, D., Goris, A., et al. International Multiple Sclerosis Genetics Consortium (IMSGC) Wellcome Trust Case Control Consortium 2 (WTCCC2), International IBD Genetics Consortium (IIBDGC). Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat. Genet. 45 (2013), 1353–1360.
34. Casella, S.J., Reiner, B.J., Chen, T.C., Holick, M.F., Harrison, H.E., A possible genetic defect in 25-hydroxylation as a cause of rickets. J. Pediatr. 124 (1994), 929–932.
35. Barresi, C., Stremnitzer, C., Mlitz, V., Kezic, S., Kammeyer, A., Ghannadan, M., Posa-Markaryan, K., Selden, C., Tschachler, E., Eckhart, L., Increased sensitivity of histidinemic mice to UVB radiation suggests a crucial role of endogenous urocanic acid in photoprotection. J. Invest. Dermatol. 131 (2011), 188–194.
36. Suchi, M., Sano, H., Mizuno, H., Wada, Y., Molecular cloning and structural characterization of the human histidase gene (HAL). Genomics 29 (1995), 98–104.