Re-Sequencing of the APOL1 - APOL4 and MYH9 Gene Regions in African Americans Does Not Identify Additional Risks for CKD Progression

American Journal of Nephrology

Volumn 42, Issue 2, 2015, Pages 99-106

  Hawkins, Gregory A ^a,b   Friedman, David J ^e   Lu, Lingyi ^a,c   McWilliams, David R ^a,c   Chou, Jeff W ^a,c   Sajuthi, Satria ^a,c   Divers, Jasmin ^a,c   Parekh, Rulan S ^g   Li, Man ^h   Genovese, Giulio ^f   Pollack, Martin R ^e   Hicks, Pamela J ^d   Bowden, Donald W ^b,d   Ma, Lijun ^a,b   Freedman, Barry I ^a,b   Langefeld, Carl D ^a,b  

^a Center for Public Health Genomics   (United States)

^b WAKE FOREST SCHOOL OF MEDICINE   (United States)

^c Department of Biostatistical Sciences ^*  (United States)

^d Center for Clinical Research   (United States)

^e BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

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

^g HOSPITAL FOR SICK CHILDREN   (Canada)

^h JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

African Americans; APOL1; DNA sequencing; FSGS; Genetics; Kidney disease

Indexed keywords

CREATININE; APOL1 PROTEIN, HUMAN; APOL2 PROTEIN, HUMAN; APOL3 PROTEIN, HUMAN; APOL4 PROTEIN, HUMAN; APOLIPOPROTEIN; HIGH DENSITY LIPOPROTEIN; MOLECULAR MOTOR; MYH9 PROTEIN, HUMAN; MYOSIN HEAVY CHAIN;

ADULT; AFRICAN AMERICAN; ALLELE; APOLIPOPROTEIN L1 GENE; APOLIPOPROTEIN L2 GENE; APOLIPOPROTEIN L3 GENE; APOLIPOPROTEIN L4 GENE; ARTICLE; BODY MASS; CHRONIC KIDNEY DISEASE; CONTROLLED STUDY; CREATININE BLOOD LEVEL; DISEASE COURSE; DISEASE DURATION; FEMALE; GENE; GENE DELETION; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; INDEL MUTATION; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; MYH9 GENE; PRIORITY JOURNAL; RENAL REPLACEMENT THERAPY; SINGLE NUCLEOTIDE POLYMORPHISM; UREA NITROGEN BLOOD LEVEL; AGED; CHRONIC KIDNEY FAILURE; COMPLICATION; DNA SEQUENCE; FOCAL GLOMERULOSCLEROSIS; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; HIV ASSOCIATED NEPHROPATHY; LUPUS ERYTHEMATOSUS NEPHRITIS; NEPHRITIS; RENAL INSUFFICIENCY, CHRONIC; RENOVASCULAR HYPERTENSION; SICKLE CELL ANEMIA;

ADULT; AFRICAN AMERICANS; AGED; AIDS-ASSOCIATED NEPHROPATHY; ANEMIA, SICKLE CELL; APOLIPOPROTEINS; DISEASE PROGRESSION; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GLOMERULOSCLEROSIS, FOCAL SEGMENTAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; HYPERTENSION, RENAL; KIDNEY FAILURE, CHRONIC; LIPOPROTEINS, HDL; LUPUS NEPHRITIS; MALE; MIDDLE AGED; MOLECULAR MOTOR PROTEINS; MYOSIN HEAVY CHAINS; NEPHRITIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RENAL INSUFFICIENCY, CHRONIC; SEQUENCE ANALYSIS, DNA;

EID: 84941211994     PISSN: 02508095     EISSN: 14219670     Source Type: Journal    
DOI: 10.1159/000439448     Document Type: Article

References (26)

1. Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI, Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, Bernhardy AJ, Hicks PJ, Nelson GW, Vanhollebeke B, Winkler CA, Kopp JB, Pays E, Pollak MR: Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 2010; 329: 841-845.
2. Palmer ND, Freedman BI: APOL1 and progression of nondiabetic nephropathy. J Am Soc Nephrol 2013; 24: 1344-1346.
3. Tzur S, Rosset S, Shemer R, Yudkovsky G, Selig S, Tarekegn A, Bekele E, Bradman N, Wasser WG, Behar DM, Skorecki K: Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene. Hum Genet 2010; 128: 345-350.
4. Freedman BI, Langefeld CD, Andringa KK, Croker JA, Williams AH, Garner NE, Birmingham DJ, Hebert LA, Hicks PJ, Segal MS, Edberg JC, Brown EE, Alarcón GS, Costenbader KH, Comeau ME, Criswell LA, Harley JB, James JA, Kamen DL, Lim SS, Merrill JT, Sivils KL, Niewold TB, Patel NM, Petri M, Ramsey-Goldman R, Reveille JD, Salmon JE, Tsao BP, Gibson KL, Byers JR, Vinnikova AK, Lea JP, Julian BA, Kimberly RP: Endstage renal disease in African Americans with lupus nephritis is associated with APOL1. Arthritis Rheumatol 2014; 66: 390-396.
5. Kanji Z, Powe CE, Wenger JB, Huang C, Ankers E, Sullivan DA, Collerone G, Powe NR, Tonelli M, Bhan I, Bernhardy AJ, Dibartolo S, Friedman D, Genovese G, Pollak MR, Thadhani R: Genetic variation in APOL1 associates with younger age at hemodialysis initiation. J Am Soc Nephrol 2011; 22: 2091-2097.
6. Tzur S, Rosset S, Skorecki K, Wasser WG: APOL1 allelic variants are associated with lower age of dialysis initiation and thereby increased dialysis vintage in African and Hispanic Americans with non-diabetic end-stage kidney disease. Nephrol Dial Transplant 2012; 27: 1498-1505.
7. Freedman BI, Skorecki K: Gene-gene and gene-environment interactions in apolipoprotein L1 gene-associated nephropathy. Clin J Am Soc Nephrol 2014; 9: 2006-2013.
8. Kopp JB, Nelson GW, Sampath K, Johnson RC, Genovese G, An P, Friedman D, Briggs W, Dart R, Korbet S, Mokrzycki MH, Kimmel PL, Limou S, Ahuja TS, Berns JS, Fryc J, Simon EE, Smith MC, Trachtman H, Michel DM, Schelling JR, Vlahov D, Pollak M, Winkler CA: APOL1 genetic variants in focal segmental glomerulosclerosis and HIV-associated nephropathy. J Am Soc Nephrol 2011; 22: 2129-2137.
9. Ashley-Koch AE, Okocha EC, Garrett ME, Soldano K, De Castro LM, Jonassaint JC, Orringer EP, Eckman JR, Telen MJ: MYH9 and APOL1 are both associated with sickle cell disease nephropathy. Br J Haematol 2011; 155: 386-394.
10. Larsen CP, Beggs ML, Saeed M, Walker PD: Apolipoprotein L1 risk variants associate with systemic lupus erythematosus-associated collapsing glomerulopathy. J Am Soc Nephrol 2013; 24: 722-725.
11. Lipkowitz MS, Freedman BI, Langefeld CD, Comeau ME, Bowden DW, Kao WH, Astor BC, Bottinger EP, Iyengar SK, Klotman PE, Freedman RG, Zhang W, Parekh RS, Choi MJ, Nelson GW, Winkler CA, Kopp JB: Apolipoprotein L1 gene variants associate with hypertension-attributed nephropathy and the rate of kidney function decline in African Americans. Kidney Int 2013; 83: 114-120.
12. Parsa A, Kao WH, Xie D, Astor BC, Li M, Hsu CY, Feldman HI, Parekh RS, Kusek JW, Greene TH, Fink JC, Anderson AH, Choi MJ, Wright JT Jr, Lash JP, Freedman BI, Ojo A, Winkler CA, Raj DS, Kopp JB, He J, Jensvold NG, Tao K, Lipkowitz MS, Appel LJ: APOL1 risk variants, race, and progression of chronic kidney disease. N Engl J Med 2013; 369: 2183-2196.
13. Cheng W, Zhou X, Zhu L, Shi S, Lv J, Liu L, Zhang H: Polymorphisms in the nonmuscle myosin heavy chain 9 gene (MYH9) are associated with the progression of IgA nephropathy in Chinese. Nephrol Dial Transplant 2011; 26: 2544-2549.
14. Cooke JN, Bostrom MA, Hicks PJ, Ng MC, Hellwege JN, Comeau ME, Divers J, Langefeld CD, Freedman BI, Bowden DW: Polymorphisms in MYH9 are associated with diabetic nephropathy in European Americans. Nephrol Dial Transplant 2012; 27: 1505-1511.
15. Kopp JB, Smith MW, Nelson GW, Johnson RC, Freedman BI, Bowden DW, Oleksyk T, McKenzie LM, Kajiyama H, Ahuja TS, Berns JS, Briggs W, Cho ME, Dart RA, Kimmel PL, Korbet SM, Michel DM, Mokrzycki MH, Schelling JR, Simon E, Trachtman H, Vlahov D, Winkler CA: MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis. Nat Genet 2008; 40: 1175-1184.
16. O'Seaghdha CM, Parekh RS, Hwang SJ, Li M, Köttgen A, Coresh J, Yang Q, Fox CS, Kao WH: The MYH9/APOL1 region and chronic kidney disease in European-Americans. Hum Mol Genet 2011; 20: 2450-2456.
17. Pattaro C, Köttgen A, Teumer A, Garnaas M, Böger CA, Fuchsberger C, Olden M, Chen MH, Tin A, Taliun D, Li M, Gao X, Gorski M, Yang Q, Hundertmark C, Foster MC, O'Seaghdha CM, Glazer N, Isaacs A, Liu CT, Smith AV, O'Connell JR, Struchalin M, Tanaka T, Li G, Johnson AD, Gierman HJ, Feitosa M, Hwang SJ, Atkinson EJ, Lohman K, Cornelis MC, Johansson Å, Tönjes A, Dehghan A, Chouraki V, Holliday EG, Sorice R, Kutalik Z, Lehtimäki T, Esko T, Deshmukh H, Ulivi S, Chu AY, Murgia F, Trompet S, Imboden M, Kollerits B, Pistis G, Harris TB, Launer LJ, Aspelund T, Eiriksdottir G, Mitchell BD, Boerwinkle E, Schmidt H, Cavalieri M, Rao M, Hu FB, Demirkan A, Oostra BA, de Andrade M, Turner ST, Ding J, Andrews JS, Freedman BI, Giulianini F, Koenig W, Illig T, Döring A, Wichmann HE, Kolcic I, Zemunik T, Boban M, Minelli C, Wheeler HE, Igl W, Zaboli G, Wild SH, Wright AF, Campbell H, Ellinghaus D, Nöthlings U, Jacobs G, Biffar R, Endlich K, Ernst F, Homuth G, Kroemer HK, Nauck M, Stracke S, Völker U, Völzke H, Kovacs P, Stumvoll M, Mägi R, Hofman A, Uitterlinden AG, Rivadeneira F, Aulchenko YS, Polasek O, Hastie N, Vitart V, Helmer C, Wang JJ, Ruggiero D, Bergmann S, Kähönen M, Viikari J, Nikopensius T, Province M, Ketkar S, Colhoun H, Doney A, Robino A, Giulianini F, Krämer BK, Portas L, Ford I, Buckley BM, Adam M, Thun GA, Paulweber B, Haun M, Sala C, Metzger M, Mitchell P, Ciullo M, Kim SK, Vollenweider P, Raitakari O, Metspalu A, Palmer C, Gasparini P, Pirastu M, Jukema JW, Probst-Hensch NM, Kronenberg F, Toniolo D, Gudnason V, Shuldiner AR, Coresh J, Schmidt R, Ferrucci L, Siscovick DS, van Duijn CM, Borecki I, Kardia SL, Liu Y, Curhan GC, Rudan I, Gyllensten U, Wilson JF, Franke A, Pramstaller PP, Rettig R, Prokopenko I, Witteman JC, Hayward C, Ridker P, Parsa A, Bochud M, Heid IM, Goessling W, Chasman DI, Kao WH, Fox CS: Genomewide association and functional follow-up reveals new loci for kidney function. PLoS Genet 2012; 8:e1002584.
18. Iyengar SK, Abboud HE, Goddard KA, Saad MF, Adler SG, Arar NH, Bowden DW, Duggirala R, Elston RC, Hanson RL, Ipp E, Kao WH, Kimmel PL, Klag MJ, Knowler WC, Meoni LA, Nelson RG, Nicholas SB, Pahl MV, Parekh RS, Quade SR, Rich SS, Rotter JI, Scavini M, Schelling JR, Sedor JR, Sehgal AR, Shah VO, Smith MW, Taylor KD, Winkler CA, Zager PG, Freedman BI: Genomewide scans for diabetic nephropathy and albuminuria in multiethnic populations: the family investigation of nephropathy and diabetes (FIND). Diabetes 2007; 56: 1577-1585.
19. Knowler WC, Coresh J, Elston RC, Freedman BI, Iyengar SK, Kimmel PL, Olson JM, Plaetke R, Sedor JR, Seldin MF: The family investigation of nephropathy and diabetes (FIND): design and methods. J Diabetes Complications 2005; 19: 1-9.
20. Freedman BI, Langefeld CD, Turner J, Núñez M, High KP, Spainhour M, Hicks PJ, Bowden DW, Reeves-Daniel AM, Murea M, Rocco MV, Divers J: Association of APOL1 variants with mild kidney disease in the first-degree relatives of African American patients with non-diabetic end-stage renal disease. Kidney Int 2012; 82: 805-811.
21. Tang H, Peng J, Wang P, Risch NJ: Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 2005; 28: 289-301.
22. Limou S, Nelson GW, Lecordier L, An P, O'Huigin CS, David VA, Binns-Roemer EA, Guiblet WM, Oleksyk TK, Pays E, Kopp JB, Winkler CA: Sequencing rare and common APOL1 coding variants to determine kidney disease risk. Kidney Int 2015, Epub ahead of print.
23. Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, Blangero J, Bowden DW, Brandslund I, Brosnan J, Burslem F, Chambers J, Cho YS, Christensen C, Douglas DA, Duggirala R, Dymek Z, Farjoun Y, Fennell T, Fontanillas P, Forsén T, Gabriel S, Glaser B, Gudbjartsson DF, Hanis C, Hansen T, Hreidarsson AB, Hveem K, Ingelsson E, Isomaa B, Johansson S, Jørgensen T, Jørgensen ME, Kathiresan S, Kong A, Kooner J, Kravic J, Laakso M, Lee JY, Lind L, Lindgren CM, Linneberg A, Masson G, Meitinger T, Mohlke KL, Molven A, Morris AP, Potluri S, Rauramaa R, Ribel-Madsen R, Richard AM, Rolph T, Salomaa V, Segrè AV, Skärstrand H, Steinthorsdottir V, Stringham HM, Sulem P, Tai ES, Teo YY, Teslovich T, Thorsteinsdottir U, Trimmer JK, Tuomi T, Tuomilehto J, Vaziri-Sani F, Voight BF, Wilson JG, Boehnke M, McCarthy MI, Njølstad PR, Pedersen O; Go-T2D Consortium; T2DGENES Consortium, Groop L, Cox DR, Stefansson K, Altshuler D: Loss-of-function mutations in SLC30A8 protect against type 2 diabetes. Nat Genet 2014; 46: 357-363.
24. Genovese G, Friedman DJ, Pollak MR: APOL1 variants and kidney disease in people of recent African ancestry. Nat Rev Nephrol 2013; 9: 240-244.
25. Ruchi R, Genovese G, Lee J, Charoonratana VT, Bernhardy AJ, Alper SL, Kopp JB, Thadhani R, Friedman DJ, Pollak MR: Copy number variation at the APOL1 locus. PLoS One 2015; 10:e0125410.
26. Khatua AK, Cheatham AM, Kruzel ED, Singhal PC, Skorecki K, Popik W: Exon 4-encoded sequence is a major determinant of cytotoxicity of apolipoprotein L1. Am J Physiol Cell Physiol 2015; 309:C22-C37.