The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip.
The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip.
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DOI：
10.1080/15592294.2022.2123898
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发表时间：
2022-12
期刊：
影响因子：
3.7
通讯作者：
Relton, Caroline
中科院分区：
文献类型：
--
作者：
Watkins, Sarah Holmes;Ho, Karen;Testa, Christian;Falk, Louise;Soule, Patrice;Nguyen, Linda, V;FitzGibbon, Sophie;Slack, Catherine;Chen, Jarvis T.;Smith, George Davey;De Vivo, Immaculata;Simpkin, Andrew J.;Tilling, Kate;Waterman, Pamela D.;Krieger, Nancy;Suderman, Matthew;Relton, Caroline
DNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilizing precious or limited DNA sources. We used a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip. We found that data are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; and that low DNA input is associated with a reduction in power to detect EWAS associations, requiring larger sample sizes. We conclude that DNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.
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影响因子：
4.6
作者：
Dugué PA;English DR;MacInnis RJ;Jung CH;Bassett JK;FitzGerald LM;Wong EM;Joo JE;Hopper JL;Southey MC;Giles GG;Milne RL
通讯作者：
Milne RL
影响因子：
3.7
作者：
Krieger, Nancy;Waterman, Pamela D.;Samuel, Latrice
通讯作者：
Samuel, Latrice
吸烟的表观遗传签名。
DOI：
10.1161/circgenetics.116.001506
发表时间：
2016-10
期刊：
Circulation. Cardiovascular genetics
影响因子：
--
作者：
Joehanes R;Just AC;Marioni RE;Pilling LC;Reynolds LM;Mandaviya PR;Guan W;Xu T;Elks CE;Aslibekyan S;Moreno-Macias H;Smith JA;Brody JA;Dhingra R;Yousefi P;Pankow JS;Kunze S;Shah SH;McRae AF;Lohman K;Sha J;Absher DM;Ferrucci L;Zhao W;Demerath EW;Bressler J;Grove ML;Huan T;Liu C;Mendelson MM;Yao C;Kiel DP;Peters A;Wang-Sattler R;Visscher PM;Wray NR;Starr JM;Ding J;Rodriguez CJ;Wareham NJ;Irvin MR;Zhi D;Barrdahl M;Vineis P;Ambatipudi S;Uitterlinden AG;Hofman A;Schwartz J;Colicino E;Hou L;Vokonas PS;Hernandez DG;Singleton AB;Bandinelli S;Turner ST;Ware EB;Smith AK;Klengel T;Binder EB;Psaty BM;Taylor KD;Gharib SA;Swenson BR;Liang L;DeMeo DL;O'Connor GT;Herceg Z;Ressler KJ;Conneely KN;Sotoodehnia N;Kardia SL;Melzer D;Baccarelli AA;van Meurs JB;Romieu I;Arnett DK;Ong KK;Liu Y;Waldenberger M;Deary IJ;Fornage M;Levy D;London SJ
通讯作者：
London SJ
影响因子：
2.5
作者：
Whalley C;Payne K;Domingo E;Blake A;Richman S;Brooks J;Batis N;Spruce R;S-CORT Consortium;Mehanna H;Nankivell P;Beggs AD
通讯作者：
Beggs AD
影响因子：
--
作者：
Battram, Thomas;Yousefi, Paul;Suderman, Matthew
通讯作者：
Suderman, Matthew