Prospective functional classification of all possible missense variants in PPARG.
Prospective functional classification of all possible missense variants in PPARG.
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DOI：
10.1038/ng.3700
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发表时间：
2016-12
期刊：
影响因子：
30.8
通讯作者：
Altshuler, David
中科院分区：
文献类型：
--
作者：
Majithia, Amit R.;Tsuda, Ben;Agostini, Maura;Gnanapradeepan, Keerthana;Rice, Robert;Peloso, Gina;Patel, Kashyap A.;Zhang, Xiaolan;Broekema, Marjoleine F.;Patterson, Nick;Duby, Marc;Sharpe, Ted;Kalkhoven, Eric;Rosen, Evan D.;Barroso, Ines;Ellard, Sian;Kathiresan, Sekar;O'Rahilly, Stephen;Chatterjee, Krishna;Florez, Jose C.;Mikkelsen, Tarjei;Savage, David B.;Altshuler, David
临床外显子组测序通常识别疾病相关基因中的错义变体，但很少进行功能表征，导致诊断不确定性。例如，PPARG突变导致孟德尔脂肪营养不良并增加2型糖尿病（T2D）的风险。虽然大约每500人中就有一人在PPARG中存在错义变体，但大多数都是未知的后果。为了前瞻性地表征PPAR γ变体，我们使用高度平行的寡核苷酸合成来构建编码所有9，595个可能的单个氨基酸取代的文库。我们在人巨噬细胞中开发了合并功能测定，实验性地评估了所有蛋白质变体，并使用实验数据通过监督机器学习来训练变体分类器（http：//www.example.com）。当应用于55种在基于人群和临床测序中鉴定的新型错义变体时，分类器将6种注释为致病性;这些随后通过单变体测定进行验证。饱和诱变和前瞻性的实验表征可以支持疾病相关基因中新发现的错义变异的即时诊断解释。
Clinical exome sequencing routinely identifies missense variants in disease-related genes, but functional characterization is rarely undertaken, leading to diagnostic uncertainty. For example, mutations in PPARG cause Mendelian lipodystrophy and increase risk of type 2 diabetes (T2D). While approximately one in 500 people harbor missense variants in PPARG, most are of unknown consequence. To prospectively characterize PPARγ variants we used highly parallel oligonucleotide synthesis to construct a library encoding all 9,595 possible single amino acid substitutions. We developed a pooled functional assay in human macrophages, experimentally evaluated all protein variants, and used the experimental data to train a variant classifier by supervised machine learning (http://miter.broadinstitute.org). When applied to 55 novel missense variants identified in population-based and clinical sequencing, the classifier annotated six as pathogenic; these were subsequently validated by single-variant assays. Saturation mutagenesis and prospective experimental characterization can support immediate diagnostic interpretation of newly discovered missense variants in disease-related genes.
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DOI：
10.1126/science.1219240
发表时间：
2012-07-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Tennessen JA;Bigham AW;O'Connor TD;Fu W;Kenny EE;Gravel S;McGee S;Do R;Liu X;Jun G;Kang HM;Jordan D;Leal SM;Gabriel S;Rieder MJ;Abecasis G;Altshuler D;Nickerson DA;Boerwinkle E;Sunyaev S;Bustamante CD;Bamshad MJ;Akey JM;Broad GO;Seattle GO;NHLBI Exome Sequencing Project
通讯作者：
NHLBI Exome Sequencing Project
影响因子：
48
作者：
Fowler, Douglas M.;Fields, Stanley
通讯作者：
Fields, Stanley
DOI：
10.1056/nejmoa1405386
发表时间：
2014-11-27
期刊：
The New England journal of medicine
影响因子：
--
作者：
Myocardial Infarction Genetics Consortium Investigators;Stitziel NO;Won HH;Morrison AC;Peloso GM;Do R;Lange LA;Fontanillas P;Gupta N;Duga S;Goel A;Farrall M;Saleheen D;Ferrario P;König I;Asselta R;Merlini PA;Marziliano N;Notarangelo MF;Schick U;Auer P;Assimes TL;Reilly M;Wilensky R;Rader DJ;Hovingh GK;Meitinger T;Kessler T;Kastrati A;Laugwitz KL;Siscovick D;Rotter JI;Hazen SL;Tracy R;Cresci S;Spertus J;Jackson R;Schwartz SM;Natarajan P;Crosby J;Muzny D;Ballantyne C;Rich SS;O'Donnell CJ;Abecasis G;Sunaev S;Nickerson DA;Buring JE;Ridker PM;Chasman DI;Austin E;Kullo IJ;Weeke PE;Shaffer CM;Bastarache LA;Denny JC;Roden DM;Palmer C;Deloukas P;Lin DY;Tang ZZ;Erdmann J;Schunkert H;Danesh J;Marrugat J;Elosua R;Ardissino D;McPherson R;Watkins H;Reiner AP;Wilson JG;Altshuler D;Gibbs RA;Lander ES;Boerwinkle E;Gabriel S;Kathiresan S
通讯作者：
Kathiresan S
影响因子：
30.8
作者：
Flannick J;Beer NL;Bick AG;Agarwala V;Molnes J;Gupta N;Burtt NP;Florez JC;Meigs JB;Taylor H;Lyssenko V;Irgens H;Fox E;Burslem F;Johansson S;Brosnan MJ;Trimmer JK;Newton-Cheh C;Tuomi T;Molven A;Wilson JG;O'Donnell CJ;Kathiresan S;Hirschhorn JN;Njølstad PR;Rolph T;Seidman JG;Gabriel S;Cox DR;Seidman CE;Groop L;Altshuler D
通讯作者：
Altshuler D
影响因子：
3.3
作者：
Starita, Lea M.;Young, David L.;Fields, Stanley
通讯作者：
Fields, Stanley