Detecting rare copy number variants from Illumina genotyping arrays with the CamCNV pipeline: Segmentation of z-scores improves detection and reliability.
Detecting rare copy number variants from Illumina genotyping arrays with the CamCNV pipeline: Segmentation of z-scores improves detection and reliability.
复制标题
DOI：
10.1002/gepi.22367
复制
发表时间：
2021-04
影响因子：
2.1
通讯作者：
Easton DF
中科院分区：
文献类型：
--
作者：
Dennis J;Walker L;Tyrer J;Michailidou K;Easton DF
来自基因分型阵列数据的强度可用于检测CNV，但数据中的高水平噪声和不同拷贝数强度分布之间的重叠产生不可靠的调用，特别是当CNV仅覆盖少数探针时。我们提出了一种新的管道（CamCNV），它具有一系列步骤来降低噪声并更可靠地检测覆盖少至三个探针的CNV。该管道旨在检测罕见的CNV（频率低于1%），用于大型队列的关联测试。该方法使用来自所有样品的信息将强度转换为z分数，从而调整探针之间的方差。我们通过在1000个基因组样本的基因分型中寻找来自1000个基因组项目的已知CNV来测试我们的管道的灵敏度。我们还比较了1，661对基因分型重复样本的CNV调用。在选定的平均z分数截止值，检测1000个基因组CNV的灵敏度对于缺失约为85%，对于重复约为65%。从重复中，我们估计缺失的错误发现率控制在约10%（超过5个探针时降至3%以下），重复的错误发现率控制在约28%。与PennCNV调用相比，该管道显示出提高的灵敏度，特别是对于仅覆盖几个探针的短缺失。对于每个调用的CNV，平均z分数是用于控制错误发现率的有用度量。
The intensities from genotyping array data can be used to detect CNVs but a high level of noise in the data and overlap between different copy-number intensity distributions produces unreliable calls, particularly when only a few probes are covered by the CNV. We present a novel pipeline (CamCNV) with a series of steps to reduce noise and detect more reliably CNVs covering as few as three probes. The pipeline aims to detect rare CNVs (below 1% frequency) for association tests in large cohorts. The method uses the information from all samples to convert intensities to z-scores, thus adjusting for variance between probes. We tested the sensitivity of our pipeline by looking for known CNVs from the 1000 Genomes project in our genotyping of 1000 Genomes samples. We also compared the CNV calls for 1,661 pairs of genotyped replicate samples. At the chosen mean z-score cut-off, sensitivity to detect the 1000 Genomes CNVs was approximately 85% for deletions and 65% for duplications. From the replicates we estimate the false discovery rate is controlled at ~10% for deletions (falling to below 3% with more than five probes) and ~28% for duplications. The pipeline demonstrates improved sensitivity when compared to calling with PennCNV, particularly for short deletions covering only a few probes. For each called CNV the mean z-score is a useful metric for controlling the false discovery rate.
登录
查看更多内容
DOI：
10.1192/bjp.bp.113.131052
发表时间：
2014-02
期刊：
The British journal of psychiatry : the journal of mental science
影响因子：
--
作者：
Rees E;Walters JT;Georgieva L;Isles AR;Chambert KD;Richards AL;Mahoney-Davies G;Legge SE;Moran JL;McCarroll SA;O'Donovan MC;Owen MJ;Kirov G
通讯作者：
Kirov G
影响因子：
64.8
作者：
Michailidou K;Lindström S;Dennis J;Beesley J;Hui S;Kar S;Lemaçon A;Soucy P;Glubb D;Rostamianfar A;Bolla MK;Wang Q;Tyrer J;Dicks E;Lee A;Wang Z;Allen J;Keeman R;Eilber U;French JD;Qing Chen X;Fachal L;McCue K;McCart Reed AE;Ghoussaini M;Carroll JS;Jiang X;Finucane H;Adams M;Adank MA;Ahsan H;Aittomäki K;Anton-Culver H;Antonenkova NN;Arndt V;Aronson KJ;Arun B;Auer PL;Bacot F;Barrdahl M;Baynes C;Beckmann MW;Behrens S;Benitez J;Bermisheva M;Bernstein L;Blomqvist C;Bogdanova NV;Bojesen SE;Bonanni B;Børresen-Dale AL;Brand JS;Brauch H;Brennan P;Brenner H;Brinton L;Broberg P;Brock IW;Broeks A;Brooks-Wilson A;Brucker SY;Brüning T;Burwinkel B;Butterbach K;Cai Q;Cai H;Caldés T;Canzian F;Carracedo A;Carter BD;Castelao JE;Chan TL;David Cheng TY;Seng Chia K;Choi JY;Christiansen H;Clarke CL;NBCS Collaborators;Collée M;Conroy DM;Cordina-Duverger E;Cornelissen S;Cox DG;Cox A;Cross SS;Cunningham JM;Czene K;Daly MB;Devilee P;Doheny KF;Dörk T;Dos-Santos-Silva I;Dumont M;Durcan L;Dwek M;Eccles DM;Ekici AB;Eliassen AH;Ellberg C;Elvira M;Engel C;Eriksson M;Fasching PA;Figueroa J;Flesch-Janys D;Fletcher O;Flyger H;Fritschi L;Gaborieau V;Gabrielson M;Gago-Dominguez M;Gao YT;Gapstur SM;García-Sáenz JA;Gaudet MM;Georgoulias V;Giles GG;Glendon G;Goldberg MS;Goldgar DE;González-Neira A;Grenaker Alnæs GI;Grip M;Gronwald J;Grundy A;Guénel P;Haeberle L;Hahnen E;Haiman CA;Håkansson N;Hamann U;Hamel N;Hankinson S;Harrington P;Hart SN;Hartikainen JM;Hartman M;Hein A;Heyworth J;Hicks B;Hillemanns P;Ho DN;Hollestelle A;Hooning MJ;Hoover RN;Hopper JL;Hou MF;Hsiung CN;Huang G;Humphreys K;Ishiguro J;Ito H;Iwasaki M;Iwata H;Jakubowska A;Janni W;John EM;Johnson N;Jones K;Jones M;Jukkola-Vuorinen A;Kaaks R;Kabisch M;Kaczmarek K;Kang D;Kasuga Y;Kerin MJ;Khan S;Khusnutdinova E;Kiiski JI;Kim SW;Knight JA;Kosma VM;Kristensen VN;Krüger U;Kwong A;Lambrechts D;Le Marchand L;Lee E;Lee MH;Lee JW;Neng Lee C;Lejbkowicz F;Li J;Lilyquist J;Lindblom A;Lissowska J;Lo WY;Loibl S;Long J;Lophatananon A;Lubinski J;Luccarini C;Lux MP;Ma ESK;MacInnis RJ;Maishman T;Makalic E;Malone KE;Kostovska IM;Mannermaa A;Manoukian S;Manson JE;Margolin S;Mariapun S;Martinez ME;Matsuo K;Mavroudis D;McKay J;McLean C;Meijers-Heijboer H;Meindl A;Menéndez P;Menon U;Meyer J;Miao H;Miller N;Taib NAM;Muir K;Mulligan AM;Mulot C;Neuhausen SL;Nevanlinna H;Neven P;Nielsen SF;Noh DY;Nordestgaard BG;Norman A;Olopade OI;Olson JE;Olsson H;Olswold C;Orr N;Pankratz VS;Park SK;Park-Simon TW;Lloyd R;Perez JIA;Peterlongo P;Peto J;Phillips KA;Pinchev M;Plaseska-Karanfilska D;Prentice R;Presneau N;Prokofyeva D;Pugh E;Pylkäs K;Rack B;Radice P;Rahman N;Rennert G;Rennert HS;Rhenius V;Romero A;Romm J;Ruddy KJ;Rüdiger T;Rudolph A;Ruebner M;Rutgers EJT;Saloustros E;Sandler DP;Sangrajrang S;Sawyer EJ;Schmidt DF;Schmutzler RK;Schneeweiss A;Schoemaker MJ;Schumacher F;Schürmann P;Scott RJ;Scott C;Seal S;Seynaeve C;Shah M;Sharma P;Shen CY;Sheng G;Sherman ME;Shrubsole MJ;Shu XO;Smeets A;Sohn C;Southey MC;Spinelli JJ;Stegmaier C;Stewart-Brown S;Stone J;Stram DO;Surowy H;Swerdlow A;Tamimi R;Taylor JA;Tengström M;Teo SH;Beth Terry M;Tessier DC;Thanasitthichai S;Thöne K;Tollenaar RAEM;Tomlinson I;Tong L;Torres D;Truong T;Tseng CC;Tsugane S;Ulmer HU;Ursin G;Untch M;Vachon C;van Asperen CJ;Van Den Berg D;van den Ouweland AMW;van der Kolk L;van der Luijt RB;Vincent D;Vollenweider J;Waisfisz Q;Wang-Gohrke S;Weinberg CR;Wendt C;Whittemore AS;Wildiers H;Willett W;Winqvist R;Wolk A;Wu AH;Xia L;Yamaji T;Yang XR;Har Yip C;Yoo KY;Yu JC;Zheng W;Zheng Y;Zhu B;Ziogas A;Ziv E;ABCTB Investigators;ConFab/AOCS Investigators;Lakhani SR;Antoniou AC;Droit A;Andrulis IL;Amos CI;Couch FJ;Pharoah PDP;Chang-Claude J;Hall P;Hunter DJ;Milne RL;García-Closas M;Schmidt MK;Chanock SJ;Dunning AM;Edwards SL;Bader GD;Chenevix-Trench G;Simard J;Kraft P;Easton DF
通讯作者：
Easton DF
影响因子：
30.8
作者：
McCarthy, Shane E.;Makarov, Vladimir;Kirov, George;Addington, Anjene M.;McClellan, Jon;Yoon, Seungtai;Perkins, Diana O.;Dickel, Diane E.;Kusenda, Mary;Krastoshevsky, Olga;Krause, Verena;Kumar, Ravinesh A.;Grozeva, Detelina;Malhotra, Dheeraj;Walsh, Tom;Zackai, Elaine H.;Kaplan, Paige;Ganesh, Jaya;Krantz, Ian D.;Spinner, Nancy B.;Roccanova, Patricia;Bhandari, Abhishek;Pavon, Kevin;Lakshmi, B.;Leotta, Anthony;Kendall, Jude;Lee, Yoon-ha;Vacic, Vladimir;Gary, Sydney;Iakoucheva, Lilia M.;Crow, Timothy J.;Christian, Susan L.;Lieberman, Jeffrey A.;Stroup, T. Scott;Lehtimaki, Terho;Puura, Kaija;Haldeman-Englert, Chad;Pearl, Justin;Goodell, Meredith;Willour, Virginia L.;DeRosse, Pamela;Steele, Jo;Kassem, Layla;Wolff, Jessica;Chitkara, Nisha;McMahon, Francis J.;Malhotra, Anil K.;Potash, James B.;Schulze, Thomas G.;Noethen, Markus M.;Cichon, Sven;Rietschel, Marcella;Leibenluft, Ellen;Kustanovich, Vlad;Lajonchere, Clara M.;Sutcliffe, James S.;Skuse, David;Gill, Michael;Gallagher, Louise;Mendell, Nancy R.;Craddock, Nick;Owen, Michael J.;O'Donovan, Michael C.;Shaikh, Tamim H.;Susser, Ezra;DeLisi, Lynn E.;Sullivan, Patrick F.;Deutsch, Curtis K.;Rapoport, Judith;Levy, Deborah L.;King, Mary-Claire;Sebat, Jonathan
通讯作者：
Sebat, Jonathan
影响因子：
64.8
作者：
Sudmant PH;Rausch T;Gardner EJ;Handsaker RE;Abyzov A;Huddleston J;Zhang Y;Ye K;Jun G;Fritz MH;Konkel MK;Malhotra A;Stütz AM;Shi X;Casale FP;Chen J;Hormozdiari F;Dayama G;Chen K;Malig M;Chaisson MJP;Walter K;Meiers S;Kashin S;Garrison E;Auton A;Lam HYK;Mu XJ;Alkan C;Antaki D;Bae T;Cerveira E;Chines P;Chong Z;Clarke L;Dal E;Ding L;Emery S;Fan X;Gujral M;Kahveci F;Kidd JM;Kong Y;Lameijer EW;McCarthy S;Flicek P;Gibbs RA;Marth G;Mason CE;Menelaou A;Muzny DM;Nelson BJ;Noor A;Parrish NF;Pendleton M;Quitadamo A;Raeder B;Schadt EE;Romanovitch M;Schlattl A;Sebra R;Shabalin AA;Untergasser A;Walker JA;Wang M;Yu F;Zhang C;Zhang J;Zheng-Bradley X;Zhou W;Zichner T;Sebat J;Batzer MA;McCarroll SA;1000 Genomes Project Consortium;Mills RE;Gerstein MB;Bashir A;Stegle O;Devine SE;Lee C;Eichler EE;Korbel JO
通讯作者：
Korbel JO
DOI：
10.1158/1055-9965.epi-16-0106
发表时间：
2017-01
期刊：
Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology
影响因子：
--
作者：
Amos CI;Dennis J;Wang Z;Byun J;Schumacher FR;Gayther SA;Casey G;Hunter DJ;Sellers TA;Gruber SB;Dunning AM;Michailidou K;Fachal L;Doheny K;Spurdle AB;Li Y;Xiao X;Romm J;Pugh E;Coetzee GA;Hazelett DJ;Bojesen SE;Caga-Anan C;Haiman CA;Kamal A;Luccarini C;Tessier D;Vincent D;Bacot F;Van Den Berg DJ;Nelson S;Demetriades S;Goldgar DE;Couch FJ;Forman JL;Giles GG;Conti DV;Bickeböller H;Risch A;Waldenberger M;Brüske-Hohlfeld I;Hicks BD;Ling H;McGuffog L;Lee A;Kuchenbaecker K;Soucy P;Manz J;Cunningham JM;Butterbach K;Kote-Jarai Z;Kraft P;FitzGerald L;Lindström S;Adams M;McKay JD;Phelan CM;Benlloch S;Kelemen LE;Brennan P;Riggan M;O'Mara TA;Shen H;Shi Y;Thompson DJ;Goodman MT;Nielsen SF;Berchuck A;Laboissiere S;Schmit SL;Shelford T;Edlund CK;Taylor JA;Field JK;Park SK;Offit K;Thomassen M;Schmutzler R;Ottini L;Hung RJ;Marchini J;Amin Al Olama A;Peters U;Eeles RA;Seldin MF;Gillanders E;Seminara D;Antoniou AC;Pharoah PD;Chenevix-Trench G;Chanock SJ;Simard J;Easton DF
通讯作者：
Easton DF