Bayesian copy number detection and association in large-scale studies

go back to reference Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S, Hurles ME. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol. 2007; 8(10):228. https://doi.org/10.1186/gb-2007-8-10-r228. Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S, Hurles ME. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol. 2007; 8(10):228. https://​doi.​org/​10.​1186/​gb-2007-8-10-r228.

go back to reference Pugh TJ, Delaney AD, Farnoud N, Flibotte S, Griffith M, Li HI, Qian H, Farinha P, Gascoyne RD, Marra MA. Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Res. 2008; 36(13):80. https://doi.org/10.1093/nar/gkn378. Pugh TJ, Delaney AD, Farnoud N, Flibotte S, Griffith M, Li HI, Qian H, Farinha P, Gascoyne RD, Marra MA. Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Res. 2008; 36(13):80. https://​doi.​org/​10.​1093/​nar/​gkn378.

go back to reference Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H., Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res. 2008; 36(19):126. https://doi.org/10.1093/nar/gkn556. Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H., Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res. 2008; 36(19):126. https://​doi.​org/​10.​1093/​nar/​gkn556.

go back to reference van de Wiel MA, Brosens R, Eilers PHC, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B. Smoothing waves in array CGH tumor profiles. Bioinformatics (Oxford, England). 2009; 25:1099–104. https://doi.org/10.1093/bioinformatics/btp132. van de Wiel MA, Brosens R, Eilers PHC, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B. Smoothing waves in array CGH tumor profiles. Bioinformatics (Oxford, England). 2009; 25:1099–104. https://​doi.​org/​10.​1093/​bioinformatics/​btp132.

go back to reference Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res. 2012; 40(10):72. https://doi.org/10.1093/nar/gks001. Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res. 2012; 40(10):72. https://​doi.​org/​10.​1093/​nar/​gks001.

go back to reference Leo A, Walker AM, Lebo MS, Hendrickson B, Scholl T, Akmaev VR. A GC-wave correction algorithm that improves the analytical performance of aCGH. J Mol Diagn JMD. 2012; 14:550–9. https://doi.org/10.1016/j.jmoldx.2012.06.002.PubMed Leo A, Walker AM, Lebo MS, Hendrickson B, Scholl T, Akmaev VR. A GC-wave correction algorithm that improves the analytical performance of aCGH. J Mol Diagn JMD. 2012; 14:550–9. https://​doi.​org/​10.​1016/​j.​jmoldx.​2012.​06.​002.PubMed

go back to reference Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genetics. 2008; 40(10):1253–60. https://doi.org/10.1038/ng.237.PubMedPubMedCentral Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genetics. 2008; 40(10):1253–60. https://​doi.​org/​10.​1038/​ng.​237.PubMedPubMedCentral

go back to reference Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D, Hurles ME. Nature Genetics. 2008; 40(10):1245–52. https://doi.org/10.1038/ng.206. Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D, Hurles ME. Nature Genetics. 2008; 40(10):1245–52. https://​doi.​org/​10.​1038/​ng.​206.

go back to reference Cardin N, Holmes C, W.T.C.C.C, Donnelly P, Marchini J.Bayesian hierarchical mixture modeling to assign copy number from a targeted cnv array. Genet Epidemiol. 2011; 35(6):536–548. https://doi.org/10.1002/gepi.20604.PubMedPubMedCentral Cardin N, Holmes C, W.T.C.C.C, Donnelly P, Marchini J.Bayesian hierarchical mixture modeling to assign copy number from a targeted cnv array. Genet Epidemiol. 2011; 35(6):536–548. https://​doi.​org/​10.​1002/​gepi.​20604.PubMedPubMedCentral

go back to reference Kumasaka N, Fujisawa H, Hosono N, Okada Y, Takahashi A, Nakamura Y, Kubo M, Kamatani N. Platinumcnv: a bayesian gaussian mixture model for genotyping copy number polymorphisms using snp array signal intensity data. Genet Epidemiol. 2011; 35(8):831–44. https://doi.org/10.1002/gepi.20633.PubMed Kumasaka N, Fujisawa H, Hosono N, Okada Y, Takahashi A, Nakamura Y, Kubo M, Kamatani N. Platinumcnv: a bayesian gaussian mixture model for genotyping copy number polymorphisms using snp array signal intensity data. Genet Epidemiol. 2011; 35(8):831–44. https://​doi.​org/​10.​1002/​gepi.​20633.PubMed

go back to reference Fromer M, Moran JL, Chambert K, Banks E, Bergen SE, Ruderfer DM, Handsaker RE, McCarroll SA, O’Donovan MC, Owen M. J., Kirov G, Sullivan PF, Hultman CM, Sklar P, Purcell SM. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am J Hum Genet. 2012; 91(4):597–607. https://doi.org/10.1016/j.ajhg.2012.08.005.PubMedPubMedCentral Fromer M, Moran JL, Chambert K, Banks E, Bergen SE, Ruderfer DM, Handsaker RE, McCarroll SA, O’Donovan MC, Owen M. J., Kirov G, Sullivan PF, Hultman CM, Sklar P, Purcell SM. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am J Hum Genet. 2012; 91(4):597–607. https://​doi.​org/​10.​1016/​j.​ajhg.​2012.​08.​005.PubMedPubMedCentral

go back to reference Packer JS, Maxwell EK, O’Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG. CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data. Bioinformatics. 2016; 32(1):133–5. https://doi.org/10.1093/bioinformatics/btv547.PubMed Packer JS, Maxwell EK, O’Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG. CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data. Bioinformatics. 2016; 32(1):133–5. https://​doi.​org/​10.​1093/​bioinformatics/​btv547.PubMed

go back to reference Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007; 3(9):161. https://doi.org/10.1371/journal.pgen.0030161. Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007; 3(9):161. https://​doi.​org/​10.​1371/​journal.​pgen.​0030161.

go back to reference Costain G, Walker S, Argiropoulos B, Baribeau DA, Bassett AS, Boot E, Devriendt K, Kellam B, Marshall CR, Prasad A, Serrano MA, Stavropoulos DJ, Twede H, Vermeesch JR, Vorstman J. A. S., Scherer SW. Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders. J Neurodevelopmental Disord. 2019; 11:3. https://doi.org/10.1186/s11689-019-9263-3. Costain G, Walker S, Argiropoulos B, Baribeau DA, Bassett AS, Boot E, Devriendt K, Kellam B, Marshall CR, Prasad A, Serrano MA, Stavropoulos DJ, Twede H, Vermeesch JR, Vorstman J. A. S., Scherer SW. Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders. J Neurodevelopmental Disord. 2019; 11:3. https://​doi.​org/​10.​1186/​s11689-019-9263-3.

go back to reference Kushima I, Aleksic B, Nakatochi M, Shimamura T, Okada T, Uno Y, Morikawa M, Ishizuka K, Shiino T, Kimura H, Arioka Y, Yoshimi A, Takasaki Y, Yu Y, Nakamura Y, Yamamoto M, Iidaka T, Iritani S, Inada T, Ogawa N, Shishido E, Torii Y, Kawano N, Omura Y, Yoshikawa T, Uchiyama T, Yamamoto T, Ikeda M, Hashimoto R, Yamamori H, Yasuda Y, Someya T, Watanabe Y, Egawa J, Nunokawa A, Itokawa M, Arai M, Miyashita M, Kobori A, Suzuki M, Takahashi T, Usami M, Kodaira M, Watanabe K, Sasaki T, Kuwabara H, Tochigi M, Nishimura F, Yamasue H, Eriguchi Y, Benner S, Kojima M, Yassin W, Munesue T, Yokoyama S, Kimura R, Funabiki Y, Kosaka H, Ishitobi M, Ohmori T, Numata S, Yoshikawa T, Toyota T, Yamakawa K, Suzuki T, Inoue Y, Nakaoka K, Goto Y-I, Inagaki M, Hashimoto N, Kusumi I, Son S, Murai T, Ikegame T, Okada N, Kasai K, Kunimoto S, Mori D, Iwata N, Ozaki N. Comparative analyses of copy-number variation in autism spectrum disorder and schizophrenia reveal etiological overlap and biological insights. Cell Rep. 2018; 24:2838–56. https://doi.org/10.1016/j.celrep.2018.08.022.PubMed Kushima I, Aleksic B, Nakatochi M, Shimamura T, Okada T, Uno Y, Morikawa M, Ishizuka K, Shiino T, Kimura H, Arioka Y, Yoshimi A, Takasaki Y, Yu Y, Nakamura Y, Yamamoto M, Iidaka T, Iritani S, Inada T, Ogawa N, Shishido E, Torii Y, Kawano N, Omura Y, Yoshikawa T, Uchiyama T, Yamamoto T, Ikeda M, Hashimoto R, Yamamori H, Yasuda Y, Someya T, Watanabe Y, Egawa J, Nunokawa A, Itokawa M, Arai M, Miyashita M, Kobori A, Suzuki M, Takahashi T, Usami M, Kodaira M, Watanabe K, Sasaki T, Kuwabara H, Tochigi M, Nishimura F, Yamasue H, Eriguchi Y, Benner S, Kojima M, Yassin W, Munesue T, Yokoyama S, Kimura R, Funabiki Y, Kosaka H, Ishitobi M, Ohmori T, Numata S, Yoshikawa T, Toyota T, Yamakawa K, Suzuki T, Inoue Y, Nakaoka K, Goto Y-I, Inagaki M, Hashimoto N, Kusumi I, Son S, Murai T, Ikegame T, Okada N, Kasai K, Kunimoto S, Mori D, Iwata N, Ozaki N. Comparative analyses of copy-number variation in autism spectrum disorder and schizophrenia reveal etiological overlap and biological insights. Cell Rep. 2018; 24:2838–56. https://​doi.​org/​10.​1016/​j.​celrep.​2018.​08.​022.PubMed

go back to reference Coe BP, Stessman HAF, Sulovari A, Geisheker MR, Bakken TE, Lake AM, Dougherty JD, Lein ES, Hormozdiari F, Bernier RA, Eichler EE. Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet. 2019; 51:106–16. https://doi.org/10.1038/s41588-018-0288-4.PubMed Coe BP, Stessman HAF, Sulovari A, Geisheker MR, Bakken TE, Lake AM, Dougherty JD, Lein ES, Hormozdiari F, Bernier RA, Eichler EE. Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet. 2019; 51:106–16. https://​doi.​org/​10.​1038/​s41588-018-0288-4.PubMed

go back to reference Huang K-L, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C., Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott A. D., Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang L-B, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim T-B, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Network CGAR, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic germline variants in 10,389 adult cancers. Cell. 2018; 173:355–37014. https://doi.org/10.1016/j.cell.2018.03.039.PubMedPubMedCentral Huang K-L, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C., Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott A. D., Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang L-B, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim T-B, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Network CGAR, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic germline variants in 10,389 adult cancers. Cell. 2018; 173:355–37014. https://​doi.​org/​10.​1016/​j.​cell.​2018.​03.​039.PubMedPubMedCentral

go back to reference Lucito R, Suresh S, Walter K, Pandey A, Lakshmi B, Krasnitz A, Sebat J, Wigler M, Klein AP, Brune K, Palmisano E, Maitra A, Goggins M, Hruban RH. Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biol Ther. 2007; 6:1592–9.PubMed Lucito R, Suresh S, Walter K, Pandey A, Lakshmi B, Krasnitz A, Sebat J, Wigler M, Klein AP, Brune K, Palmisano E, Maitra A, Goggins M, Hruban RH. Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biol Ther. 2007; 6:1592–9.PubMed

go back to reference Willis JA, Mukherjee S, Orlow I, Viale A, Offit K, Kurtz RC, Olson SH, Klein RJ. Genome-wide analysis of the role of copy-number variation in pancreatic cancer risk. Front Genet. 2014; 5:29. https://doi.org/10.3389/fgene.2014.00029.PubMedPubMedCentral Willis JA, Mukherjee S, Orlow I, Viale A, Offit K, Kurtz RC, Olson SH, Klein RJ. Genome-wide analysis of the role of copy-number variation in pancreatic cancer risk. Front Genet. 2014; 5:29. https://​doi.​org/​10.​3389/​fgene.​2014.​00029.PubMedPubMedCentral

go back to reference Childs EJ, Mocci E, Campa D, Bracci PM, Gallinger S, Goggins M, Li D, Neale RE, Olson SH, Scelo G, Amundadottir LT, Bamlet WR, Bijlsma MF, Blackford A, Borges M, Brennan P, Brenner H, Bueno-de-Mesquita HB, Canzian F, Capurso G, Cavestro GM, Chaffee KG, Chanock SJ, Cleary SP, Cotterchio M, Foretova L, Fuchs C, Funel N, Gazouli M, Hassan M, Herman JM, Holcatova I, Holly EA, Hoover RN, Hung RJ, Janout V, Key TJ, Kupcinskas J, Kurtz RC, Landi S, Lu L., Malecka-Panas E, Mambrini A, Mohelnikova-Duchonova B, Neoptolemos JP, Oberg AL, Orlow I, Pasquali C, Pezzilli R, Rizzato C, Saldia A, Scarpa A, Stolzenberg-Solomon RZ, Strobel O, Tavano F, Vashist YK, Vodicka P, Wolpin BM, Yu H, Petersen GM, Risch HA, Klein AP. Common variation at 2p13.3, 3q29, 7p13 and 17q25.1 associated with susceptibility to pancreatic cancer. Nat Genet. 2015; 47:911–6. https://doi.org/10.1038/ng.3341.PubMedPubMedCentral Childs EJ, Mocci E, Campa D, Bracci PM, Gallinger S, Goggins M, Li D, Neale RE, Olson SH, Scelo G, Amundadottir LT, Bamlet WR, Bijlsma MF, Blackford A, Borges M, Brennan P, Brenner H, Bueno-de-Mesquita HB, Canzian F, Capurso G, Cavestro GM, Chaffee KG, Chanock SJ, Cleary SP, Cotterchio M, Foretova L, Fuchs C, Funel N, Gazouli M, Hassan M, Herman JM, Holcatova I, Holly EA, Hoover RN, Hung RJ, Janout V, Key TJ, Kupcinskas J, Kurtz RC, Landi S, Lu L., Malecka-Panas E, Mambrini A, Mohelnikova-Duchonova B, Neoptolemos JP, Oberg AL, Orlow I, Pasquali C, Pezzilli R, Rizzato C, Saldia A, Scarpa A, Stolzenberg-Solomon RZ, Strobel O, Tavano F, Vashist YK, Vodicka P, Wolpin BM, Yu H, Petersen GM, Risch HA, Klein AP. Common variation at 2p13.3, 3q29, 7p13 and 17q25.1 associated with susceptibility to pancreatic cancer. Nat Genet. 2015; 47:911–6. https://​doi.​org/​10.​1038/​ng.​3341.PubMedPubMedCentral

go back to reference Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I. Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat. 2008; 2(2):687–713.PubMedPubMedCentral Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I. Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat. 2008; 2(2):687–713.PubMedPubMedCentral

go back to reference Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, Macdonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol. 2011; 29(6):512–20.PubMedPubMedCentral Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, Macdonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol. 2011; 29(6):512–20.PubMedPubMedCentral

go back to reference Peel D, McLachlan GJ. Robust mixture modelling using the t distribution. Stat Comput. 2000; 10(4):339–48. Peel D, McLachlan GJ. Robust mixture modelling using the t distribution. Stat Comput. 2000; 10(4):339–48.

go back to reference Vounatsou P, Smith AFM. Simulation-based bayesian inferences for two-variance components linear models. J Stat Plan Infer. 1997; 59(1):139–61. https://doi.org/10.1016/S0378-3758(96)00093-6. Vounatsou P, Smith AFM. Simulation-based bayesian inferences for two-variance components linear models. J Stat Plan Infer. 1997; 59(1):139–61. https://​doi.​org/​10.​1016/​S0378-3758(96)00093-6.

go back to reference Lin TI, Lee JC, Ni HF. Bayesian analysis of mixture modelling using the multivariate t distribution. Stat Comput. 2004; 14(2):119–30. https://doi.org/10.1023/B:STCO.0000021410.33077.10. Lin TI, Lee JC, Ni HF. Bayesian analysis of mixture modelling using the multivariate t distribution. Stat Comput. 2004; 14(2):119–30. https://​doi.​org/​10.​1023/​B:​STCO.​0000021410.​33077.​10.

go back to reference Chib S. Marginal likelihood from the Gibbs output. J Am Stat Assoc. 1995; 90(432):1313–21. https://doi.org/10.1080/01621459.1995.10476635. Chib S. Marginal likelihood from the Gibbs output. J Am Stat Assoc. 1995; 90(432):1313–21. https://​doi.​org/​10.​1080/​01621459.​1995.​10476635.

go back to reference Gelman A, Rubin DB. Inference from iterative simulation using multiple sequences. Stat Sci. 1992; 7(4):457–472. https://doi.org/10.1214/ss/1177011136. Gelman A, Rubin DB. Inference from iterative simulation using multiple sequences. Stat Sci. 1992; 7(4):457–472. https://​doi.​org/​10.​1214/​ss/​1177011136.

go back to reference International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C., Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X., He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MMY, Tsui S. K. W., Xue H, Wong JT-F, Galver LM, Fan J-B, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier J-F, Phillips MS, Roumy S, Sall-e C, Verner A, Hudson TJ, Kwok P-Y, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui L-C, Mak W, Song YQ, Tam PKH, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PIW, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe’er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CDM, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H., Kang L, Godbout M, Wallenburg JC, L’Archev-que P, Bellemare G., Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007; 449(7164):851–61. https://doi.org/10.1038/nature06258. International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C., Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X., He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MMY, Tsui S. K. W., Xue H, Wong JT-F, Galver LM, Fan J-B, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier J-F, Phillips MS, Roumy S, Sall-e C, Verner A, Hudson TJ, Kwok P-Y, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui L-C, Mak W, Song YQ, Tam PKH, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PIW, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe’er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CDM, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H., Kang L, Godbout M, Wallenburg JC, L’Archev-que P, Bellemare G., Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007; 449(7164):851–61. https://​doi.​org/​10.​1038/​nature06258.

go back to reference Plummer M. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the third international workshop on distributed statistical computing. 2003; 124(125.10):1–10. Plummer M. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the third international workshop on distributed statistical computing. 2003; 124(125.10):1–10.

go back to reference 1000 Genomes Project Consortium, Auton A, Brooks L, Durbin R, Garrison E, Kang H, Korbel J, Marchini J, McCarthy S, McVean G, Abecasis G. A global reference for human genetic variation. Nature. 2015; 526(7571):68–74. https://doi.org/10.1038/nature15393. 1000 Genomes Project Consortium, Auton A, Brooks L, Durbin R, Garrison E, Kang H, Korbel J, Marchini J, McCarthy S, McVean G, Abecasis G. A global reference for human genetic variation. Nature. 2015; 526(7571):68–74. https://​doi.​org/​10.​1038/​nature15393.

go back to reference Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, Cardin N., Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews T. D, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JMC, Cooper JD, Dominiczak AF, Downes K, Drummond H. E., Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JMM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DCO, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O’Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JRB, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K., Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DPM, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SCL, Hall AS, Hattersley AT, Hill AVS, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski D. P., McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature. 2010; 464(7289):713–20. https://doi.org/10.1038/nature08979. Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, Cardin N., Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews T. D, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JMC, Cooper JD, Dominiczak AF, Downes K, Drummond H. E., Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JMM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DCO, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O’Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JRB, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K., Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DPM, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SCL, Hall AS, Hattersley AT, Hill AVS, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski D. P., McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature. 2010; 464(7289):713–20. https://​doi.​org/​10.​1038/​nature08979.

go back to reference Gutiérrez VF, Marcos C. l., Llorente JL, Guervós MA, Iglesias FD, Tamargo LA, Hermsen M. Genetic profile of second primary tumors and recurrences in head and neck squamous cell carcinomas. Head Neck. 2012; 34:830–9. https://doi.org/10.1002/hed.21824.PubMed Gutiérrez VF, Marcos C. l., Llorente JL, Guervós MA, Iglesias FD, Tamargo LA, Hermsen M. Genetic profile of second primary tumors and recurrences in head and neck squamous cell carcinomas. Head Neck. 2012; 34:830–9. https://​doi.​org/​10.​1002/​hed.​21824.PubMed

go back to reference Gu Y, Wang Q, Guo K, Qin W, Liao W, Wang S, Ding Y, Lin J. Tusc3 promotes colorectal cancer progression and epithelial-mesenchymal transition (emt) through wnt/-catenin and mapk signalling. J Pathol. 2016; 239:60–71. https://doi.org/10.1002/path.4697.PubMed Gu Y, Wang Q, Guo K, Qin W, Liao W, Wang S, Ding Y, Lin J. Tusc3 promotes colorectal cancer progression and epithelial-mesenchymal transition (emt) through wnt/-catenin and mapk signalling. J Pathol. 2016; 239:60–71. https://​doi.​org/​10.​1002/​path.​4697.PubMed

go back to reference Gu Y, Pei X, Ren Y, Cai K, Guo K, Chen J, Qin W, Lin M, Wang Q, Tang N, Cheng Z, Ding Y, Lin J. Oncogenic function of tusc3 in non-small cell lung cancer is associated with hedgehog signalling pathway. Biochim Biophys Acta Mol Basis Dis. 2017; 1863:1749–60. https://doi.org/10.1016/j.bbadis.2017.05.005.PubMed Gu Y, Pei X, Ren Y, Cai K, Guo K, Chen J, Qin W, Lin M, Wang Q, Tang N, Cheng Z, Ding Y, Lin J. Oncogenic function of tusc3 in non-small cell lung cancer is associated with hedgehog signalling pathway. Biochim Biophys Acta Mol Basis Dis. 2017; 1863:1749–60. https://​doi.​org/​10.​1016/​j.​bbadis.​2017.​05.​005.PubMed

go back to reference Vašíčková K, Horak P, Vaňhara P. Tusc3: functional duality of a cancer gene. Cell Mol Life Sci CMLS. 2018; 75:849–57. https://doi.org/10.1007/s00018-017-2660-4.PubMed Vašíčková K, Horak P, Vaňhara P. Tusc3: functional duality of a cancer gene. Cell Mol Life Sci CMLS. 2018; 75:849–57. https://​doi.​org/​10.​1007/​s00018-017-2660-4.PubMed

go back to reference Grisanzio C, Freedman ML. Chromosome 8q24-associated cancers and MYC. Genes Cancer. 2010; 1:555–9. https://doi.org/10.1177/1947601910381380.PubMedPubMedCentral Grisanzio C, Freedman ML. Chromosome 8q24-associated cancers and MYC. Genes Cancer. 2010; 1:555–9. https://​doi.​org/​10.​1177/​1947601910381380​.PubMedPubMedCentral

go back to reference Wolpin BM, Rizzato C, Kraft P, Kooperberg C, Petersen GM, Wang Z, Arslan AA, Beane-Freeman L, Bracci PM, Buring J, Canzian F, Duell EJ, Gallinger S, Giles GG, Goodman GE, Goodman PJ, Jacobs EJ, Kamineni A, Klein AP, Kolonel LN, Kulke MH, Li D, Malats N, Olson SH, Risch HA, Sesso H. D, Visvanathan K, White E, Zheng W, Abnet CC, Albanes D, Andreotti G, Austin MA, Barfield R, Basso D, Berndt SI, Boutron-Ruault M-C, Brotzman M, Bachler MW, Bueno-de-Mesquita HB, Bugert P, Burdette L, Campa D, Caporaso NE, Capurso G, Chung C, Cotterchio M, Costello E, Elena J, Funel N, Gaziano JM, Giese NA, Giovannucci EL, Goggins M, Gorman MJ, Gross M, Haiman CA, Hassan M, Helzlsouer KJ, Henderson BE, Holly EA, Hu N, Hunter DJ, Innocenti F, Jenab M, Kaaks R, Key TJ, Khaw K-T, Klein EA, Kogevinas M, Krogh V, Kupcinskas J, Kurtz RC, LaCroix A, Landi MT, Landi S, Le Marchand L, Mambrini A, Mannisto S, Milne RL, Nakamura Y, Oberg AL, Owzar K, Patel AV, Peeters PHM, Peters U, Pezzilli R, Piepoli A, Porta M, Real FX, Riboli E, Rothman N, Scarpa A, Shu X-O, Silverman DT, Soucek P, Sund M, Talar-Wojnarowska R, Taylor PR, Theodoropoulos GE, Thornquist M, Tjanneland A, Tobias GS, Trichopoulos D, Vodicka P., Wactawski-Wende J, Wentzensen N, Wu C, Yu H, Yu K, Zeleniuch-Jacquotte A, Hoover R, Hartge P, Fuchs C, Chanock SJ, Stolzenberg-Solomon RS, Amundadottir LT. Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer. Nat Genet. 2014; 46:994–1000. https://doi.org/10.1038/ng.3052.PubMedPubMedCentral Wolpin BM, Rizzato C, Kraft P, Kooperberg C, Petersen GM, Wang Z, Arslan AA, Beane-Freeman L, Bracci PM, Buring J, Canzian F, Duell EJ, Gallinger S, Giles GG, Goodman GE, Goodman PJ, Jacobs EJ, Kamineni A, Klein AP, Kolonel LN, Kulke MH, Li D, Malats N, Olson SH, Risch HA, Sesso H. D, Visvanathan K, White E, Zheng W, Abnet CC, Albanes D, Andreotti G, Austin MA, Barfield R, Basso D, Berndt SI, Boutron-Ruault M-C, Brotzman M, Bachler MW, Bueno-de-Mesquita HB, Bugert P, Burdette L, Campa D, Caporaso NE, Capurso G, Chung C, Cotterchio M, Costello E, Elena J, Funel N, Gaziano JM, Giese NA, Giovannucci EL, Goggins M, Gorman MJ, Gross M, Haiman CA, Hassan M, Helzlsouer KJ, Henderson BE, Holly EA, Hu N, Hunter DJ, Innocenti F, Jenab M, Kaaks R, Key TJ, Khaw K-T, Klein EA, Kogevinas M, Krogh V, Kupcinskas J, Kurtz RC, LaCroix A, Landi MT, Landi S, Le Marchand L, Mambrini A, Mannisto S, Milne RL, Nakamura Y, Oberg AL, Owzar K, Patel AV, Peeters PHM, Peters U, Pezzilli R, Piepoli A, Porta M, Real FX, Riboli E, Rothman N, Scarpa A, Shu X-O, Silverman DT, Soucek P, Sund M, Talar-Wojnarowska R, Taylor PR, Theodoropoulos GE, Thornquist M, Tjanneland A, Tobias GS, Trichopoulos D, Vodicka P., Wactawski-Wende J, Wentzensen N, Wu C, Yu H, Yu K, Zeleniuch-Jacquotte A, Hoover R, Hartge P, Fuchs C, Chanock SJ, Stolzenberg-Solomon RS, Amundadottir LT. Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer. Nat Genet. 2014; 46:994–1000. https://​doi.​org/​10.​1038/​ng.​3052.PubMedPubMedCentral

go back to reference Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou J-Y, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu K-H, Tabb DL, Fenya D, Bafna V, Wang Y, Rodriguez H., Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih I-M, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD, Investigators C. Integrated proteogenomic characterization of human high-grade serous ovarian cancer. Cell. 2016; 166:755–65. https://doi.org/10.1016/j.cell.2016.05.069.PubMedPubMedCentral Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou J-Y, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu K-H, Tabb DL, Fenya D, Bafna V, Wang Y, Rodriguez H., Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih I-M, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD, Investigators C. Integrated proteogenomic characterization of human high-grade serous ovarian cancer. Cell. 2016; 166:755–65. https://​doi.​org/​10.​1016/​j.​cell.​2016.​05.​069.PubMedPubMedCentral

go back to reference Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006; 78(4):629–44. https://doi.org/10.1086/502802.PubMedPubMedCentral Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006; 78(4):629–44. https://​doi.​org/​10.​1086/​502802.PubMedPubMedCentral

go back to reference Scharpf RB, Mireles L, Yang Q, Köttgen A, Ruczinski I., Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A., Boerwinkle E, Fox CS, Coresh J, Linda Kao WH. Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations. BMC Genet. 2014; 15:81. https://doi.org/10.1186/1471-2156-15-81.PubMedPubMedCentral Scharpf RB, Mireles L, Yang Q, Köttgen A, Ruczinski I., Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A., Boerwinkle E, Fox CS, Coresh J, Linda Kao WH. Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations. BMC Genet. 2014; 15:81. https://​doi.​org/​10.​1186/​1471-2156-15-81.PubMedPubMedCentral

go back to reference Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q., Wang L-E, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu S. M., Regnier C, Lowe WL, Hayes MG, Marazita ML, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, Weir BS. Detectable clonal mosaicism from birth to old age and its relationship to cancer. 2012; 44(6):642–50. https://doi.org/10.1038/ng.2271. Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q., Wang L-E, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu S. M., Regnier C, Lowe WL, Hayes MG, Marazita ML, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, Weir BS. Detectable clonal mosaicism from birth to old age and its relationship to cancer. 2012; 44(6):642–50. https://​doi.​org/​10.​1038/​ng.​2271.

go back to reference Vattathil S, Scheet P. Haplotype-based profiling of subtle allelic imbalance with snp arrays. Genome Res. 2013; 23:152–158. https://doi.org/10.1101/gr.141374.112.PubMedPubMedCentral Vattathil S, Scheet P. Haplotype-based profiling of subtle allelic imbalance with snp arrays. Genome Res. 2013; 23:152–158. https://​doi.​org/​10.​1101/​gr.​141374.​112.PubMedPubMedCentral

go back to reference Freed D, Stevens EL, Pevsner J. Somatic mosaicism in the human genome. Genes. 2014; 5:1064–94. https://doi.org/10.3390/genes5041064.PubMedPubMedCentral Freed D, Stevens EL, Pevsner J. Somatic mosaicism in the human genome. Genes. 2014; 5:1064–94. https://​doi.​org/​10.​3390/​genes5041064.PubMedPubMedCentral

go back to reference Vattathil S, Scheet P. Extensive hidden genomic mosaicism revealed in normal tissue. Am J Hum Genet. 2016; 98:571–578. https://doi.org/10.1016/j.ajhg.2016.02.003.PubMedPubMedCentral Vattathil S, Scheet P. Extensive hidden genomic mosaicism revealed in normal tissue. Am J Hum Genet. 2016; 98:571–578. https://​doi.​org/​10.​1016/​j.​ajhg.​2016.​02.​003.PubMedPubMedCentral