novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data

被引:5
作者
Mohanty, Anwoy Kumar [1 ,2 ,6 ]
Vuzman, Dana [1 ,2 ]
Francioli, Laurent [3 ,4 ]
Cassa, Christopher [1 ,2 ]
Toth-Petroczy, Agnes [1 ,2 ]
Sunyaev, Shamil [1 ,2 ,5 ]
机构
[1] Brigham & Womens Hosp, Dept Med, Div Genet, 75 Francis St, Boston, MA 02115 USA
[2] Harvard Med Sch, Boston, MA 02115 USA
[3] Broad Inst MIT & Harvard, Program Med & Populat Genet, Cambridge, MA 02142 USA
[4] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA
[5] Harvard Med Sch, Dept Biomed Informat, Boston, MA 02115 USA
[6] Indian Inst Technol Bhubaneswar, Sch Elect Sci, Bhubaneswar 752050, Odisha, India
基金
美国国家卫生研究院;
关键词
MUTATIONS; GENES;
D O I
10.1093/bioinformatics/bty749
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation De novo mutations (i.e. newly occurring mutations) are a pre-dominant cause of sporadic dominant monogenic diseases and play a significant role in the genetics of complex disorders. De novo mutation studies also inform population genetics models and shed light on the biology of DNA replication and repair. Despite the broad interest, there is room for improvement with regard to the accuracy of de novo mutation calling. Results We designed novoCaller, a Bayesian variant calling algorithm that uses information from read-level data both in the pedigree and in unrelated samples. The method was extensively tested using large trio-sequencing studies, and it consistently achieved over 97% sensitivity. We applied the algorithm to 48 trio cases of suspected rare Mendelian disorders as part of the Brigham Genomic Medicine gene discovery initiative. Its application resulted in a significant reduction in the resources required for manual inspection and experimental validation of the calls. Three de novo variants were found in known genes associated with rare disorders, leading to rapid genetic diagnosis of the probands. Another 14 variants were found in genes that are likely to explain the phenotype, and could lead to novel disease-gene discovery. Availability and implementation Source code implemented in C++ and Python can be downloaded from https://github.com/bgm-cwg/novoCaller. Supplementary information Supplementary data are available at Bioinformatics online.
引用
收藏
页码:1174 / 1180
页数:7
相关论文
共 21 条
[1]   De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies [J].
Appenzeller, Silke ;
Balling, Rudi ;
Barisic, Nina ;
Baulac, Stephanie ;
Caglayan, Hande ;
Craiu, Dana ;
De Jonghe, Peter ;
Depienne, Christel ;
Dimova, Petia ;
Djemie, Tania ;
Gormley, Padhraig ;
Guerrini, Renzo ;
Helbig, Ingo ;
Hjalgrim, Helle ;
Hoffman-Zacharska, Dorota ;
Jaehn, Johanna ;
Klein, Karl Martin ;
Koeleman, Bobby ;
Komarek, Vladimir ;
Krause, Roland ;
Kuhlenbaeumer, Gregor ;
Leguern, Eric ;
Lehesjoki, Anna-Elina ;
Lemke, Johannes R. ;
Lerche, Holger ;
Linnankivi, Tarja ;
Marini, Carla ;
May, Patrick ;
Moller, Rikke S. ;
Muhle, Hiltrud ;
Pal, Deb ;
Palotie, Aarno ;
Pendziwiat, Manuela ;
Robbiano, Angela ;
Roelens, Filip ;
Rosenow, Felix ;
Selmer, Kaja ;
Serratosa, Jose M. ;
Sisodiya, Sanjay ;
Stephani, Ulrich ;
Sterbova, Katalin ;
Striano, Pasquale ;
Suls, Arvid ;
Talvik, Tiina ;
von Spiczak, Sarah ;
Weber, Yvonne ;
Weckhuysen, Sarah ;
Zara, Federico ;
Abou-Khalil, Bassel ;
Alldredge, Brian K. .
AMERICAN JOURNAL OF HUMAN GENETICS, 2014, 95 (04) :360-370
[2]   Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data [J].
Cleary, John G. ;
Braithwaite, Ross ;
Gaastra, Kurt ;
Hilbush, Brian S. ;
Inglis, Stuart ;
Irvine, Sean A. ;
Jackson, Alan ;
Littin, Richard ;
Nohzadeh-Malakshah, Sahar ;
Rathod, Mehul ;
Ware, David ;
Trigg, Len ;
De La Vega, Francisco M. .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2014, 21 (06) :405-419
[3]   Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of Distal Arthrogryposis [J].
Coste, Bertrand ;
Houge, Gunnar ;
Murray, Michael F. ;
Stitziel, Nathan ;
Bandell, Michael ;
Giovanni, Monica A. ;
Philippakis, Anthony ;
Hoischen, Alexander ;
Riemer, Gunnar ;
Steen, Unni ;
Steen, Vidar Martin ;
Mathur, Jayanti ;
Cox, James ;
Lebo, Matthew ;
Rehm, Heidi ;
Weiss, Scott T. ;
Wood, John N. ;
Maas, Richard L. ;
Sunyaev, Shamil R. ;
Patapoutian, Ardem .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (12) :4667-4672
[4]   Synaptic, transcriptional and chromatin genes disrupted in autism [J].
De Rubeis, Silvia ;
He, Xin ;
Goldberg, Arthur P. ;
Poultney, Christopher S. ;
Samocha, Kaitlin ;
Cicek, A. Ercument ;
Kou, Yan ;
Liu, Li ;
Fromer, Menachem ;
Walker, Susan ;
Singh, Tarjinder ;
Klei, Lambertus ;
Kosmicki, Jack ;
Fu, Shih-Chen ;
Aleksic, Branko ;
Biscaldi, Monica ;
Bolton, Patrick F. ;
Brownfeld, Jessica M. ;
Cai, Jinlu ;
Campbell, Nicholas G. ;
Carracedo, Angel ;
Chahrour, Maria H. ;
Chiocchetti, Andreas G. ;
Coon, Hilary ;
Crawford, Emily L. ;
Crooks, Lucy ;
Curran, Sarah R. ;
Dawson, Geraldine ;
Duketis, Eftichia ;
Fernandez, Bridget A. ;
Gallagher, Louise ;
Geller, Evan ;
Guter, Stephen J. ;
Hill, R. Sean ;
Ionita-Laza, Iuliana ;
Gonzalez, Patricia Jimenez ;
Kilpinen, Helena ;
Klauck, Sabine M. ;
Kolevzon, Alexander ;
Lee, Irene ;
Lei, Jing ;
Lehtimaeki, Terho ;
Lin, Chiao-Feng ;
Ma'ayan, Avi ;
Marshall, Christian R. ;
McInnes, Alison L. ;
Neale, Benjamin ;
Owen, Michael J. ;
Ozaki, Norio ;
Parellada, Mara .
NATURE, 2014, 515 (7526) :209-+
[5]   A framework for the detection of de novo mutations in family-based sequencing data [J].
Francioli, Laurent C. ;
Cretu-Stancu, Mircea ;
Garimella, Kiran V. ;
Fromer, Menachem ;
Kloosterman, Wigard P. ;
Samocha, Kaitlin E. ;
Neale, Benjamin M. ;
Daly, Mark J. ;
Banks, Eric ;
DePristo, Mark A. ;
de Bakker, Paul I. W. .
EUROPEAN JOURNAL OF HUMAN GENETICS, 2017, 25 (02) :227-233
[6]   Genome-wide patterns and properties of de novo mutations in humans [J].
Francioli, Laurent C. ;
Polak, Paz P. ;
Koren, Amnon ;
Menelaou, Androniki ;
Chun, Sung ;
Renkens, Ivo ;
van Duijn, Cornelia M. ;
Swertz, Morris ;
Wijmenga, Cisca ;
van Ommen, Gertjan ;
Slagboom, P. Eline ;
Boomsma, Dorret I. ;
Ye, Kai ;
Guryev, Victor ;
Arndt, Peter F. ;
Kloosterman, Wigard P. ;
de Bakker, Paul I. W. ;
Sunyaev, Shamil R. .
NATURE GENETICS, 2015, 47 (07) :822-+
[7]   Whole-genome sequence variation, population structure and demographic history of the Dutch population [J].
Francioli, Laurent C. ;
Menelaou, Andronild ;
Pulit, Sara L. ;
Van Dijk, Freerk ;
Palamara, Pier Francesco ;
Elbers, Clara C. ;
Neerincx, Pieter B. T. ;
Ye, Kai ;
Guryev, Victor ;
Kloosterman, Wigard P. ;
Deelen, Patrick ;
Abdellaoui, Abdel ;
Van Leeuwen, Elisabeth M. ;
Van Oven, Mannis ;
Vermaat, Martijn ;
Li, Mingkun ;
Laros, Jeroen F. J. ;
Karssen, Lennart C. ;
Kanterakis, Alexandros ;
Amin, Najaf ;
Hottenga, Jouke Jan ;
Lameijer, Eric-Wubbo ;
Kattenberg, Mathijs ;
Dijkstra, Martijn ;
Byelas, Heorhiy ;
Van Settenl, Jessica ;
Van Schaik, Barbera D. C. ;
Bot, Jan ;
Nijman, Isaac J. ;
Renkens, Ivo ;
Marscha, Tobias ;
Schonhuth, Alexander ;
Hehir-Kwa, Jayne Y. ;
Handsaker, Robert E. ;
Polak, Paz ;
Sohail, Mashaal ;
Vuzman, Dana ;
Hormozdiari, Fereydoun ;
Van Enckevort, David ;
Mei, Hailiang ;
Koval, Vyacheslav ;
Moed, Ma-Tthijs H. ;
Van der Velde, K. Joeri ;
Rivadeneira, Fernando ;
Estrada, Karol ;
Medina-Gomez, Carolina ;
Isaacs, Aaron ;
McCarroll, Steven A. ;
Beekrnan, Marian ;
De Craen, Anton J. M. .
NATURE GENETICS, 2014, 46 (08) :818-825
[8]   De novo mutations in schizophrenia implicate synaptic networks [J].
Fromer, Menachem ;
Pocklington, Andrew J. ;
Kavanagh, David H. ;
Williams, Hywel J. ;
Dwyer, Sarah ;
Gormley, Padhraig ;
Georgieva, Lyudmila ;
Rees, Elliott ;
Palta, Priit ;
Ruderfer, Douglas M. ;
Carrera, Noa ;
Humphreys, Isla ;
Johnson, Jessica S. ;
Roussos, Panos ;
Barker, Douglas D. ;
Banks, Eric ;
Milanova, Vihra ;
Grant, Seth G. ;
Hannon, Eilis ;
Rose, Samuel A. ;
Chambert, Kimberly ;
Mahajan, Milind ;
Scolnick, Edward M. ;
Moran, Jennifer L. ;
Kirov, George ;
Palotie, Aarno ;
McCarroll, Steven A. ;
Holmans, Peter ;
Sklar, Pamela ;
Owen, Michael J. ;
Purcell, Shaun M. ;
O'Donovan, Michael C. .
NATURE, 2014, 506 (7487) :179-+
[9]   SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors [J].
Goya, Rodrigo ;
Sun, Mark G. F. ;
Morin, Ryan D. ;
Leung, Gillian ;
Ha, Gavin ;
Wiegand, Kimberley C. ;
Senz, Janine ;
Crisan, Anamaria ;
Marra, Marco A. ;
Hirst, Martin ;
Huntsman, David ;
Murphy, Kevin P. ;
Aparicio, Sam ;
Shah, Sohrab P. .
BIOINFORMATICS, 2010, 26 (06) :730-736
[10]   An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery [J].
Haghighi, Alireza ;
Krier, Joel B. ;
Toth-Petroczy, Agnes ;
Cassa, Christopher A. ;
Frank, Natasha Y. ;
Carmichael, Nikkola ;
Fieg, Elizabeth ;
Bjonnes, Andrew ;
Mohanty, Anwoy ;
Briere, Lauren C. ;
Lincoln, Sharyn ;
Lucia, Stephanie ;
Gupta, Vandana A. ;
Soylemez, Onuralp ;
Sutti, Sheila ;
Kooshesh, Kameron ;
Qiu, Haiyan ;
Fay, Christopher J. ;
Perroni, Victoria ;
Valerius, Jamie ;
Hanna, Meredith ;
Frank, Alexander ;
Ouahed, Jodie ;
Snapper, Scott B. ;
Pantazi, Angeliki ;
Chopra, Sameer S. ;
Leshchiner, Ignaty ;
Stitziel, Nathan O. ;
Feldweg, Anna ;
Mannstadt, Michael ;
Loscalzo, Joseph ;
Sweetser, David A. ;
Liao, Eric ;
Stoler, Joan M. ;
Nowak, Catherine B. ;
Sanchez-Lara, Pedro A. ;
Klein, Ophir D. ;
Perry, Hazel ;
Patsopoulos, Nikolaos A. ;
Raychaudhuri, Soumya ;
Goessling, Wolfram ;
Green, Robert C. ;
Seidman, Christine E. ;
MacRae, Calum A. ;
Sunyaev, Shamil R. ;
Maas, Richard L. ;
Vuzman, Dana .
NPJ GENOMIC MEDICINE, 2018, 3