Twelve years of SAMtools and BCFtools

Authors: Danecek, Petr, Bonfield, James K., Liddle, Jennifer, Marshall, John, Ohan, Valeriu, Pollard, Martin O, Whitwham, Andrew, Keane, Thomas, McCarthy, Shane A., Davies, Robert M., Li, Heng

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/2012.10295

Detection and characterization of copy-number variants from exome sequencing in the DDD study

Authors: Danecek, Petr, Gardner, Eugene J., Fitzgerald, Tomas W., Gallone, Giuseppe, Kaplanis, Joanna, Eberhardt, Ruth Y., Wright, Caroline F., Firth, Helen V., Hurles, Matthew E.

Source: In Genetics in Medicine Open 2024 2

Somatic mutations alter the differentiation outcomes of iPSC-derived neurons

Authors: Puigdevall, Pau, Jerber, Julie, Danecek, Petr, Castellano, Sergi, Kilpinen, Helena

Source: In Cell Genomics 12 April 2023 3(4)

Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms

Authors: Wright, Caroline F., Quaife, Nicholas M., Ramos-Hernández, Laura, Danecek, Petr, Ferla, Matteo P., Samocha, Kaitlin E., Kaplanis, Joanna, Gardner, Eugene J., Eberhardt, Ruth Y., Chao, Katherine R., Karczewski, Konrad J., Morales, Joannella, Gallone, Giuseppe, Balasubramanian, Meena, Banka, Siddharth, Gompertz, Lianne, Kerr, Bronwyn, Kirby, Amelia, Lynch, Sally A., Morton, Jenny E.V., Pinz, Hailey, Sansbury, Francis H., Stewart, Helen, Zuccarelli, Britton D., Cook, Stuart A., Taylor, Jenny C., Juusola, Jane, Retterer, Kyle, Firth, Helen V., Hurles, Matthew E., Lara-Pezzi, Enrique, Barton, Paul J.R., Whiffin, Nicola

Source: In The American Journal of Human Genetics 3 June 2021 108(6):1083-1094

Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders

Authors: Gardner, Eugene J., Sifrim, Alejandro, Lindsay, Sarah J., Prigmore, Elena, Rajan, Diana, Danecek, Petr, Gallone, Giuseppe, Eberhardt, Ruth Y., Martin, Hilary C., Wright, Caroline F., FitzPatrick, David R., Firth, Helen V., Hurles, Matthew E.

Source: American journal of human genetics. 108(11):2186-2194

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100147868387.0x000001&indx=1&recIds=ETOCvdc_100147868387.0x000001

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Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations

Authors: Chundru, V. Kartik, Zhang, Zhancheng, Walter, Klaudia, Lindsay, Sarah J., Danecek, Petr, Eberhardt, Ruth Y., Gardner, Eugene J., Malawsky, Daniel S., Wigdor, Emilie M., Torene, Rebecca, Retterer, Kyle, Wright, Caroline F., Ólafsdóttir, Hildur, Guillen Sacoto, Maria J., Ayaz, Akif, Akbeyaz, Ismail Hakki, Türkdoğan, Dilşad, Al Balushi, Aaisha Ibrahim, Bertoli-Avella, Aida, Bauer, Peter, Szenker-Ravi, Emmanuelle, Reversade, Bruno, McWalter, Kirsty, Sheridan, Eamonn, Firth, Helen V., Hurles, Matthew E., Samocha, Kaitlin E., Ustach, Vincent D., Martin, Hilary C.

Source: Nature Genetics; October 2024, Vol. 56 Issue: 10 p2046-2053, 8p

Ancient human parallel lineages within North America contributed to a coastal expansion

Authors: Scheib, C. L., Li, Hongjie, Desai, Tariq, Link, Vivian, Kendall, Christopher, Dewar, Genevieve, Griffith, Peter William, Mörseburg, Alexander, Johnson, John R., Potter, Amiee, Kerr, Susan L., Endicott, Phillip, Lindo, John, Haber, Marc, Xue, Yali, Tyler-Smith, Chris, Sandhu, Manjinder S., Lorenz, Joseph G., Randall, Tori D., Faltyskova, Zuzana, Pagani, Luca, Danecek, Petr, O’Connell, Tamsin C., Martz, Patricia, Boraas, Alan S., Byrd, Brian F., Leventhal, Alan, Cambra, Rosemary, Williamson, Ronald, Lesage, Louis, Holguin, Brian, Soto, Ernestine Ygnacio-De, Rosas, JohnTommy, Metspalu, Mait, Stock, Jay T., Manica, Andrea, Scally, Aylwyn, Wegmann, Daniel, Malhi, Ripan S., Kivisild, Toomas

Source: Science, 2018 Jun 01. 360(6392), 1024-1027.

Access URL: https://www.jstor.org/stable/26498847

Contribution of retrotransposition to developmental disorders

Authors: Gardner, Eugene, Prigmore, Elena, Gallone, Giuseppe, Danecek, Petr, Samocha, Kaitlin, Handsaker, Juliet, Gerety, Sebastian, Ironfield, Holly, Short, Patrick, Sifrim, Alejandro, Singh, Tarjinder, Chandler, Kate, Clement, Emma, Lachlan, Katherine, Prescott, Katrina, Rosser, Elisabeth, FitzPatrick, David, Firth, Helen, Hurles, Matthew

Source: Nature communications. 10(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190848164.0x000001&indx=1&recIds=ETOCvdc_100190848164.0x000001

Very low-depth whole-genome sequencing in complex trait association studies

Authors: Gilly, Arthur, Southam, Lorraine, Suveges, Daniel, Kuchenbaecker, Karoline, Moore, Rachel, Melloni, Giorgio E M, Hatzikotoulas, Konstantinos, Farmaki, Aliki-Eleni, Ritchie, Graham, Schwartzentruber, Jeremy, Danecek, Petr, Kilian, Britt, Pollard, Martin O, Ge, Xiangyu, Tsafantakis, Emmanouil, Dedoussis, George, Zeggini, Eleftheria

Source: Bioinformatics. 35(15):2555-2561

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100087529880.0x000001&indx=1&recIds=ETOCvdc_100087529880.0x000001

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits

Authors: Tachmazidou, Ioanna, Süveges, Dániel, Min, Josine L., Ritchie, Graham R.S., Steinberg, Julia, Walter, Klaudia, Iotchkova, Valentina, Schwartzentruber, Jeremy, Huang, Jie, Memari, Yasin, McCarthy, Shane, Crawford, Andrew A., Bombieri, Cristina, Cocca, Massimiliano, Farmaki, Aliki-Eleni, Gaunt, Tom R., Jousilahti, Pekka, Kooijman, Marjolein N., Lehne, Benjamin, Malerba, Giovanni, Männistö, Satu, Matchan, Angela, Medina-Gomez, Carolina, Metrustry, Sarah J., Nag, Abhishek, Ntalla, Ioanna, Paternoster, Lavinia, Rayner, Nigel W., Sala, Cinzia, Scott, William R., Shihab, Hashem A., Southam, Lorraine, St Pourcain, Beate, Traglia, Michela, Trajanoska, Katerina, Zaza, Gialuigi, Zhang, Weihua, Artigas, María S., Bansal, Narinder, Benn, Marianne, Chen, Zhongsheng, Danecek, Petr, Lin, Wei-Yu, Locke, Adam, Luan, Jian’an, Manning, Alisa K., Mulas, Antonella, Sidore, Carlo, Tybjaerg-Hansen, Anne, Varbo, Anette, Zoledziewska, Magdalena, Finan, Chris, Hatzikotoulas, Konstantinos, Hendricks, Audrey E., Kemp, John P., Moayyeri, Alireza, Panoutsopoulou, Kalliope, Szpak, Michal, Wilson, Scott G., Boehnke, Michael, Cucca, Francesco, Di Angelantonio, Emanuele, Langenberg, Claudia, Lindgren, Cecilia, McCarthy, Mark I., Morris, Andrew P., Nordestgaard, Børge G., Scott, Robert A., Tobin, Martin D., Wareham, Nicholas J., Burton, Paul, Chambers, John C., Smith, George Davey, Dedoussis, George, Felix, Janine F., Franco, Oscar H., Gambaro, Giovanni, Gasparini, Paolo, Hammond, Christopher J., Hofman, Albert, Jaddoe, Vincent W.V., Kleber, Marcus, Kooner, Jaspal S., Perola, Markus, Relton, Caroline, Ring, Susan M., Rivadeneira, Fernando, Salomaa, Veikko, Spector, Timothy D., Stegle, Oliver, Toniolo, Daniela, Uitterlinden, André G., Barroso, Inês, Greenwood, Celia M.T., Perry, John R.B., Walker, Brian R., Butterworth, Adam S., Xue, Yali, Durbin, Richard, Small, Kerrin S., Soranzo, Nicole, Timpson, Nicholas J., Zeggini, Eleftheria

Source: In The American Journal of Human Genetics 1 June 2017 100(6):865-884

Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences

Authors: Haber, Marc, Doumet-Serhal, Claude, Scheib, Christiana, Xue, Yali, Danecek, Petr, Mezzavilla, Massimo, Youhanna, Sonia, Martiniano, Rui, Prado-Martinez, Javier, Szpak, Michał, Matisoo-Smith, Elizabeth, Schutkowski, Holger, Mikulski, Richard, Zalloua, Pierre, Kivisild, Toomas, Tyler-Smith, Chris

Source: American journal of human genetics. 101(2):274-282

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100056145443.0x000001&indx=1&recIds=ETOCvdc_100056145443.0x000001

De novo variants in the RNU4-2snRNA cause a frequent neurodevelopmental syndrome

Authors: Chen, Yuyang, Dawes, Ruebena, Kim, Hyung Chul, Ljungdahl, Alicia, Stenton, Sarah L., Walker, Susan, Lord, Jenny, Lemire, Gabrielle, Martin-Geary, Alexandra C., Ganesh, Vijay S., Ma, Jialan, Ellingford, Jamie M., Delage, Erwan, D’Souza, Elston N., Dong, Shan, Adams, David R., Allan, Kirsten, Bakshi, Madhura, Baldwin, Erin E., Berger, Seth I., Bernstein, Jonathan A., Bhatnagar, Ishita, Blair, Ed, Brown, Natasha J., Burrage, Lindsay C., Chapman, Kimberly, Coman, David J., Compton, Alison G., Cunningham, Chloe A., D’Souza, Precilla, Danecek, Petr, Délot, Emmanuèle C., Dias, Kerith-Rae, Elias, Ellen R., Elmslie, Frances, Evans, Care-Anne, Ewans, Lisa, Ezell, Kimberly, Fraser, Jamie L., Gallacher, Lyndon, Genetti, Casie A., Goriely, Anne, Grant, Christina L., Haack, Tobias, Higgs, Jenny E., Hinch, Anjali G., Hurles, Matthew E., Kuechler, Alma, Lachlan, Katherine L., Lalani, Seema R., Lecoquierre, François, Leitão, Elsa, Fevre, Anna Le, Leventer, Richard J., Liebelt, Jan E., Lindsay, Sarah, Lockhart, Paul J., Ma, Alan S., Macnamara, Ellen F., Mansour, Sahar, Maurer, Taylor M., Mendez, Hector R., Metcalfe, Kay, Montgomery, Stephen B., Moosajee, Mariya, Nassogne, Marie-Cécile, Neumann, Serena, O’Donoghue, Michael, O’Leary, Melanie, Palmer, Elizabeth E., Pattani, Nikhil, Phillips, John, Pitsava, Georgia, Pysar, Ryan, Rehm, Heidi L., Reuter, Chloe M., Revencu, Nicole, Riess, Angelika, Rius, Rocio, Rodan, Lance, Roscioli, Tony, Rosenfeld, Jill A., Sachdev, Rani, Shaw-Smith, Charles J., Simons, Cas, Sisodiya, Sanjay M., Snell, Penny, St Clair, Laura, Stark, Zornitza, Stewart, Helen S., Tan, Tiong Yang, Tan, Natalie B., Temple, Suzanna E. L., Thorburn, David R., Tifft, Cynthia J., Uebergang, Eloise, VanNoy, Grace E., Vasudevan, Pradeep, Vilain, Eric, Viskochil, David H., Wedd, Laura, Wheeler, Matthew T., White, Susan M., Wojcik, Monica, Wolfe, Lynne A., Wolfenson, Zoe, Wright, Caroline F., Xiao, Changrui, Zocche, David, Rubenstein, John L., Markenscoff-Papadimitriou, Eirene, Fica, Sebastian M., Baralle, Diana, Depienne, Christel, MacArthur, Daniel G., Howson, Joanna M. M., Sanders, Stephan J., O’Donnell-Luria, Anne, Whiffin, Nicola

Source: Nature; 20240101, Issue: Preprints p1-9, 9p

25. DISSECTING THE CONTRIBUTION OF COMMON VARIANTS TO RISK OF RARE NEURODEVELOPMENTAL CONDITIONS

Authors: Huang, Qinqin, Wigdor, Emilie, Campbell, Patrick, Malawsky, Daniel, Samocha, Kaitlin, Chundru, Kartik, Danecek, Petr, Radford, Elizabeth, Barrett, Jeffrey, Wright, Caroline, Firth, Helen, Warrier, Varun, Young, Alexander, Hurles, Matt, Martin, Hilary

Source: In European Neuropsychopharmacology October 2024 87 Supplement 1:61-61

Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland.

Authors: Wright, Caroline F.¹, caroline.wright@exeter.ac.uk, Campbell, Patrick^2,3, Eberhardt, Ruth Y.², Aitken, Stuart⁴, Perrett, Daniel^2,5, Brent, Simon^2,5, Danecek, Petr², Gardner, Eugene J.², Kartik Chundru, V.², Lindsay, Sarah J.², Andrews, Katrina², Hampstead, Juliet², Kaplanis, Joanna², Samocha, Kaitlin E.², Middleton, Anna⁶, Foreman, Julia^2,5, Hobson, Rachel J.², Parker, Michael J.⁷, Martin, Hilary C.², FitzPatrick, David R.⁴

Source: New England Journal of Medicine; 4/27/2023, Vol. 388 Issue 17, p1559-1571, 13p

PCP Consensus Sequences of Flaviviruses: Correlating Variance with Vector Competence and Disease Phenotype

Authors: Danecek, Petr, Lu, Wenzhe, Schein, Catherine H.

Source: In Journal of Molecular Biology 26 February 2010 396(3):550-563

Flavitrack analysis of the structure and function of West Nile non-structural proteins

Authors: Danecek, Petr, Schein, Catherine H.

Source: International journal of bioinformatics research and applications. 6(2):134-146

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100079049969.0x000001&indx=1&recIds=ETOCvdc_100079049969.0x000001

Mouse genomic variation and its effect on phenotypes and gene regulation.

Authors: Keane, Thomas M., Goodstadt, Leo, Danecek, Petr

Source: Nature; September 15 2011, Vol. 477 Issue 7364, p289-294, 6p

Genetic and chemotherapeutic influences on germline hypermutation.

Authors: Kaplanis, Joanna, Ide, Benjamin, Sanghvi, Rashesh, Neville, Matthew, Danecek, Petr, Coorens, Tim, Prigmore, Elena, Short, Patrick, Gallone, Giuseppe, McRae, Jeremy, Moutsianas, Loukas, Odhams, Chris, Carmichael, Jenny, Barnicoat, Angela, Firth, Helen, O’Brien, Patrick, Rahbari, Raheleh, Hurles, Matthew

Source: Nature; May2022, Vol. 605 Issue 7910, p503-508, 6p

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

Authors: Danecek, Petr¹ pd3@sanger.ac.uk, McCarthy, Shane A.¹, null, null, Durbin, Richard¹ rd@sanger.ac.uk

Source: PLoS ONE. 5/13/2016, Vol. 11 Issue 5, p1-13. 13p.

Subject Terms: *CELL lines, *CELL culture, *SINGLE nucleotide polymorphisms, *GENOTYPES, *GENETIC testing, *DNA copy number variations