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Publicações

Publicações por LIAAD

2022

Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes

Autores
Garg, M; Couturier, D; Nsengimana, J; Fonseca, NA; Wongchenko, M; Yan, Y; Lauss, M; Jönsson, GB; Newton-Bishop, J; Parkinson, C; Middleton, MR; Bishop, DT; McDonald, S; Stefanos, N; Tadross, J; Vergara, IA; Lo, S; Newell, F; Wilmott, JS; Thompson, JF; Long, GV; Scolyer, RA; Corrie, P; Adams, DJ; Brazma, A; Rabbie, R;

Publicação
Nature Communications

Abstract

2022

Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison

Autores
Egeter, B; Verissimo, J; Lopes Lima, M; Chaves, C; Pinto, J; Riccardi, N; Beja, P; Fonseca, NA;

Publicação
MOLECULAR ECOLOGY RESOURCES

Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was nonsignificant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.

2022

Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations (Nature Communications, (2020), 11, 1, (736), 10.1038/s41467-019-13885-w)

Autores
Zhang, Y; Chen, F; Fonseca, NA; He, Y; Fujita, M; Nakagawa, H; Zhang, Z; Brazma, A; Amin, SB; Awadalla, P; Bailey, PJ; Brazma, A; Brooks, AN; Calabrese, C; Chateigner, A; Cortés-Ciriano, I; Craft, B; Craft, D; Creighton, CJ; Davidson, NR; Demircioglu, D; Erkek, S; Fonseca, NA; Frenkel-Morgenstern, M; Goldman, MJ; Greger, L; Göke, J; He, Y; Hoadley, KA; Hou, Y; Huska, MR; Kahles, A; Khurana, E; Kilpinen, H; Korbel, JO; Lamaze, FC; Lehmann, K; Li, C; Li, S; Li, X; Li, X; Liu, D; Liu, F; Liu, X; Marin, MG; Markowski, J; Meyerson, M; Nandi, T; Nielsen, MM; Ojesina, AI; Ouellette, BFF; Pan-Hammarström, Q; Park, PJ; Pedamallu, CS; Pedersen, JS; Perry, MD; Rätsch, G; Schwarz, RF; Shiraishi, Y; Siebert, R; Soulette, CM; Stark, SG; Stegle, O; Su, H; Tan, P; Teh, BT; Urban, L; Wang, J; Waszak, SM; Wu, K; Xiang, Q; Xiong, H; Yakneen, S; Yang, H; Ye, C; Yung, CK; Zhang, F; Zhang, J; Zhang, X; Zhang, Z; Zheng, L; Zhu, J; Zhu, S; Akdemir, KC; Alvarez, EG; Baez-Ortega, A; Beroukhim, R; Boutros, PC; Bowtell, DDL; Brors, B; Burns, KH; Campbell, PJ; Chan, K; Chen, K; Cortés-Ciriano, I; Dueso-Barroso, A; Dunford, AJ; Edwards, PA; Estivill, X; Etemadmoghadam, D; Feuerbach, L; Fink, JL; Frenkel-Morgenstern, M; Garsed, DW; Gerstein, M; Gordenin, DA; Haan, D; Haber, JE; Hess, JM; Hutter, B; Imielinski, M; Jones, DTW; Ju, YS; Kazanov, MD; Klimczak, LJ; Koh, Y; Korbel, JO; Kumar, K; Lee, EA; Lee, JJ; Li, Y; Lynch, AG; Macintyre, G; Markowetz, F; Martincorena, I; Martinez-Fundichely, A; Meyerson, M; Miyano, S; Nakagawa, H; Navarro, FCP; Ossowski, S; Park, PJ; Pearson, JV; Puiggròs, M; Rippe, K; Roberts, ND; Roberts, SA; Rodriguez-Martin, B; Schumacher, SE; Scully, R; Shackleton, M; Sidiropoulos, N; Sieverling, L; Stewart, C; Torrents, D; Tubio, JMC; Villasante, I; Waddell, N; Wala, JA; Weischenfeldt, J; Yang, L; Yao, X; Yoon, S; Zamora, J; Zhang, C; Creighton, CJ; Aaltonen, LA; Abascal, F; Abeshouse, A; Aburatani, H; Adams, DJ; Agrawal, N; Ahn, KS; Ahn, S; Aikata, H; Akbani, R; Akdemir, KC; Al-Ahmadie, H; Al-Sedairy, ST; Al-Shahrour, F; Alawi, M; Albert, M; Aldape, K; Alexandrov, LB; Ally, A; Alsop, K; Alvarez, EG; Amary, F; Amin, SB; Aminou, B; Ammerpohl, O; Anderson, MJ; Ang, Y; Antonello, D; Anur, P; Aparicio, S; Appelbaum, EL; Arai, Y; Aretz, A; Arihiro, K; Ariizumi, S; Armenia, J; Arnould, L; Asa, S; Assenov, Y; Atwal, G; Aukema, S; Auman, JT; Aure, MRR; Awadalla, P; Aymerich, M; Bader, GD; Baez-Ortega, A; Bailey, MH; Bailey, PJ; Balasundaram, M; Balu, S; Bandopadhayay, P; Banks, RE; Barbi, S; Barbour, AP; Barenboim, J; Barnholtz-Sloan, J; Barr, H; Barrera, E; Bartlett, J; Bartolome, J; Bassi, C; Bathe, OF; Baumhoer, D; Bavi, P; Baylin, SB; Bazant, W; Beardsmore, D; Beck, TA; Behjati, S; Behren, A; Niu, B; Bell, C; Beltran, S; Benz, C; Berchuck, A; Bergmann, AK; Bergstrom, EN; Berman, BP; Berney, DM; Bernhart, SH; Beroukhim, R; Berrios, M; Bersani, S; Bertl, J; Betancourt, M; Bhandari, V; Bhosle, SG; Biankin, AV; Bieg, M; Bigner, D; Binder, H; Birney, E; Birrer, M; Biswas, NK; Bjerkehagen, B; Bodenheimer, T; Boice, L; Bonizzato, G; De Bono, JS; Boot, A; Bootwalla, MS; Borg, A; Borkhardt, A; Boroevich, KA; Borozan, I; Borst, C; Bosenberg, M; Bosio, M; Boultwood, J; Bourque, G; Boutros, PC; Bova, GS; Bowen, DT; Bowlby, R; Bowtell, DDL; Boyault, S; Boyce, R; Boyd, J; Brazma, A; Brennan, P; Brewer, DS; Brinkman, AB; Bristow, RG; Broaddus, RR; Brock, JE; Brock, M; Broeks, A; Brooks, AN; Brooks, D; Brors, B; Brunak, S; Bruxner, TJC; Bruzos, AL; Buchanan, A; Buchhalter, I; Buchholz, C; Bullman, S; Burke, H; Burkhardt, B; Burns, KH; Busanovich, J; Bustamante, CD; Butler, AP; Butte, AJ; Byrne, NJ; Børresen-Dale, A; Caesar-Johnson, SJ; Cafferkey, A; Cahill, D; Calabrese, C; Caldas, C; Calvo, F; Camacho, N; Campbell, PJ; Campo, E; Cantù, C; Cao, S; Carey, TE; Carlevaro-Fita, J; Carlsen, R; Cataldo, I; Cazzola, M; Cebon, J; Cerfolio, R; Chadwick, DE; Chakravarty, D; Chalmers, D; Chan, CWY; Chan, K; Chan-Seng-Yue, M; Chandan, VS; Chang, DK; Chanock, SJ; Chantrill, LA; Chateigner, A; Chatterjee, N; Chayama, K; Chen, H; Chen, J; Chen, K; Chen, Y; Chen, Z; Cherniack, AD; Chien, J; Chiew, Y; Chin, S; Cho, J; Cho, S; Choi, JK; Choi, W; Chomienne, C; Chong, Z; Choo, SP; Chou, A; Christ, AN; Christie, EL; Chuah, E; Cibulskis, C; Cibulskis, K; Cingarlini, S; Clapham, P; Claviez, A; Cleary, S; Cloonan, N; Cmero, M; Collins, CC; Connor, AA; Cooke, SL; Cooper, CS; Cope, L; Corbo, V; Cordes, MG; Cordner, SM; Cortés-Ciriano, I; Covington, K; Cowin, PA; Craft, B; Craft, D; Creighton, CJ; Cun, Y; Curley, E; Cutcutache, I; Czajka, K; Czerniak, B; Dagg, RA; Danilova, L; Davi, MV; Davidson, NR; Davies, H; Davis, IJ; Davis-Dusenbery, BN; Dawson, KJ; De La Vega, FM; De Paoli-Iseppi, R; Defreitas, T; Tos, APD; Delaneau, O; Demchok, JA; Demeulemeester, J; Demidov, GM; Demircioglu, D; Dennis, NM; Denroche, RE; Dentro, SC; Desai, N; Deshpande, V; Deshwar, AG; Desmedt, C; Deu-Pons, J; Dhalla, N; Dhani, NC; Dhingra, P; Dhir, R; DiBiase, A; Diamanti, K; Ding, L; Ding, S; Dinh, HQ; Dirix, L; Doddapaneni, H; Donmez, N; Dow, MT; Drapkin, R; Drechsel, O; Drews, RM; Serge, S; Dudderidge, T; Dueso-Barroso, A; Dunford, AJ; Dunn, M; Dursi, LJ; Duthie, FR; Dutton-Regester, K; Eagles, J; Easton, DF; Edmonds, S; Edwards, PA; Edwards, SE; Eeles, RA; Ehinger, A; Eils, J; Eils, R; El-Naggar, A; Eldridge, M; Ellrott, K; Erkek, S; Escaramis, G; Espiritu, SMG; Estivill, X; Etemadmoghadam, D; Eyfjord, JE; Faltas, BM; Fan, D; Fan, Y; Faquin, WC; Farcas, C; Fassan, M; Fatima, A; Favero, F; Fayzullaev, N; Felau, I; Fereday, S; Ferguson, ML; Ferretti, V; Feuerbach, L; Field, MA; Fink, JL; Finocchiaro, G; Fisher, C; Fittall, MW; Fitzgerald, A; Fitzgerald, RC; Flanagan, AM; Fleshner, NE; Flicek, P; Foekens, JA; Fong, KM; Fonseca, NA; Foster, CS; Fox, NS; Fraser, M; Frazer, S; Frenkel-Morgenstern, M; Friedman, W; Frigola, J; Fronick, CC; Fujimoto, A; Fujita, M; Fukayama, M; Fulton, LA; Fulton, RS; Furuta, M; Futreal, PA; Füllgrabe, A; Gabriel, SB; Gallinger, S; Gambacorti-Passerini, C; Gao, J; Gao, S; Garraway, L; Garred, Ø; Garrison, E; Garsed, DW; Gehlenborg, N; Gelpi, JLL; George, J; Gerhard, DS; Gerhauser, C; Gershenwald, JE; Gerstein, M; Gerstung, M; Getz, G; Ghori, M; Ghossein, R; Giama, NH; Gibbs, RA; Gibson, B; Gill, AJ; Gill, P; Giri, DD; Glodzik, D; Gnanapragasam, VJ; Goebler, ME; Goldman, MJ; Gomez, C; Gonzalez, S; Gonzalez-Perez, A; Gordenin, DA; Gossage, J; Gotoh, K; Govindan, R; Grabau, D; Graham, JS; Grant, RC; Green, AR; Green, E; Greger, L; Grehan, N; Grimaldi, S; Grimmond, SM; Grossman, RL; Grundhoff, A; Gundem, G; Guo, Q; Gupta, M; Gupta, S; Gut, IG; Gut, M; Göke, J; Ha, G; Haake, A; Haan, D; Haas, S; Haase, K; Haber, JE; Habermann, N; Hach, F; Haider, S; Hama, N; Hamdy, FC; Hamilton, A; Hamilton, MP; Han, L; Hanna, GB; Hansmann, M; Haradhvala, NJ; Harismendy, O; Harliwong, I; Harmanci, AO; Harrington, E; Hasegawa, T; Haussler, D; Hawkins, S; Hayami, S; Hayashi, S; Hayes, DN; Hayes, SJ; Hayward, NK; Hazell, S; He, Y; Heath, AP; Heath, SC; Hedley, D; Hegde, AM; Heiman, DI; Heinold, MC; Heins, Z; Heisler, LE; Hellstrom-Lindberg, E; Helmy, M; Heo, SG; Hepperla, AJ; Heredia-Genestar, JM; Herrmann, C; Hersey, P; Hess, JM; Hilmarsdottir, H; Hinton, J; Hirano, S; Hiraoka, N; Hoadley, KA; Hobolth, A; Hodzic, E; Hoell, JI; Hoffmann, S; Hofmann, O; Holbrook, A; Holik, AZ; Hollingsworth, MA; Holmes, O; Holt, RA; Hong, C; Hong, EP; Hong, JH; Hooijer, GK; Hornshøj, H; Hosoda, F; Hou, Y; Hovestadt, V; Howat, W; Hoyle, AP; Hruban, RH; Hu, J; Hu, T; Hua, X; Huang, K; Huang, M; Huang, MN; Huang, V; Huang, Y; Huber, W; Hudson, TJ; Hummel, M; Hung, JA; Huntsman, D; Hupp, TR; Huse, J; Huska, MR; Hutter, B; Hutter, CM; Hübschmann, D; Iacobuzio-Donahue, CA; Imbusch, CD; Imielinski, M; Imoto, S; Isaacs, WB; Isaev, K; Ishikawa, S; Iskar, M; Islam, SMA; Ittmann, M; Ivkovic, S; Izarzugaza, JMG; Jacquemier, J; Jakrot, V; Jamieson, NB; Jang, GH; Jang, SJ; Jayaseelan, JC; Jayasinghe, R; Jefferys, SR; Jegalian, K; Jennings, JL; Jeon, S; Jerman, L; Ji, Y; Jiao, W; Johansson, PA; Johns, AL; Johns, J; Johnson, R; Johnson, TA; Jolly, C; Joly, Y; Jonasson, JG; Jones, CD; Jones, DR; Jones, DTW; Jones, N; Jones, SJM; Jonkers, J; Ju, YS; Juhl, H; Jung, J; Juul, M; Juul, RI; Juul, S; Jäger, N; Kabbe, R; Kahles, A; Kahraman, A; Kaiser, VB; Kakavand, H; Kalimuthu, S; von Kalle, C; Kang, KJ; Karaszi, K; Karlan, B; Karlic, R; Karsch, D; Kasaian, K; Kassahn, KS; Katai, H; Kato, M; Katoh, H; Kawakami, Y; Kay, JD; Kazakoff, SH; Kazanov, MD; Keays, M; Kebebew, E; Kefford, RF; Kellis, M; Kench, JG; Kennedy, CJ; Kerssemakers, JNA; Khoo, D; Khoo, V; Khuntikeo, N; Khurana, E; Kilpinen, H; Kim, HK; Kim, H; Kim, H; Kim, H; Kim, J; Kim, J; Kim, JK; Kim, Y; King, TA; Klapper, W; Kleinheinz, K; Klimczak, LJ; Knappskog, S; Kneba, M; Knoppers, BM; Koh, Y; Jan Komorowski; Komura, D; Komura, M; Kong, G; Kool, M; Korbel, JO; Korchina, V; Korshunov, A; Koscher, M; Koster, R; Kote-Jarai, Z; Koures, A; Kovacevic, M; Kremeyer, B; Kretzmer, H; Kreuz, M; Krishnamurthy, S; Kube, D; Kumar, K; Kumar, P; Kumar, S; Kumar, Y; Kundra, R; Kübler, K; Küppers, R; Lagergren, J; Lai, PH; Laird, PW; Lakhani, SR; Lalansingh, CM; Lalonde, E; Lamaze, FC; Lambert, A; Lander, E; Landgraf, P; Landoni, L; Langerød, A; Lanzós, A; Larsimont, D; Larsson, E; Lathrop, M; Lau, LMS; Lawerenz, C; Lawlor, RT; Lawrence, MS; Lazar, AJ; Lazic, AM; Le, X; Lee, D; Lee, D; Lee, EA; Lee, HJ; Lee, JJ; Lee, J; Lee, J; Lee, MTM; Lee-Six, H; Lehmann, K; Lehrach, H; Lenze, D; Leonard, CR; Leongamornlert, DA; Leshchiner, I; Letourneau, L; Letunic, I; Levine, DA; Lewis, L; Ley, T; Li, C; Li, CH; Li, HI; Li, J; Li, L; Li, S; Li, S; Li, X; Li, X; Li, X; Li, Y; Liang, H; Liang, S; Lichter, P; Lin, P; Lin, Z; Linehan, WM; Lingjærde, OC; Liu, D; Liu, EM; Liu, FF; Liu, F; Liu, J; Liu, X; Livingstone, J; Livitz, D; Livni, N; Lochovsky, L; Loeffler, M; Long, GV; Lopez-Guillermo, A; Lou, S; Louis, DN; Lovat, LB; Lu, Y; Lu, Y; Lu, Y; Luchini, C; Lungu, I; Luo, X; Luxton, HJ; Lynch, AG; Lype, L; López, C; López-Otín, C; Ma, EZ; Ma, Y; MacGrogan, G; MacRae, S; Macintyre, G; Madsen, T; Maejima, K; Mafficini, A; Maglinte, DT; Maitra, A; Majumder, PP; Malcovati, L; Malikic, S; Malleo, G; Mann, GJ; Mantovani-Löffler, L; Marchal, K; Marchegiani, G; Mardis, ER; Margolin, AA; Marin, MG; Markowetz, F; Markowski, J; Marks, J; Marques-Bonet, T; Marra, MA; Marsden, L; Martens, JWM; Martin, S; Martin-Subero, JI; Martincorena, I; Martinez-Fundichely, A; Maruvka, YE; Mashl, RJ; Massie, CE; Matthew, TJ; Matthews, L; Mayer, E; Mayes, S; Mayo, M; Mbabaali, F; McCune, K; McDermott, U; McGillivray, PD; McLellan, MD; McPherson, JD; McPherson, JR; McPherson, TA; Meier, SR; Meng, A; Meng, S; Menzies, A; Merrett, ND; Merson, S; Meyerson, M; Meyerson, W; Mieczkowski, PA; Mihaiescu, GL; Mijalkovic, S; Mikkelsen, T; Milella, M; Mileshkin, L; Miller, CA; Miller, DK; Miller, JK; Mills, GB; Milovanovic, A; Minner, S; Miotto, M; Arnau, GM; Mirabello, L; Mitchell, C; Mitchell, TJ; Miyano, S; Miyoshi, N; Mizuno, S; Molnár-Gábor, F; Moore, MJ; Moore, RA; Morganella, S; Morris, QD; Morrison, C; Mose, LE; Moser, CD; Muiños, F; Mularoni, L; Mungall, AJ; Mungall, K; Musgrove, EA; Mustonen, V; Mutch, D; Muyas, F; Muzny, DM; Muñoz, A; Myers, J; Myklebost, O; Möller, P; Nagae, G; Nagrial, AM; Nahal-Bose, HK; Nakagama, H; Nakagawa, H; Nakamura, H; Nakamura, T; Nakano, K; Nandi, T; Nangalia, J; Nastic, M; Navarro, A; Navarro, FCP; Neal, DE; Nettekoven, G; Newell, F; Newhouse, SJ; Newton, Y; Ng, AWT; Ng, A; Nicholson, J; Nicol, D; Nie, Y; Nielsen, GP; Nielsen, MM; Nik-Zainal, S; Noble, MS; Nones, K; Northcott, PA; Notta, F; O’Connor, BD; O’Donnell, P; O’Donovan, M; O’Meara, S; O’Neill, BP; O’Neill, JR; Ocana, D; Ochoa, A; Oesper, L; Ogden, C; Ohdan, H; Ohi, K; Ohno-Machado, L; Oien, KA; Ojesina, AI; Ojima, H; Okusaka, T; Omberg, L; Ong, CK; Ossowski, S; Ott, G; Ouellette, BFF; P’ng, C; Paczkowska, M; Paiella, S; Pairojkul, C; Pajic, M; Pan-Hammarström, Q; Papaemmanuil, E; Papatheodorou, I; Paramasivam, N; Park, JW; Park, J; Park, K; Park, K; Park, PJ; Parker, JS; Parsons, SL; 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Publicação
Nature Communications

Abstract
In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArticle has been corrected to include the members and affiliations of the PCAWG Consortium in the main paper; the corrections have been made to the HTML version of the Article but not the PDF version. In the PCAWG Transcriptome Working Group, the affiliation ‘BioForA, French National Institute for Agriculture, Food, and Environment (INRAE),ONF,Orléans, France’ for Aurélien Chateignerwas alsomissing. The original Article has been corrected. Additional corrections to affiliations have been made to the PDF and HTML versions of the original Article for consistency of information between the PCAWG list and the main paper. © The Author(s) 2022.

2022

Impact in the quality of life of parents of children with chronic diseases using psychoeducational interventions - A systematic review with meta- analysis

Autores
Rodrigues, MG; Rodrigues, JD; Pereira, AT; Azevedo, LF; Rodrigues, PP; Areias, JC; Areias, ME;

Publicação
PATIENT EDUCATION AND COUNSELING

Abstract
Objective: This study aimed to identify psychoeducational interventions applied to parents of children with chronic diseases and evaluate their impact on their quality of life (QoL). Methods: It was conducted in six databases, complemented by references from the included studies and other reviews, manual search, and contact with experts. We included primary studies on parents of children with chronic diseases that studied psychoeducational interventions versus standard care. Results: We screened 6604 titles and abstracts, reviewed the full text of 60 records, and included 37 primary studies. Half of the studies were on Asthma. We found three intervention formats: one-to-one (43%), groups (49%), and combined approach with individual and group settings (8%). More than 60% of the included studies found statistically significant differences between the intervention and the control group (p < 0.05). Conclusion: Several interventions have shown efficacy in improving parental QoL. Despite that, there is insufficient evidence of interventions' implementation. Practice implications: A holistic approach encompassing the patient and the family's biopsychosocial dimensions is fundamental in successfully managing chronic disease in children. It is vital to design and implement interventions accommodating the common issues experienced by children, parents, and families that deal with chronic childhood conditions. Systematic review registration number PROSPERO 2018 CRD42018092135.

2022

Biomarkers for Alzheimer's Disease in the Current State: A Narrative Review

Autores
Gunes, S; Aizawa, Y; Sugashi, T; Sugimoto, M; Rodrigues, PP;

Publicação
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Abstract
Alzheimer's disease (AD) has become a problem, owing to its high prevalence in an aging society with no treatment available after onset. However, early diagnosis is essential for preventive intervention to delay disease onset due to its slow progression. The current AD diagnostic methods are typically invasive and expensive, limiting their potential for widespread use. Thus, the development of biomarkers in available biofluids, such as blood, urine, and saliva, which enables low or non-invasive, reasonable, and objective evaluation of AD status, is an urgent task. Here, we reviewed studies that examined biomarker candidates for the early detection of AD. Some of the candidates showed potential biomarkers, but further validation studies are needed. We also reviewed studies for non-invasive biomarkers of AD. Given the complexity of the AD continuum, multiple biomarkers with machine-learning-classification methods have been recently used to enhance diagnostic accuracy and characterize individual AD phenotypes. Artificial intelligence and new body fluid-based biomarkers, in combination with other risk factors, will provide a novel solution that may revolutionize the early diagnosis of AD.

2022

Partial Multiple Imputation With Variational Autoencoders: Tackling Not at Randomness in Healthcare Data

Autores
Pereira, RC; Abreu, PH; Rodrigues, PP;

Publicação
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS

Abstract
Missing data can pose severe consequences in critical contexts, such as clinical research based on routinely collected healthcare data. This issue is usually handled with imputation strategies, but these tend to produce poor and biased results under the Missing Not At Random (MNAR) mechanism. A recent trend that has been showing promising results for MNAR is the use of generative models, particularly Variational Autoencoders. However, they have a limitation: the imputed values are the result of a single sample, which can be biased. To tackle it, an extension to the Variational Autoencoder that uses a partial multiple imputation procedure is introduced in this work. The proposed method was compared to 8 state-of-the-art imputation strategies, in an experimental setup with 34 datasets from the medical context, injected with the MNAR mechanism (10% to 80% rates). The results were evaluated through the Mean Absolute Error, with the new method being the overall best in 71% of the datasets, significantly outperforming the remaining ones, particularly for high missing rates. Finally, a case study of a classification task with heart failure data was also conducted, where this method induced improvements in 50% of the classifiers.

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