2022
Autores
Sarmento, C; Guimaraes, S; Kilinc, GM; Gotherstrom, A; Pires, AE; Ginja, C; Fonseca, NA;
Publicação
PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY & BIOINFORMATICS, PACBB 2021
Abstract
The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint.
2022
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
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
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; 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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; 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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
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
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.
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