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Article: Applications of second generation sequencing technologies in complex disorders.

Bayés, Mònica / Heath, Simon / Gut, Ivo Glynne

Current topics in behavioral neurosciences

2012 Volume 12, Page(s) 321–343

Abstract: Second generation sequencing (2ndGS) technologies generate unprecedented amounts of sequence data very rapidly and at relatively limited costs, allowing the sequence of a human genome to be completed in a few weeks. The principle is on the basis of ... ...

Abstract	Second generation sequencing (2ndGS) technologies generate unprecedented amounts of sequence data very rapidly and at relatively limited costs, allowing the sequence of a human genome to be completed in a few weeks. The principle is on the basis of generating millions of relatively short reads from amplified single DNA fragments using iterative cycles of nucleotide extensions. However, the data generated on this scale present new challenges in interpretation, data analysis and data management. 2ndGS technologies are becoming widespread and are profoundly impacting biomedical research. Common applications include whole-genome sequencing, target resequencing, characterization of structural and copy number variation, profiling epigenetic modifications, transcriptome sequencing and identification of infectious agents. New methodologies and instruments that will enable to sequence the complete human genome in less than a day at a cost of less than $1,000 are currently in development.
MeSH term(s)	Computational Biology ; Epigenesis, Genetic ; Genetic Research ; Genome, Human/genetics ; Genomics/instrumentation ; Genomics/methods ; Humans ; Sequence Analysis, DNA/instrumentation ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2012
Publishing country	Germany
Document type	Journal Article
ISSN	1866-3370
ISSN	1866-3370
DOI	10.1007/7854_2011_196
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Article ; Online: Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes

Torrico, Bàrbara / Shaw, Alex D. / Mosca, Roberto / Vivó-Luque, Norma / Hervás, Amaia / Fernàndez-Castillo, Noèlia / Aloy, Patrick / Bayés, Mònica / Fullerton, Janice M. / Cormand, Bru / Toma, Claudio

Journal of psychiatry & neuroscience : JPN

2019 Volume 44, Issue 5, Page(s) 350–359

Abstract: Background: Previous research has implicated de novo and inherited truncating mutations in autism-spectrum disorder. We aim to investigate whether the load of inherited truncating mutations contributes similarly to high-functioning autism, and to ... ...

Abstract	Background: Previous research has implicated de novo and inherited truncating mutations in autism-spectrum disorder. We aim to investigate whether the load of inherited truncating mutations contributes similarly to high-functioning autism, and to characterize genes that harbour de novo variants in high-functioning autism. Methods: We performed whole-exome sequencing in 20 high-functioning autism families (average IQ = 100). Results: We observed no difference in the number of transmitted versus nontransmitted truncating alleles for high-functioning autism (117 v. 130, p = 0.78). Transmitted truncating and de novo variants in high-functioning autism were not enriched in gene ontology (GO) or Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, or in autism-related gene sets. However, in a patient with high-functioning autism we identified a de novo variant in a canonical splice site of LRP1, a postsynaptic density gene that is a target for fragile X mental retardation protein (FRMP). This de novo variant leads to in-frame skipping of exon 29, removing 2 of 6 blades of the β-propeller domain 4 of LRP1, with putative functional consequences. Large data sets implicate LRP1 across a number of psychiatric disorders: de novo variants are associated with autism-spectrum disorder (p = 0.039) and schizophrenia (p = 0.008) from combined sequencing projects; common variants using genome-wide association study data sets from the Psychiatric Genomics Consortium show gene-based association in schizophrenia (p = 6.6 × E−07) and in a meta-analysis across 7 psychiatric disorders (p = 2.3 × E−03); and the burden of ultra-rare pathogenic variants has been shown to be higher in autism-spectrum disorder (p = 1.2 × E−05), using whole-exome sequencing from 6135 patients with schizophrenia, 1778 patients with autism-spectrum disorder and 7875 controls. Limitations: We had a limited sample of patients with high-functioning autism, related to difficulty in recruiting probands with high cognitive performance and no family history of psychiatric disorders. Conclusion: Previous studies and ours suggest an effect of truncating mutations restricted to severe autism-spectrum disorder phenotypes that are associated with intellectual disability. We provide evidence for pleiotropic effects of common and rare variants in the LRP1 gene across psychiatric phenotypes.
MeSH term(s)	Adolescent ; Adult ; Alleles ; Autism Spectrum Disorder/genetics ; Autistic Disorder/genetics ; Databases, Genetic ; Epilepsy/genetics ; Family ; Female ; Gene Regulatory Networks ; Genetic Pleiotropy ; Humans ; Intellectual Disability/genetics ; Low Density Lipoprotein Receptor-Related Protein-1/genetics ; Male ; Models, Molecular ; Mutation ; RNA Splicing ; Schizophrenia/genetics ; Siblings ; Spain ; Whole Exome Sequencing ; Young Adult
Chemical Substances	LRP1 protein, human ; Low Density Lipoprotein Receptor-Related Protein-1
Language	English
Publishing date	2019-05-16
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1077443-9
ISSN	1488-2434 ; 1180-4882
ISSN (online)	1488-2434
ISSN	1180-4882
DOI	10.1503/jpn.180184
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Article: The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons.

Simões, João / Bezerra, Ana R / Moura, Gabriela R / Araújo, Hugo / Gut, Ivo / Bayes, Mónica / Santos, Manuel A S

Frontiers in microbiology

2016 Volume 7, Page(s) 401

Abstract: The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic ... ...

Abstract	The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.
Language	English
Publishing date	2016-03-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.00401
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Article ; Online: Design and evaluation of a panel of single-nucleotide polymorphisms in microRNA genomic regions for association studies in human disease.

Muiños-Gimeno, Margarita / Montfort, Magda / Bayés, Mònica / Estivill, Xavier / Espinosa-Parrilla, Yolanda

European journal of human genetics : EJHG

2009 Volume 18, Issue 2, Page(s) 218–226

Abstract: MicroRNAs (miRNA) are recognized posttranscriptional gene repressors involved in the control of almost every biological process. Allelic variants in these regions may be an important source of phenotypic diversity and contribute to disease susceptibility. ...

Abstract	MicroRNAs (miRNA) are recognized posttranscriptional gene repressors involved in the control of almost every biological process. Allelic variants in these regions may be an important source of phenotypic diversity and contribute to disease susceptibility. We analyzed the genomic organization of 325 human miRNAs (release 7.1, miRBase) to construct a panel of 768 single-nucleotide polymorphisms (SNPs) covering approximately 1 Mb of genomic DNA, including 131 isolated miRNAs (40%) and 194 miRNAs arranged in 48 miRNA clusters, as well as their 5-kb flanking regions. Of these miRNAs, 37% were inside known protein-coding genes, which were significantly associated with biological functions regarding neurological, psychological or nutritional disorders. SNP coverage analysis revealed a lower SNP density in miRNAs compared with the average of the genome, with only 24 SNPs located in the 325 miRNAs studied. Further genotyping of 340 unrelated Spanish individuals showed that more than half of the SNPs in miRNAs were either rare or monomorphic, in agreement with the reported selective constraint on human miRNAs. A comparison of the minor allele frequencies between Spanish and HapMap population samples confirmed the applicability of this SNP panel to the study of complex disorders among the Spanish population, and revealed two miRNA regions, hsa-mir-26a-2 in the CTDSP2 gene and hsa-mir-128-1 in the R3HDM1 gene, showing geographical allelic frequency variation among the four HapMap populations, probably because of differences in natural selection. The designed miRNA SNP panel could help to identify still hidden links between miRNAs and human disease.
MeSH term(s)	Chromosome Mapping ; DNA/genetics ; DNA/isolation & purification ; Gene Frequency ; Genetic Diseases, Inborn/genetics ; Genetic Variation ; Genome, Human ; Genome-Wide Association Study/methods ; Genotype ; Geography ; Humans ; Lymphocytes/physiology ; MicroRNAs/genetics ; Polymorphism, Single Nucleotide/genetics ; Reference Values ; Spain
Chemical Substances	MicroRNAs ; DNA (9007-49-2)
Language	English
Publishing date	2009-10-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/ejhg.2009.165
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Article ; Online: Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.

Castellano, Sergi / Andrés, Aida M / Bosch, Elena / Bayes, Mònica / Guigó, Roderic / Clark, Andrew G

Molecular biology and evolution

2009 Volume 26, Issue 9, Page(s) 2031–2040

Abstract: Selenocysteine (Sec), the 21st amino acid, is incorporated into proteins through the recoding of a termination codon, an inefficient translational process mediated by a complex molecular machinery. Sec is a rare amino acid in extant proteins, chemically ... ...

Abstract	Selenocysteine (Sec), the 21st amino acid, is incorporated into proteins through the recoding of a termination codon, an inefficient translational process mediated by a complex molecular machinery. Sec is a rare amino acid in extant proteins, chemically similar to cysteine (Cys), found in homologous position to Cys of nonselenoprotein families. Selenoproteins account for the dependence of vertebrates on environmental selenium (Se) and have an important role in several Se-deficiency diseases. Selenoproteins are poorly characterized enzymes and reports on the functional exchangeability of Sec with Cys are limited and controversial. Whether the unique role of Sec in some selenoenzymes illustrates the broader contribution of Se to protein function is unknown (Gromer S, Johansson L, Bauer H, Arscott LD, Rauch S, Ballou DP, Williams CH Jr, Schirmer RH, Arnér ES. 2003. Active sites of thioredoxin reductases: why selenoproteins? Proc Natl Acad Sci USA. 100:12618-12623). Here, we address this question from an evolutionary perspective by the simultaneous identification of the patterns of divergence in almost half a billion years of vertebrate evolution and diversity within the human lineage for the full complement of enzymatic Sec residues in these proteomes. We complete this analysis with data for the homologous Cys residues in the same genomes. Our results indicate concerted purifying selection across Sec and Cys sites in all selenoproteomes, consistent with a unique role of Sec in protein function, low exchangeability, and an unknown degree of functional divergence with Cys homologs. The distinct biochemical properties of Sec, rather than the geographical distribution of Se, global O(2) levels or Sec metabolic cost, appear to play a major role in driving adaptive changes in vertebrate selenoproteomes. A better understanding of the selenoproteomes and neutral evolutionary patterns in other taxa will be necessary to fully assess the generality of this conclusion.
MeSH term(s)	Animals ; Evolution, Molecular ; Humans ; Oxygen/metabolism ; Phylogeny ; Proteins/genetics ; Proteins/metabolism ; Proteome/genetics ; Selenocysteine/genetics ; Selenocysteine/metabolism ; Selenoproteins/genetics ; Vertebrates/metabolism
Chemical Substances	Proteins ; Proteome ; Selenoproteins ; Selenocysteine (0CH9049VIS) ; Oxygen (S88TT14065)
Language	English
Publishing date	2009-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msp109
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Article: Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in

Weil, Tobias / Santamaría, Rodrigo / Lee, Wanseon / Rung, Johan / Tocci, Noemi / Abbey, Darren / Bezerra, Ana R / Carreto, Laura / Moura, Gabriela R / Bayés, Mónica / Gut, Ivo G / Csikasz-Nagy, Attila / Cavalieri, Duccio / Berman, Judith / Santos, Manuel A S

mSphere

2017 Volume 2, Issue 4

Abstract: Regulated erroneous protein translation (adaptive mistranslation) increases proteome diversity and produces advantageous phenotypic variability in the human ... ...

Abstract	Regulated erroneous protein translation (adaptive mistranslation) increases proteome diversity and produces advantageous phenotypic variability in the human pathogen
Language	English
Publishing date	2017-07
Publishing country	United States
Document type	Journal Article
ISSN	2379-5042
ISSN	2379-5042
DOI	10.1128/mSphere.00167-17
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Article ; Online: Correction: Colorectal adenomas contain multiple somatic mutations that do not coincide with synchronous adenocarcinoma specimens.

Vaqué, José P / Martínez, Nerea / Varela, Ignacio / Fernández, Fidel / Mayorga, Marta / Derdak, Sophia / Beltrán, Sergi / Moreno, Thaidy / Almaraz, Carmen / De Las Heras, Gonzalo / Bayés, Mónica / Gut, Ivo / Crespo, Javier / Piris, Miguel A

PloS one

2015 Volume 10, Issue 4, Page(s) e0125459

Language	English
Publishing date	2015
Publishing country	United States
Document type	Published Erratum
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0125459
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Article ; Online: Colorectal adenomas contain multiple somatic mutations that do not coincide with synchronous adenocarcinoma specimens.

PloS one

2015 Volume 10, Issue 3, Page(s) e0119946

Abstract: We have performed a comparative ultrasequencing study of multiple colorectal lesions obtained simultaneously from four patients. Our data show that benign lesions (adenomatous or hyperplastic polyps) contain a high mutational load. Additionally multiple ... ...

Abstract	We have performed a comparative ultrasequencing study of multiple colorectal lesions obtained simultaneously from four patients. Our data show that benign lesions (adenomatous or hyperplastic polyps) contain a high mutational load. Additionally multiple synchronous colorectal lesions show non overlapping mutational signatures highlighting the degree of heterogeneity between multiple specimens in the same patient. Observations in these cases imply that considering not only the number of mutations but an effective oncogenic combination of mutations can determine the malignant progression of colorectal lesions.
MeSH term(s)	Adenocarcinoma/genetics ; Adenocarcinoma/pathology ; Adenoma/genetics ; Adenoma/pathology ; Aged ; Aged, 80 and over ; Clonal Evolution ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Female ; Humans ; Male ; Mutation
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0119946
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Article ; Online: Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover.

Kalapis, Dorottya / Bezerra, Ana R / Farkas, Zoltán / Horvath, Peter / Bódi, Zoltán / Daraba, Andreea / Szamecz, Béla / Gut, Ivo / Bayes, Mónica / Santos, Manuel A S / Pál, Csaba

PLoS biology

2015 Volume 13, Issue 11, Page(s) e1002291

Abstract: Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was ... ...

Abstract	Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome-mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature.
MeSH term(s)	Adaptation, Physiological ; Candida albicans/enzymology ; Candida albicans/genetics ; Candida albicans/growth & development ; Candida albicans/physiology ; Codon ; Evolution, Molecular ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Gene Dosage ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Models, Genetic ; Mutation ; Proteasome Endopeptidase Complex/metabolism ; Protein Stability ; Proteome/genetics ; Proteome/metabolism ; Ribosomes/enzymology ; Ribosomes/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Selection, Genetic ; Stress, Physiological ; Ubiquitin-Protein Ligase Complexes/genetics ; Ubiquitin-Protein Ligase Complexes/metabolism ; Ubiquitination
Chemical Substances	Codon ; Fungal Proteins ; Proteome ; Saccharomyces cerevisiae Proteins ; Ubiquitin-Protein Ligase Complexes (EC 2.3.2.23) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2015-11-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.1002291
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Article ; Online: The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases.

Laurie, Steven / Piscia, Davide / Matalonga, Leslie / Corvó, Alberto / Fernández-Callejo, Marcos / Garcia-Linares, Carles / Hernandez-Ferrer, Carles / Luengo, Cristina / Martínez, Inés / Papakonstantinou, Anastasios / Picó-Amador, Daniel / Protasio, Joan / Thompson, Rachel / Tonda, Raul / Bayés, Mònica / Bullich, Gemma / Camps-Puchadas, Jordi / Paramonov, Ida / Trotta, Jean-Rémi /

Alonso, Angel / Attimonelli, Marcella / Béroud, Christophe / Bros-Facer, Virginie / Buske, Orion J / Cañada-Pallarés, Andrés / Fernández, José M / Hansson, Mats G / Horvath, Rita / Jacobsen, Julius O B / Kaliyaperumal, Rajaram / Lair-Préterre, Séverine / Licata, Luana / Lopes, Pedro / López-Martín, Estrella / Mascalzoni, Deborah / Monaco, Lucia / Pérez-Jurado, Luis A / Posada de la Paz, Manuel / Rambla, Jordi / Rath, Ana / Riess, Olaf / Robinson, Peter N / Salgado, David / Smedley, Damian / Spalding, Dylan / 't Hoen, Peter A C / Töpf, Ana / Zaharieva, Irina / Graessner, Holm / Gut, Ivo G / Lochmüller, Hanns / Beltran, Sergi

Human mutation

2022 Volume 43, Issue 6, Page(s) 717–733

Abstract: Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed ... ...

Abstract	Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.
MeSH term(s)	Exome ; Genetic Association Studies ; Genomics/methods ; Humans ; Phenotype ; Rare Diseases/diagnosis ; Rare Diseases/genetics
Language	English
Publishing date	2022-02-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.24353
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