Evolutionary analysis of genetic variants involved in rare diseases

Treball de fi de grau en Biologia HumanaSupervisor: Ferran Casals LópezNext-generation sequencing techniques such as exome sequencing can successfully detect all genetic variants in a human exome and it has been useful together with the implementation of variant filters to identify causing-disease mutations. Two filters are/nmainly used for the mutations identification: low allele frequency and the computational annotation of the genetic variant. Bioinformatic tools to predict the effect of a given/nvariant may have errors due to the existing bias in databases and sometimes show a limited coincidence among them. Advances in functional and comparative genomics are needed in order to properly annotate these variants./nThe goal of this study is to: first, functionally annotate Common Variable Immunodeficiency disease (CVID) variants with the available bioinformatic methods in order to assess the reliability of these strategies. Sencondly, as the development of new methods to reduce the number of candidate genetic variants is an active and necessary field of research, we are exploring the utility of gene function information at organism level as a filter for rare disease genes identification. Recently, it has been proposed that only 10-15% of human genes are essential and therefore we would expect that severe rare diseases are mostly caused by mutations on them. Our goal is to determine whether or not these rare and severe diseases are caused by deleterious mutations in these essential genes. If this hypothesis were true, taking into account essential genes as a filter would be an interesting parameter to identify causingdisease mutations

Insights into the adaptative history of African human populations from whole-genome sequence data

Africa is the origin source of modern humans. Despite that African populations harbor the highest levels of genetic diversity worldwide, they remain underrepresented in genetic studies. Therefore, in order to fully understand modern human evolutionary history it is fundamental to include more African populations in genetic studies. The work in this thesis is a small contribution to the study of African evolutionary history. In particular we have focused on two different locations of Africa, eastern and southern Africa. We have tried to unravel candidates of positive (or adaptive) selection through the analysis of whole-genome sequences of five Ethiopian populations and one KhoeSan population. Moreover, we have tried to fill the gap between genotype and phenotype of a candidate of adaptive selection in an Ethiopian population.Àfrica és la font d'origen dels humans moderns. Malgrat que les poblacions Africanes són les que contenen la major diversitat genètica al món, estan molt poc representades en estudis genètics. Així doncs, per poder plenament entendre la història evolutiva humana és fonamental incloure més poblacions Africanes en estudis genètics. Aquesta tesi és una petita contribució en l'estudi de la història evolutiva humana a l'Àfrica. Ens hem centrat en dos localitzacions diferents, a l'est i al sud de l'Àfrica. Hem intentat dilucidar les possibles senyals de selecció positiva (o adaptativa) a través de l'anàlisi de seqüències completes de genomes de cinc poblacions d'Etiòpia i una KhoeSan. A més a més, en l'última part de la tesi s'ha intentat entendre a nivell funcional la relació entre el genotip i el fenotip d'un candidat de selecció adaptativa descobert en una població d'Etiòpia

Insights into the adaptative history of African human populations from whole-genome sequence data

Africa is the origin source of modern humans. Despite that African populations harbor the highest levels of genetic diversity worldwide, they remain underrepresented in genetic studies. Therefore, in order to fully understand modern human evolutionary history it is fundamental to include more African populations in genetic studies. The work in this thesis is a small contribution to the study of African evolutionary history. In particular we have focused on two different locations of Africa, eastern and southern Africa. We have tried to unravel candidates of positive (or adaptive) selection through the analysis of whole-genome sequences of five Ethiopian populations and one KhoeSan population. Moreover, we have tried to fill the gap between genotype and phenotype of a candidate of adaptive selection in an Ethiopian population.Àfrica és la font d'origen dels humans moderns. Malgrat que les poblacions Africanes són les que contenen la major diversitat genètica al món, estan molt poc representades en estudis genètics. Així doncs, per poder plenament entendre la història evolutiva humana és fonamental incloure més poblacions Africanes en estudis genètics. Aquesta tesi és una petita contribució en l'estudi de la història evolutiva humana a l'Àfrica. Ens hem centrat en dos localitzacions diferents, a l'est i al sud de l'Àfrica. Hem intentat dilucidar les possibles senyals de selecció positiva (o adaptativa) a través de l'anàlisi de seqüències completes de genomes de cinc poblacions d'Etiòpia i una KhoeSan. A més a més, en l'última part de la tesi s'ha intentat entendre a nivell funcional la relació entre el genotip i el fenotip d'un candidat de selecció adaptativa descobert en una població d'Etiòpia

Positive selection in admixed populations from Ethiopia

Background: In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history. Results: Here, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world. The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens. Conclusions: Signals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.This study has been possible thanks to the F.P.I. grant BES-2014-068994 to SW, and grant BFU2016–77961-P (AEI/FEDER, UE) both awarded by the Agencia Estatal de Investigación (MINECO, Spain) and with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 702). Part of the “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018–000792-M). YX and CTS are supported by Wellcome Trust (098051), LP is supported by the European Union through the European Regional Development Fund Project No. 2014–2020.4.01.16–0024, MOBTT53. Publication costs were funded by Wellcome (grant 098051). The funding body has not played any role in the design of the study and collection, analysis, and interpretation of data and in writing of the manuscript

Teleconsultations between patients and healthcare professionals in primary care in Catalonia: the evaluation of text classification algorithms using supervised machine learning

Background: The primary care service in Catalonia has operated an asynchronous teleconsulting service between GPs and patients since 2015 (eConsulta), which has generated some 500,000 messages. New developments in big data analysis tools, particularly those involving natural language, can be used to accurately and systematically evaluate the impact of the service. Objective: The study was intended to assess the predictive potential of eConsulta messages through di erent combinations of vector representation of text and machine learning algorithms and to evaluate their performance. Methodology: Twenty machine learning algorithms (based on five types of algorithms and four text representation techniques) were trained using a sample of 3559 messages (169,102 words) corresponding to 2268 teleconsultations (1.57 messages per teleconsultation) in order to predict the three variables of interest (avoiding the need for a face-to-face visit, increased demand and type of use of the teleconsultation). The performance of the various combinations was measured in terms of precision, sensitivity, F-value and the ROC curve. Results: The best-trained algorithms are generally e ective, proving themselves to be more robust when approximating the two binary variables “avoiding the need of a face-to-face visit” and “increased demand” (precision = 0.98 and 0.97, respectively) rather than the variable “type of query” (precision = 0.48). Conclusion: To the best of our knowledge, this study is the first to investigate a machine learning strategy for text classification using primary care teleconsultation datasets. The study illustrates the possible capacities of text analysis using artificial intelligence. The development of a robust text classification tool could be feasible by validating it with more data, making it potentially more useful for decision support for health professionals

Clinical characteristics of COVID-19 in older adults: a retrospective study in long-term nursing homes in Catalonia

The natural history of COVID-19 and predictors of mortality in older adults need to be investigated to inform clinical operations and healthcare policy planning. A retrospective study took place in 80 long-term nursing homes in Catalonia, Spain collecting data from March 1st to May 31st, 2020. Demographic and clinical data from 2,092 RT-PCR confirmed cases of SARS-CoV-2 infection were registered, including structural characteristics of the facilities. Descriptive statistics to describe the demographic, clinical, and molecular characteristics of our sample were prepared, both overall and by their symptomatology was performed and an analysis of statistically significant bivariate differences and constructions of a logistic regression model were carried out to assess the relationship between variables. The incidence of the infection was 28%. 71% of the residents showed symptoms. Five major symptoms included: fever, dyspnea, dry cough, asthenia and diarrhea. Fever and dyspnea were by far the most frequent (50% and 28%, respectively). The presentation was predominantly acute and symptomatology persisted from days to weeks (mean 9.1 days, SD = 10,9). 16% of residents had confirmed pneumonia and 22% required hospitalization. The accumulated mortality rate was 21.75% (86% concentrated during the first 28 days at onset). A multivariate logistic regression analysis showed a positive predictive value for mortality for some variables such as age, pneumonia, fever, dyspnea, stupor refusal to oral intake and dementia (p<0.01 for all variables). Results suggest that density in the nursing homes did not account for differences in the incidence of the infection within the facilities. This study provides insights into the natural history of the disease in older adults with high dependency living in long-term nursing homes during the first pandemic wave of March-May 2020 in the region of Catalonia, and suggests that some comorbidities and symptoms have a strong predictive value for mortality

Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population

TRPP3 (also called PKD2L1) is a nonselective, cation-permeable channel activated by multiple stimuli, including extracellular pH changes. TRPP3 had been considered a candidate for sour sensor in humans, due to its high expression in a subset of tongue receptor cells detecting sour, along with its membership to the TRP channel family known to function as sensory receptors. Here, we describe the functional consequences of two non-synonymous genetic variants (R278Q and R378W) found to be under strong positive selection in an Ethiopian population, the Gumuz. Electrophysiological studies and 3D modelling reveal TRPP3 loss-of-functions produced by both substitutions. R278Q impairs TRPP3 activation after alkalinisation by mislocation of H+ binding residues at the extracellular polycystin mucolipin domain. R378W dramatically reduces channel activity by altering conformation of the voltage sensor domain and hampering channel transition from closed to open state. Sour sensitivity tests in R278Q/R378W carriers argue against both any involvement of TRPP3 in sour detection and the role of such physiological process in the reported evolutionary positive selection past event.This work was funded by the Spanish Ministry of Science and Innovation, the State Research Agency (AEI, Agencia Estatal de Investigación) and FEDER Funds (Fondo Europeo de Desarrollo Regional): Grants BFU2016-77961-P to J.B. and E.B., RTI2018-094809-B-I00 to J.M.F.F., PID2019-110933GB-I00/AEI/10.13039/501100011033 to E.B. and J.B., and CEX2018-000792-M through the “María de Maeztu” Programme for Units of Excellence in R&D to “Departament de Ciències Experimentals i de la Salut”. With the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 702). S.W. has had a F.P.I. grant (BES-2014-068994) and M.I.-S. a “Juan de la Cierva-Incorporación” Fellowship funded by the Spanish Ministry of Science and Innovation

Exploring adaptive phenotypes for the human calcium-sensing receptor polymorphism R990G

Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter-gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter-gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests.This work was supported by Agencia Estatal de Investigación (AEI, DOI: 10.13039/501100011033), Fondo Europeo de Desarrollo Regional, Ministerio de Ciencia e Innovación, and Ministerio de Ciencia, Innovación y Universidades with project grants BFU2016-77961-P, PID2019-110933GB-I00, and the Unidad de Excelencia María de Maeztu Ref. CEX2018-000792-M; and by Agència de Gestió d'Ajuts Universitaris i de la Recerca, Generalitat de Catalunya (2017SGR00702). B.S. was supported with an FPI-MINECO PhD fellowship (BES-2017-080343). S.A. was supported by Beatriu de Pinós 2017 BP 00176 and by the Serra Hunter Fellowship from Generalitat de Catalunya