Дисертації з теми "Clinical exome sequencing"

Motivation: The advent of clinical exome sequencing will require new tools to handlecoverage data and making it relevant to clinicians. That means genes over targets, smartsoftware over BED-files, and full stack, automated solutions from BAM-files to genetic testreport. Fresh ideas can also provide new insights into the factors that cause certain regionsof the exome to receive poor coverage.Results: A novel coverage analysis tool for analyzing clinical exome sequencing data has beendeveloped. Named Chanjo, it’s capable of converting between different elements such astargets and exons, supports custom annotations, and provides powerful statistics andplotting options. A coverage investigation using Chanjo linked both extreme GC content andlow sequence complexity to poor coverage. High bait density was shown to increasereliability of exome capture but not improve coverage of regions that had already proventricky. To improve coverage of especially very G+C rich regions, developing new ways toamplify rather than enrich DNA will likely make the biggest difference.

[ES] Durante las últimas décadas, se han realizado importantes avances en el estudio de las causas genéticas de enfermedades raras y comunes, donde un gran número de variantes han sido identificadas y asociadas a múltiples enfermedades. Con las tecnologías de secuenciación de nueva generación, hoy en día somos capaces de investigar, con un alto rendimiento, la contribución de variantes de alta y baja frecuencia a distintos tipos de enfermedades, permitiéndonos así estudiar su importancia en el desarrollo de las mismas. En ésta tesis se ha utilizado la secuenciación del exoma como tecnología para el estudio de variantes raras en una enfermedad compleja, la alergia gastrointestinal inducida por múltiples alimentos. Para ello, se realizó la secuenciación del exoma completo de una cohorte de 31 individuos (ocho afectados y 23 no afectados) provenientes de siete familias diferentes. Se desarrolló un flujo de trabajo para procesar los datos generados a partir de diferentes librerías e instrumentos de secuenciación, así como un control de calidad exhaustivo con el fin de maximizar el número de variantes de alta calidad. Diferentes tipos de mutaciones fueron investigadas, incluyendo polimorfismos de nucleótido único, inserciones/deleciones, variantes del número de copia y haplotipos HLA, y se realizaron diferentes métodos de filtrado para su interpretación. Finalmente, se encontraron una serie de mutaciones que podrían estar asociadas con la enfermedad y se describe su posible papel en la patogénesis de las alergias gastrointestinales. Los resultados de esta tesis suponen importantes avances en el estudio de la compleja arquitectura genética de las alergias gastrointestinales y abren las puertas a futuras líneas de investigación, que serán necesarias para entender completamente las bases genéticas de esta enfermedad.
[CAT] Durant les últimes dècades, s'han realitzat importants avanços en l'estudi de les causes genètiques de malalties rares i comunes, on un gran nombre de variants han sigut identificades i associades a múltiples malalties. Amb les tecnologies de seqüenciació de nova generació, avui en dia som capaços d'investigar, amb un alt rendiment, la contribució de variants d'alta i baixa freqüència a diferents tipus de malalties, permetent-nos així estudiar la seva importància en el desenvolupament de les mateixes. En aquesta tesis s'ha utilitzat la seqüenciació del exoma com a tecnologia per a l'estudi de variants rares en una malaltia complexa, l'al·lèrgia gastrointestinal induïda per múltiples aliments. Per això, es va realitzar la seqüenciació del exoma complet d'una cohort de 31 individus (vuit afectats i 23 no afectats) provinents de set famílies diferents. Es va desenvolupar un flux de treball per a processar les dades generades a partir de diferents llibreries e instruments de seqüenciació, així com un control de qualitat exhaustiu amb la fi de maximitzar el nombre de variants d'alta qualitat. Diferents tipus de mutacions foren investigades, incloïent polimorfismes de nucleòtid únic, insercions/delecions, variants del nombre de còpia i haplotips HLA, i es realitzaren diferent mètodes de filtrat per a la seva interpretació. Finalment, es trobaren una sèrie de mutacions que podrien estar associades amb la malaltia i es descriu el seu possible paper en la patogènesis de les al·lèrgies gastrointestinals. Els resultats d'aquesta tesis suposen importants avanços en l'estudi de la complexa arquitectura genètica de les al·lèrgies gastrointestinals i obrin les portes a futures línies d'investigació, que seran necessàries per entendre completament les bases genètiques d'aquesta malaltia.
[EN] The study of genetics has been making significant progress towards understanding the causes of rare and common disease during the past decades. Across a wide range of disorders, there have been hundreds of associated loci identified and associated with multiple disorders. Now, with the advent of next-generation sequencing technologies, we are able to interrogate the contribution of high and low frequency variation to disease in a high throughput manner. This provides an opportunity to investigate the role of rare variation in complex disease risk, potentially offering insights into disease pathogenesis and biological mechanisms. In this thesis, it has been assessed the use of whole-exome sequencing technology to investigate the role of rare variation in a complex disease, gastrointestinal food allergy induced by multiple food proteins. For that, a cohort of 31 individuals (eight affected and 23 non-affected) from seven different families was whole exome sequenced. Data obtained from multiple sequencing systems and libraries were analysed, and a workflow was developed, focusing on a comprehensive quality control to maximise the number of real positive calls. Different types of genome variations were investigated, including single nucleotide variants, insertions/deletions, copy number variants and HLA haplotypes. By approaching different methods of variant filtering, a set of rare variants that could be associated with the disease was identified. The possible role of these candidate variants in the pathogenesis of gastrointestinal food allergies was also discussed. These results reveal important insights into the genetic architecture of gastrointestinal food allergies and lead to additional lines of investigation that will be required in order to fully understand the genetic basis of this disease.
Sanchis Juan, A. (2019). Exome Sequencing in Gastrointestinal Food Allergy Induced by Multiple Food Protein [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/134361
TESIS

Importance. The American College of Medical Genetics and Genomics recommends informing individuals who carry mutations in a set of Mendelian disease genes that might require clinical action regardless of genetic testing indication. However, whether such mutations lead to an increased risk for diseases in individuals not referred for clinical genetic testing has not been evaluated. Objective. To evaluate whether those in the unselected general population who carry potentially actionable mutations are more likely to manifest the associated diseases than those without such mutations. Design, Setting, and Participants. Cross-sectional observational study of participants enrolled in the Jackson Heart Study (Jackson, MS) between 2000 and 2004 who underwent whole exome sequencing (n = 3223). All participants were on African descent. Exposures. Mutations across a set of 56 recommended clinically actionable genes ascertained by whole exome sequencing. Main Outcomes and Measures. Evidence for pathogenicity for all mutations identified in 56 genes was determined by bioinformatic analyses and extensive literature review. Anticipated clinical findings for each of the 56 genes were extracted from study surveys, echocardiography, electrocardiography, and lipid panels across all participants without knowledge of mutation carrier status. The main outcome was the difference in expected clinical findings in those with mutations compared to those without. Results. 3,223 African Americans had a total of 4,429 mutations across the 56 genes. Bioinformatic filters yielded 462 candidate pathogenic variants in 1945 participants (60%). Subsequent manual review of the evidence yielded 30 pathogenic variants in 44 (1.3 %) participants and 12 likely pathogenic variants in 23 (0.7 %). Participants with pathogenic or likely pathogenic variants were more likely to display suggested clinical features (19.6 %) compared with expected (7.1 %; one-sided P = 0.002) by a factor of 2.75 (95% CI , 1.37 to 4.92). In secondary analyses, the excess of observed clinical features was apparent in cardiovascular and cancer genes by 2.67-fold (95% CI, 1.07 to 5.51) and 2.89-fold (95% CI, 0.78 to 7.39), respectively. Conclusions and Relevance. Unselected African Americans in the general population with pathogenic or likely pathogenic variants have an increased risk of displaying features associated with clinical disease.

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Doctorat en Sciences biomédicales et pharmaceutiques (Médecine)
info:eu-repo/semantics/nonPublished

There are more than 7000 described rare genetic disorders; however, the molecular basis underlying approximately half of these disorders is unknown, and the majority are currently untreatable. Stature and growth abnormalities are a common clinical feature of many rare disorders including: Floating-Harbor syndrome (FHS), a short stature syndrome characterized by delayed osseous maturation, language deficits, and unique dysmorphic facial features; Weaver syndrome, an overgrowth syndrome characterized by advanced osseous maturation, developmental delay, and macrocephaly; and Sotos syndrome with cutis laxa, an overgrowth syndrome with marked tissue laxity in addition to the typical Sotos characteristics of developmental delay, macrocephaly, and a unique facial gestalt. The genetic basis underlying these three rare stature conditions were unknown at the outset of this study. We utilized high-throughput exome sequencing approaches to investigate the molecular etiology of these rare disorders and identified truncating mutations in the final exon of SRCAP as the genetic cause underlying FHS, missense mutations in EZH2 in Weaver syndrome, and novel mutations in the Sotos syndrome gene NSD1 in Sotos syndrome with cutis laxa. Next, we investigated the spectrum of SRCAP mutations in FHS and established the clustering of truncating SRCAP mutations in the final exon as being highly suggestive of a non-haploinsufficiency mutational mechanism in FHS. Finally, global methylation array analysis identified a unique methylation ‘epi-signature’ in FHS individuals, providing further insight into FHS disease mechanism and a diagnostic signature. These studies have delineated the molecular etiology of these three rare stature/growth disorders, furthered our understanding of the associated clinical spectrum, and provided biological insight into disease pathogenesis.

Next-generation sequencing methods now allow rapid and cost-effective sequencing of DNA on a scale not previously possible. This offers great opportunities for the research of Mendelian disorders, but also significant challenges. The sequencing of exomes, or whole genomes, has emerged as a powerful clinical research tool, with targeted gene analyses generally being preferred in the clinical diagnostic setting. These methods have been employed here with the aim of identifying novel genetic causes of inherited heart disorders and to gain insights into the utility and limitations of these techniques for clinical diagnosis in these disorders. Data produced from the introduction of a targeted multi-gene next-generation sequencing test into clinical practice has been studied. Variation within the mitochondrial genome has been analysed to assess the importance of mitochondrial DNA variants in patients with hypertrophic cardiomyopathy. The m.4300A>G mutation is identified as an important cause of this disorder, with other previously cardiomyopathy-associated and novel variants also identified. Such multi-gene tests can facilitate interpretable and phenotype-relevant results, but at the expense of limiting more extensive data acquisition. Whole-genome sequencing has been performed in five families with different autosomal dominant inherited heart disease phenotypes of unknown genetic aetiology. In two of these likely pathogenic variants were identified, one in the gene encoding titin (TTN) and the other in the calcium channel subunit gene CACNA1C. In vitro studies were undertaken to support the pathogenicity of the TTN variant and understand the functional effects of this. In the other three families either multiple candidate gene variants were identified or no clear candidate variant was identified. This highlights the difficulties in interpreting these results, even in carefully selected families. Overall, although the research benefits of exome or genome studies are evident, the interpretation and validation of genetic variant data produced remains highly challenging for clinical diagnosis.

This thesis further delineates the molecular genetic basis of a relatively common craniofacial condition, coronal craniosynostosis. It used whole-exome sequencing to identify novel disease genes in patients with non-syndromic coronal synostosis and negative genetic testing. Initially, 2 patients were identified with damaging, frameshift mutations in a gene not previously linked with craniosynostosis – Transcription Factor 12 (TCF12). A further intronic mutation was identified in a third patient. This gene encodes a transcription factor that dimerises with TWIST1, mutations of which cause Saethre-Chotzen syndrome, also associated with coronal synostosis. Screening 344 undiagnosed patients identified 35 further mutations, all with coronal synostosis with 14 cases arising de novo. This work was published and testing for TCF12-related craniosynostosis was translated clinically. Significant non-penetrance (60%) was identified in mutation-positive relatives and the genetic background was investigated. Firstly, analysis of parental origins of de novo mutations identified 6 of paternal origin and helped refine haplotype assignment. Secondly, haplotype analysis of TCF12-mutation carriers revealed modest correlation with phenotypic status, but this was insufficient to be useful in clinical testing. Thirdly, TCF12 haplotypes were analysed for association with non-syndromic coronal synostosis, but no significant association was found. Further exome sequencing revealed a de novo frameshift mutation in Transcription Factor 20 (TCF20) in a patient with coronal synostosis and autism, although the mutation only correlated with the latter phenotype. Analysis of 5 trios revealed a novel variant in myosin heavy chain 4 (MYH4) in 1 family, although its role in suture development is uncertain. Reviewing pooled exome data from 19 mutation-negative patients revealed no further disease genes. In summary, this thesis describes novel gene discovery, defines a new clinical entity and investigates genetic background of penetrant and non-penetrant individuals. Further exome sequencing identified another disease gene, a de novo mutation and compiled lists of damaging variants to allow future work.

Les paragangliomes (PGL) sont des tumeurs neuroendocrines rares, génétiquement déterminées dans 40 % des cas. Malgré les évolutions récentes des connaissances sur la génétique des PGL, il reste toujours environ 15 % des patients pour lesquels aucune cause génétique ne peut être identifiée alors que leur présentation clinique évoque une forme génétiquement déterminée. De plus, il n’a jamais été démontré que l’identification d’une mutation constitutionnelle dans l’un de ces gènes de prédisposition avait un impact positif sur la prise en charge et l’évolution des patients. Mon travail de thèse a été organisé autour de deux grands objectifs : 1) évaluer le bénéfice pour les patients de l’identification d’une mutation constitutionnelle sur un gène de prédisposition au moment du diagnostic du PGL ; 2) mettre en évidence de nouveaux gènes de prédisposition aux PGL et/ou de nouveaux mécanismes d’inactivation des gènes de prédisposition connus pouvant expliciter les formes suspectes d’être génétiques sans mutation identifiée. Grâce à une étude rétrospective multicentrique rassemblant 221 patients ayant un PGL secondaire à une mutation sur les gènes SDHB, SDHD, SDHC ou VHL, j’ai pu observer que les patients ayant bénéficié de l’analyse génétique au moment du diagnostic de leur PGL avaient été mieux suivis que ceux ayant bénéficié du diagnostic génétique à distance de leur prise en charge initiale. La connaissance d’un statut génétique positif dans la période du diagnostic du PGL a permis de dépister des PGL plus petits en cas de récidive et une maladie métastatique moins étendue en cas de malignité et d’améliorer la survie. Ces résultats valident les recommandations internationales qui proposent un test génétique à tous patients avec PGL au moment du diagnostic initial. Sur le plan fondamental, j’ai identifié par une stratégie de séquençage d’exome des mutations dans un nouveau gène de prédisposition au PGL, SLC25A11, qui code pour le transporteur mitochondrial du 2-oxoglutarate/malate et montré que les mutations constitutionnelles de SLC25A11 prédisposent à des formes malignes de PGL. J’ai de plus démontré que les tumeurs humaines ainsi que le modèle expérimental cellulaire inactivé pour ce gène développent une pseudo-hypoxie et une hyperméthylation globale de l’ADN expliquant la tumorigenèse secondaire à l’inactivation de ce gène. L’identification de ce nouveau gène de prédisposition étend le champ des dysfonctions mitochondriales dans la tumorigenèse et dans la cancérogénèse des PGL et révèle un nouveau lien entre mitochondrie et cancer
Paragangliomas (PGL) are rare neuroendocrine tumors, genetically determined in around 40% of cases. Despite recent developments in PGL genetics, there is still about 15% of patients for whom no genetic cause can be identified, while their clinical presentation is suspicious of a genetic form. Moreover, it has never been demonstrated that the identification of a germline mutation in any of the PPGL predisposition genes has a positive impact on the patients’ management and clinical outcome. My PhD research project has been organized around two main objectives: 1) to evaluate the benefits for the patients of the identification of a germline mutation on one susceptibility gene at the time of PGL diagnosis; 2) to search for new PGL genes and / or new mechanisms of inactivation of the previously known genes, which could explain PGL suspected to be a genetic form but without detected mutation. Thanks to a retrospective multicenter study involving 221 patients with a PGL due to a mutation on the SDHB, SDHD, SDHC or VHL genes, I observed that the patients who benefited from the genetic analysis at the time of the diagnosis of PGL had a better follow-up than those who had the data of their genetic test later on after the initial PGL diagnosis. Knowledge of a positive genetic status in the PGL diagnosis period favored the detection of smaller recurrent PGLs and less extensive metastatic disease and improved the median of survival. These results validate the international recommendations of offering a PPGL genetic testing to all affected patients at the time of initial diagnosis. I identified germline mutations in a novel PGL gene, SLC25A11 with a whole-exome sequencing strategy, which encodes for the mitochondrial 2-oxoglutarate/malate carrier and showed that SLC25A11 germline mutations predispose to malignant PGL. I demonstrated that human tumors as well as the knockout of slc25a11 gene in a murine experimental model induces a pseudo-hypoxia and a global hypermethylation of the DNA, which explains the tumourigenesis secondary to the inactivation of this gene. The identification of this new PGL susceptibility gene expands the role of mitochondrial dysfunction in paraganglioma tumorigenesis and reveals a new pathway linking metabolic defects and cancer

Les causes génétiques des syndromes avec déficiences intellectuelles sont encore peu élucidées. Les données actuelles disponibles sont très récentes et encore incomplètes. Le syndrome de Mowat-Wilson appartient à ce cadre nosologique. Il associe une déficience intellectuelle profonde et un syndrome polymalformatif comprenant une maladie de Hirschsprung, des anomalies du corps calleux, des anomalies cardiaques et urogénitales. Les causes moléculaires sont, dans la très grande majorité des cas, des mutations tronquantes de ZEB2 (ou SIP1 ou ZFHX1B). Ces anomalies surviennent de novo à l'état hétérozygote. Récemment, nous avons identifié dans notre laboratoire, trois nouvelles mutation faux-sens de ZEB2 chez trois patients ayant un phénotype modéré de la maladie. Nous montrons que ces anomalies moléculaires induisent une perte de fonction de la protéine. Les techniques de sauvetage du phénotype par injection d'ARN ZEB2 sauvage et muté montrent que, chez les embryons morphants sip1b, les protéines mutées participent partiellement au développement des dérivés neuraux et des crêtes neurales.Parallèlement à cette étude, par séquençage de l'exome, nous avons identifié chez un patient atteint de déficience intellectuelle syndromique, une mutation de CSDE1. Ce gène code une protéine à 5 domaines cold-shock, liant l'ARN et régulant la traduction dépendante de l'IRES. C'est la première fois que CSDE1 est impliqué en pathologie. Nous montrons que la mutation entraine une haploinsuffisance et dérégule la traduction de ZEB2
[Translated by Reverso web site - The genetic causes of the syndromes with intellectual deficiencies are again little clarified. The available current data are very recent and still incomplete. The syndrome of Mowat-Wilson belongs to this nosologique frame(executive). He(it) associates a deep intellectual deficiency and a polymalformatif syndrome understanding(including) a disease of Hirschsprung, anomalies of the corpus callusum, the cardiac anomalies and urogénitales. The molecular causes are, in her(it) very great majority of the cases, tronquantes transfers(transformations) of ZEB2 (or SIP1 or ZFHX1B). These anomalies arise of novo in the heterozygous state. Recently, we identified in our laboratory, three news(short stories) transfer(transformation) misinterpretation of ZEB2 at three patients having a moderate phenotype of the disease. We show that these molecular anomalies lead(infer) a loss of function(office) of the protein. The techniques of rescue of the phenotype by injection of wild and moved ARN ZEB2 show that, to morphants embryos sip1b, moved proteins participate partially in the development of by-products neuraux and neurales crests. In a parallel to(at the same time as) this study, by sequencing of the exome, we identified at a patient's reached(affected) by intellectual syndromique deficiency, a transfer(transformation) of CSDE1. This gene codes a protein in 5 domains cold-shock, linking(binding) ARN and regulating the dependent translation of IRES. It is the first time when CSDE1 is involved in pathology. We show that the transfer(transformation) entraine a haploinsuffisance and deregulate the translation of ZEB2.]

The advent of next-generation sequencing, now nearing a decade in age, has enabled, among other capabilities, measurement of genome-wide sequence features at unprecedented scale and resolution.

In this dissertation, I describe work to understand the genetic underpinnings of non-Hodgkin’s lymphoma through exploration of the epigenetics of its cell of origin, initial characterization and interpretation of driver mutations, and finally, a larger-scale, population-level study that incorporates mutation interpretation with clinical outcome.

In the first research chapter, I describe genomic characteristics of lymphomas through the lens of their cells of origin. Just as many other cancers, such as breast cancer or lung cancer, are categorized based on their cell of origin, lymphoma subtypes can be examined through the context of their normal B Cells of origin, Naïve, Germinal Center, and post-Germinal Center. By applying integrative analysis of the epigenetics of normal B Cells of origin through chromatin-immunoprecipitation sequencing, we find that differences in normal B Cell subtypes are reflected in the mutational landscapes of the cancers that arise from them, namely Mantle Cell, Burkitt, and Diffuse Large B-Cell Lymphoma.

In the next research chapter, I describe our first endeavor into understanding the genetic heterogeneity of Diffuse Large B Cell Lymphoma, the most common form of non-Hodgkin’s lymphoma, which affects 100,000 patients in the world. Through whole-genome sequencing of 1 case as well as whole-exome sequencing of 94 cases, we characterize the most recurrent genetic features of DLBCL and lay the groundwork for a larger study.

In the last research chapter, I describe work to characterize and interpret the whole exomes of 1001 cases of DLBCL in the largest single-cancer study to date. This highly-powered study enabled sub-gene, gene-level, and gene-network level understanding of driver mutations within DLBCL. Moreover, matched genomic and clinical data enabled the connection of these driver mutations to clinical features such as treatment response or overall survival. As sequencing costs continue to drop, whole-exome sequencing will become a routine clinical assay, and another diagnostic dimension in addition to existing methods such as histology. However, to unlock the full utility of sequencing data, we must be able to interpret it. This study undertakes a first step in developing the understanding necessary to uncover the genomic signals of DLBCL hidden within its exomes. However, beyond the scope of this one disease, the experimental and analytical methods can be readily applied to other cancer sequencing studies.

Thus, this dissertation leverages next-generation sequencing analysis to understand the genetic underpinnings of lymphoma, both by examining its normal cells of origin as well as through a large-scale study to sensitively identify recurrently mutated genes and their relationship to clinical outcome.

Dissertation

Next-Generation Sequencing has opened the doors to nearly limitless amounts of genomic data, but the clinical utility of this data is not yet clear. From examining at sequencing data of known familial cancer genes in hereditary cancer patients, the NCGENES study found a clear molecular diagnosis in about 5% of patients and an uncertain molecular result in about 15% of patients. The remaining 80% of hereditary cancer patients received a negative result for the screening of known cancer genes. These latter patients were followed up by whole exome sequencing analysis, and the data was used to perform a research sweep to potentially identify mutation(s) in gene(s) that have yet to be clearly associated with their phenotype. Hereditary breast cancer has a relatively well-established set of susceptibility genes, yet a large percentage of the molecular etiology is still unknown. There are many genes that are good candidates for breast cancer genes based on their protein's function, but they may not actually contribute to breast cancer susceptibility. The ClinGen consortium is aiming to establish the clinical validity of gene-disease associations so that clinicians and patients can better interpret and utilize sequencing results. Six breast cancer susceptibility genes were evaluated using the ClinGen clinical validity framework with the goal of both evaluating the genes already on hereditary breast cancer panels and evaluating genes not yet widely tested to determine if there is enough evidence to support their role in disease to warrant widespread testing. These genes have varying levels of evidence supporting their role in breast cancer susceptibility. The variants in each of the six genes were compared between a cancer patient cohort and a non-cancer patient cohort enrolled in the NCGENES whole exome sequencing study. One likely pathogenic variant and several variants of unknown significance were identified in various genes, and the burden of variants in cancer cases versus controls was evaluated, although the controls were not matched to the cancer cohort in any way. Research sweeps were performed for patients with VUSs to ensure that there were no other mutations in genes that would better fit the phenotype. This thesis presents a method for evaluating gene-disease associations and for utilizing whole exome sequencing data to pinpoint a molecular diagnosis in hereditary breast cancer patients. Overall, it was found that the ClinGen method of evaluating clinical validity of gene-disease associations could be helpful when determining if variants are pathogenic or benign. A new gene, RINT1, was found to have enough evidence to be moderately associated with hereditary breast cancer and it was subsequently added to the diagnostic list so that all cancer patients will now be screened for RINT1 variants. In addition, it was found that two of the genes currently on the diagnostic list, RAD51C and RAD51D, have "disputed" evidence with respect to breast cancer susceptibility. Interestingly, they have much more evidence for an association with ovarian cancer, so if variants are found in these genes, the patient's phenotype should be considered when evaluating them. It was also shown that PALB2, an established breast cancer susceptibility gene, indeed is definitively associated with breast cancer, and the NCGENES cancer patients have more truncating variants than the controls, further validating the clinical validity assertion. Finally, an ovarian cancer patient with two interesting variants, one in SLX4 and one in GEN1, were evaluated. Studies showed that knocking out both of these genes' pathways was highly destructive to the cell. A VUS was found in each of these genes, and it was hypothesized that perhaps these two variants together may be sufficient to contribute to this patient's cancer susceptibility.

Yes
Currently, out of the 82 US FDA-approved targeted therapies for adult cancer treatments, only three are approved for use in children irrespective of their genomic status. Apart from leukemia, only a handful of genomic-based trials involving children with solid tumors are ongoing. Emerging genomic data for pediatric solid tumors may facilitate the development of precision medicine in pediatric patients. Here, we provide an up-to-date review of all reported genomic aberrations in the eight most common pediatric solid tumors with whole-exome sequencing or whole-genome sequencing data (from cBioPortal database, Pediatric Cancer Genome Project, Therapeutically Applicable Research to Generate Effective Treatments) and additional non-whole-exome sequencing studies. Potential druggable events are highlighted and discussed so as to facilitate preclinical and clinical research in this area.
Seed Grant of Strategic Research Theme for Cancer, The University of Hong Kong of AKSC. VWY Lui is funded by the Research Grant Council, Hong Kong (#17114814, #17121616, General Research Fund; T12–401/13-R, Theme-based Research Scheme), and the Start-up Fund, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong. W Piao is funded by the Faculty Postdoctoral Fellowship Scheme, Faculty of Medicine, the Chinese University of Hong Kong.

L’anémie falciforme est une maladie monogénique causée par une mutation dans le locus de la β-globine. Malgré le fait que l’anémie falciforme soit une maladie monogénique, cette maladie présente une grande hétérogénéité clinique. On présume que des facteurs environnementaux et génétiques contribuent à cette hétérogénéité. Il a été observé qu’un haut taux d’hémoglobine fœtale (HbF) diminuait la sévérité et la mortalité des patients atteints de l’anémie falciforme. Le but de mon projet était d’identifier des variations génétiques modifiant la sévérité clinique de l’anémie falciforme. Dans un premier temps, nous avons effectué la cartographie-fine de trois régions précédemment associées avec le taux d’hémoglobine fœtale. Nous avons ensuite effectué des études d’association pan-génomiques avec deux complications cliniques de l’anémie falciforme ainsi qu’avec le taux d’hémoglobine fœtale. Hormis les régions déjà identifiées comme étant associées au taux d’hémoglobine fœtale, aucun locus n’a atteint le niveau significatif de la puce de génotypage. Pour identifier des groupes de gènes modérément associés au taux d’hémoglobine fœtale qui seraient impliqués dans de mêmes voies biologiques, nous avons effectué une étude des processus biologiques. Finalement, nous avons effectué l’analyse de 19 exomes de patients Jamaïcains ayant des complications cliniques mineures de l’anémie falciforme. Compte tenu de la taille des cohortes de réplication disponibles, nous n’avons pas les moyens de valider statistiquement les variations identifiées par notre étude. Cependant, nos résultats fournissent de bons gènes candidats pour des études fonctionnelles et pour les réplications futures. Nos résultats suggèrent aussi que le β-hydroxybutyrate en concentration endogène pourraient influencer le taux d’hémoglobine fœtale. De plus, nous montrons que la cartographie-fine des régions associées par des études pan-génomiques peut identifier des signaux d’association additionnels et augmenter la variation héritable expliquée par cette région.
Sickle cell disease is a monogenic disease caused by a mutation in the β-globin locus. Although it is a monogenic disease, it shows a high clinical heterogeneity. Environmental and genetic factors are thought to play a role in this heterogeneity. It has been observed that a high fetal hemoglobin (HbF) levels correlates with a diminution of the severity and mortality of patients with sickle cell disease. The goal of my project was to identify genetic modifiers of the clinical severity of sickle cell disease. First, I performed the fine-mapping of three regions previously associated with HbF levels. Second, I performed genome-wide association studies with two clinical complications of sickle cell disease as well as with HbF levels. Since no new loci reached array-wide significance for HbF levels, I performed a pathway analysis to identify additional HbF loci of smaller effect size that might implicate shared biological processes. Finally, I performed the analysis of 19 whole exomes from Jamaican sickle cell disease patients with very mild complications. In conclusion, given the sample size of the replication cohorts available, we do not currently have the means to statistically validate the association signals. However, these results provide good candidate genes for functional studies and for future replication. Our results also suggest that β-hydroxybutyrate in endogenous levels could influence HbF levels. Furthermore, we show that fine-mapping the loci associated in genome-wide association studies can identify additional signals and increase the explained heritable variation.