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Doctoral Thesis
DOI
https://doi.org/10.11606/T.5.2021.tde-07012022-092142
Document
Author
Full name
Bruna Lucheze Freire
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
São Paulo, 2021
Supervisor
Committee
Jorge, Alexander Augusto de Lima (President)
Longui, Carlos Alberto
Kim, Chong Ae
Miachon, Adriana Aparecida Siviero
Title in Portuguese
O sequenciamento completo do exoma deve ser a primeira abordagem genético-molecular para crianças com baixa estatura sindrômica sem diagnóstico clínico
Keywords in Portuguese
Genética
Insuficiência de crescimento/ genética
Mutação/genética
Retardo do crescimento/ genética
Sequenciamento completo do exoma
Sequenciamento de nucleotídeos em larga escala
Abstract in Portuguese
As doenças que comprometem o crescimento humano apresentam uma forte influência genética. O objetivo geral do projeto foi avaliar a utilidade do sequenciamento completo do exoma como primeira abordagem genético-molecular na investigação da etiologia da baixa estatura sindrômica de pacientes sem diagnóstico clínico reconhecido. Para tanto os pacientes com características sindrômicas foram submetidos a extensa avaliação clínica em nosso ambulatório e nos casos selecionados, foi utilizado o sequenciamento completo do exoma para estabelecer etiologia genética responsável pelo distúrbio de crescimento. Desta forma foram selecionados de forma prospectiva 86 pacientes com baixa estatura (escore-Z de altura menor ou igual a -2) ou baixa estatura em relação ao seu padrão familiar (escore-Z da altura do paciente menos escore-Z da altura alvo -2) associado a dismorfismos, malformações congênitas maiores, distúrbios de desenvolvimento neuropsicomotor ou déficit intelectual. Os pacientes selecionados não apresentam diagnóstico clínico ou a suspeita clínica inicial foi afastada por estudo molecular prévio baseado em gene candidato. Foram selecionados 86 pacientes que foram avaliados em nosso ambulatório. Estes foram submetidos ao sequenciamento do exoma com captura das regiões alvo pela tecnologia SureSelect (Agilent) ou xGen Exome Research Panel v2 (IDT). Em casos 61 casos apenas o probando foi inicialmente analisado em 25 houve a análise conjunta com outros familiares (trios). A análise das amostras gerou uma cobertura média de 152 vezes e com mais de 98,15% da região alvo com cobertura > 10 reads. Nestas amostras foram identificadas 47 variantes deletérias em 41 pacientes. Em 22 pacientes as variantes foram consideradas patogênicas e em 19 provavelmente patogênicas. Dentre as variantes consideradas patogênicas ou provavelmente patogênicas houve uma grande heterogeneidade entre os genes, sendo identificadas variantes nos genes ACTB, AFF4, ANKRD11, BCL11B(x2), BRCA1, CHD7,COL2A1(x3), DPH1, DYRK1A, FBN1, FOXP1, GINS1, HDAC8. IGF1R, INPP5K, KIF11, KDM5C, KMT2A, KIF11, KRAS, MVK, PCNT, PDHA1, POC1A, POLG1, PUF60, RPL5, RPS6KA3, SCN1A, SCUBE3, SETD5, SMARCA4, SRCAP(x2), STAT5B, TERT, além de 3 duplicações e 1 deleção encontradas pela análise de CNVs. Podemos concluir que a técnica de sequenciamento paralelo em larga escala de exoma foi eficiente em estabelecer o diagnóstico molecular da baixa estatura sindrômica, e foi possível identificar a etiologia genética em 47,7% da casuística estudada
Title in English
Whole exome sequencing should be the first genetic-molecular approach for children with syndromic short stature without clinical diagnosis
Keywords in English
Failure to thrive /genetics
Fetal growth retardation/genetics
Genetics
High-throughput nucleotide sequencing
Mutation/genetics
Whole exome sequencing
Abstract in English
Diseases that compromise human growth have a strong genetic influence. The main aim of the current project was to evaluate the usefulness of complete exome sequencing as the first molecular-genetic approach in the investigation of the etiology of syndromic short stature in patients without a recognized clinical diagnosis. Therefore, patients with syndromic characteristics underwent extensive clinical evaluation in our clinic and, in selected cases, complete exome sequencing was used to establish the genetic etiology responsible for the growth disorder. Thus, 86 patients with short stature (Z-score for height less than or equal to -2) or short stature in relation to their family pattern (Z-score of patient height minus Z-score of target height -2) associated with dysmorphisms, major congenital malformations, neuropsychomotor development disorders or intellectual deficit were prospectively selected for WES. The selected patients do not have a clinical diagnosis or the initial clinical suspicion was ruled out by a previous molecular study based on a candidate gene. These were subjected to exome sequencing with capture of target regions by SureSelect (Agilent) or xGen Exome Research Panel v2 (IDT) technology. In 61 cases only the proband was initially analyzed and in 25 there was a joint analysis with other family members (trios). The analysis of the samples generated an average coverage of 152 times with more than 98.15% of the target region with coverage > 10 reads. In these samples, 47 deleterious variants were identified in 41 patients. In 22 patients the variants were considered pathogenic and in 19 probably pathogenic. Among the variants considered pathogenic or probably pathogenic, there was great heterogeneity between the genes, with variants being identified in ACTB, AFF4, ANKRD11, BCL11B(x2), BRCA1, CHD7, COL2A1(x3), DPH1, DYRK1A, FBN1, FOXP1, GINS1 genes. , HDAC8. IGF1R, INPP5K, KIF11, KDM5C, KMT2A, KIF11, KRAS, MVK, PCNT, PDHA1, POC1A, POLG1, PUF60, RPL5, RPS6KA3, SCN1A, SCUBE3, SETD5, SMARCA4, SRCAP(x2), STAT5B, and 3 duplications and one deletion found by CNV analysis. We can conclude that the massive parallel sequencing technique of the exome was efficient in establishing the molecular diagnosis of syndromic short stature, and it was possible to identify the genetic etiology in 47,7% of the studied cohort
 
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Publishing Date
2022-01-07
 
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