Copy number variation detection in next generation sequencing data
Data
2020-09-28
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As variações genéticas no genoma humano podem ser desde grandes anomalias cromossómicas (aneuploidias segmentais), variações de um único nucleótido (SNVs) a pequenas inserções ou deleções (indels). Ganhos ou uma perdas do número de cópias vão corresponder, respectivamente, a duplicações ou deleções estruturais genómicas. Estes ganhos e perdas de cópias de genes são uma fonte comum de variação genética que têm sido implicados em muitas doenças genómicas. Os objetivos deste trabalho são a validação da deteção de CNVs com dados de NGS, o calculo da percentagem de diagnóstico com esta deteção tanto em amostras para paineis oncológicos como em WES, determinação de parâmetros de qualidade e respectivo limiar de deteção. A validação da análise de CNVs com o programa VarSeq consistiu na junção de casos positivos (com deleções ou duplicações) e negativos confirmados por outro método, na sua análise para calcular a especificidade, sensibilidade, exatidão e valores preditivos positivo e negativo. Depois da validação do software obteve-se a percentagem de diagnóstico. Foram incluidos neste estudo 902 pacientes para análise oncológica e o diagnóstico obtido foi de 2.54% para CNVs. Para as amostras de exoma foram utilizadas um total de 540 amostras cuja análise resultou num diagnóstco para CNVs de 8.15%. Foi possível detetar CNVs com uma sensibilidade de 99.15%, especificidade de 98.85% e exatidão de 98.90% para paineis oncológicos; para WES foi obtida uma sensibilidade de 87.50%, especificificidade de 99.30% e exatidão de 97.84%. CNVs podem ser detetados com exatidão e com uma taxa de diagnóstico entre 3−8% o que é relevante para a gestão clínica e para o aconselhamento genético tanto para os pacientes como para os seus familiares. Este estudo evidencia o potencial da sequenciação de nova geração como método para deteção de CNVs robusto e com uma boa relação custo-benefício, tanto para painéis oncológicos como para exomas.
Genetic variation in the human genome can range from large chromosomic anomalies to single nucleotide variations (SNVs), including structural variations, copy number variations (CNVs), small indels, and individual base alterations. Copy number gains or losses correspond to genomic structural duplications or deletions, respectively, and these alterations can directly influence genic dosage, which has direct implications in genomic diseases. This work focuses on patients that made oncologic genetic tests and in the detection of potential causal CNVs. The main goals are the validation of CNVs detected with NGS data, calculation of the diagnostic yield with CNV detection in oncologic, and whole exome sequencing samples diagnostic. Determination of quality parameters and respective detection thresholds. CNVs analysis validation involving CNV detection program VarSeq consisted of gathering positive (with deletions/duplications) and negative cases confirmed by another method, analyzing NGS data for the detection and calculating specificity, sensitivity, accuracy, and positive, and negative predictive values. After software validation, the diagnostic yield was calculated. There were included in this study 902 patients from oncologic testing with a diagnostic yield for CNVs was 2.54%. For WES samples, a total of 540 patients were analyzed with a diagnostic rate of 8.15% for CNVs. CNV accurate detection is possible, with a sensitivity of 99.15%, specificity of 98.85% and accuracy of 98.90% for cancer panels. For exomes, accounting all the alterations, the sensitivity is 87.50%, the specificity achieved of 99.30% and the accuracy of 97.84%. CNVs can accurately be detected and increase diagnostic yield by 3 − 8%, which is relevant for clinical management and genetic counseling to patients and their relatives. This study proves the potential of NGS as a reliable and affordable method to detect CNVs, both in target panel (as cancer panels) and WES.
Genetic variation in the human genome can range from large chromosomic anomalies to single nucleotide variations (SNVs), including structural variations, copy number variations (CNVs), small indels, and individual base alterations. Copy number gains or losses correspond to genomic structural duplications or deletions, respectively, and these alterations can directly influence genic dosage, which has direct implications in genomic diseases. This work focuses on patients that made oncologic genetic tests and in the detection of potential causal CNVs. The main goals are the validation of CNVs detected with NGS data, calculation of the diagnostic yield with CNV detection in oncologic, and whole exome sequencing samples diagnostic. Determination of quality parameters and respective detection thresholds. CNVs analysis validation involving CNV detection program VarSeq consisted of gathering positive (with deletions/duplications) and negative cases confirmed by another method, analyzing NGS data for the detection and calculating specificity, sensitivity, accuracy, and positive, and negative predictive values. After software validation, the diagnostic yield was calculated. There were included in this study 902 patients from oncologic testing with a diagnostic yield for CNVs was 2.54%. For WES samples, a total of 540 patients were analyzed with a diagnostic rate of 8.15% for CNVs. CNV accurate detection is possible, with a sensitivity of 99.15%, specificity of 98.85% and accuracy of 98.90% for cancer panels. For exomes, accounting all the alterations, the sensitivity is 87.50%, the specificity achieved of 99.30% and the accuracy of 97.84%. CNVs can accurately be detected and increase diagnostic yield by 3 − 8%, which is relevant for clinical management and genetic counseling to patients and their relatives. This study proves the potential of NGS as a reliable and affordable method to detect CNVs, both in target panel (as cancer panels) and WES.
Descrição
Dissertação submetida à UNIVERSIDADE DE TRAS-OS-MONTES E ALTO DOURO para obtenção do grau de MESTRE em Biotecnologia para as Ciências da Saúde
Palavras-chave
Variação-Número-Cópias , Sequenciação-Nova-Geração