Dataset Information

Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases.

ABSTRACT:

Background

Exome sequencing (ES) has become the most powerful and cost-effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%-40% in solo-ES and 50% in trio-ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio-ES.

Methods

We pooled six (Agilent-CRE-v2-100X) or five parental DNA (TWIST-HCE-70X) aiming to detect allelic balance around 8-10% for heterozygous status. The strategies were applied as second-tier (74 individuals after negative solo-ES) and first-tier approaches (324 individuals without previous ES).

Results

The allelic balance of parental-pool variants was around 8.97%. Sanger sequencing uncovered false positives in 1.5% of sporadic variants. In the second-tier approach, we evaluated than two thirds of the Sanger validations performed after solo-ES (41/59-69%) would have been saved if the parental-pool segregations had been available from the start. The parental-pool strategy identified a causative diagnosis in 18/74 individuals (24%) in the second-tier and in 116/324 individuals (36%) in the first-tier approaches, including 19 genes newly associated with human disorders.

Conclusions

Parental-pooling is an efficient alternative to trio-ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.

SUBMITTER: Tran Mau-Them F

PROVIDER: S-EPMC8683640 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Publications

Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases.

Tran Mau-Them Frederic F Duffourd Yannis Y Vitobello Antonio A Bruel Ange-Line AL Denommé-Pichon Anne-Sophie AS Nambot Sophie S Delanne Julian J Moutton Sebastien S Sorlin Arthur A Couturier Victor V Bourgeois Valentin V Chevarin Martin M Poe Charlotte C Mosca-Boidron Anne-Laure AL Callier Patrick P Safraou Hana H Faivre Laurence L Philippe Christophe C Thauvin-Robinet Christel C

Molecular genetics & genomic medicine 20211030 12

<h4>Background</h4>Exome sequencing (ES) has become the most powerful and cost-effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%-40% in solo-ES and 50% in trio-ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio-ES.<h4>Methods</h4>We pooled six (Agilent-CRE-v2-100X) or five parental DNA (TWIST-HCE-70X) aiming to detect allelic balance around 8-10% for heterozygo ...[more]

PMID: 34716697

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Project description:Consanguineous marriages have a prevalence rate of 24% in Turkey. These carry an increased risk of autosomal recessive genetic conditions, leading to severe disability or premature death, with a significant health and economic burden. A definitive molecular diagnosis could not be achieved in these children previously, as infrastructures and access to sophisticated diagnostic options were limited. We studied the cause of neurogenetic disease in 246 children from 190 consanguineous families recruited in three Turkish hospitals between 2016 and 2020. All patients underwent deep phenotyping and trio whole exome sequencing, and data were integrated in advanced international bioinformatics platforms. We detected causative variants in 119 known disease genes in 72% of families. Due to overlapping phenotypes 52% of the confirmed genetic diagnoses would have been missed on targeted diagnostic gene panels. Likely pathogenic variants in 27 novel genes in 14% of the families increased the diagnostic yield to 86%. Eighty-two per cent of causative variants (141/172) were homozygous, 11 of which were detected in genes previously only associated with autosomal dominant inheritance. Eight families carried two pathogenic variants in different disease genes. De novo (9.3%), X-linked recessive (5.2%) and compound heterozygous (3.5%) variants were less frequent compared to non-consanguineous populations. This cohort provided a unique opportunity to better understand the genetic characteristics of neurogenetic diseases in a consanguineous population. Contrary to what may be expected, causative variants were often not on the longest run of homozygosity and the diagnostic yield was lower in families with the highest degree of consanguinity, due to the high number of homozygous variants in these patients. Pathway analysis highlighted that protein synthesis/degradation defects and metabolic diseases are the most common pathways underlying paediatric neurogenetic disease. In our cohort 164 families (86%) received a diagnosis, enabling prevention of transmission and targeted treatments in 24 patients (10%). We generated an important body of genomic data with lasting impacts on the health and wellbeing of consanguineous families and economic benefit for the healthcare system in Turkey and elsewhere. We demonstrate that an untargeted next generation sequencing approach is far superior to a more targeted gene panel approach, and can be performed without specialized bioinformatics knowledge by clinicians using established pipelines in populations with high rates of consanguinity.

Dataset Information

Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases.

Background

Methods

Results

Conclusions

Publications

Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases.

Similar Datasets

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