[State of knowledge: principles and criteria to guide the use of genome-wide sequencing versus targeted sequencing of a limited number of genes for the search of germline variants ]
Provost C, Gravel C, Nshimyumukiza L
Record ID 32018013192
French
Original Title:
Principes et critères permettant de baliser le recours au séquençage pangénomique par rapport au séquençage ciblé d’un nombre limité de gènes pour la recherche de variants germinaux
Authors' objectives:
The mandate of the Réseau québécois de diagnostic moléculaire (RQDM), of which the
Centre québécois de génomique clinique (CQGC) is a part, is to meet the current and
future needs of the health and social services network in terms of molecular diagnostics
and personalized medicine, mainly in the fields of rare diseases and cancer.
With a view to standardizing, providing a framework for and ensuring the quality of the
next-generation sequencing (NGS) services currently being developed in Quebec, the
MSSS has asked the Institut national d’excellence en santé et en services sociaux
(INESSS) to review the current state of knowledge on the principles and criteria that
should guide the use of genome-wide sequencing versus targeted sequencing of a
limited number of genes to search for germline variants. In general terms, the questions
addressed to INESSS are intended to stimulate global reflection on the analytical
approach and completeness of the genomic analyses that should be offered in different
clinical contexts.
Authors' results and conclusions:
RESULTS (#1 TECHNICAL AND ORGANIZATIONAL FEATURES): According to a comparative analysis of the technical characteristics of NGS approaches,
targeted panels offer the advantage of relatively short library generation and data
analysis times. Whole genome sequencing (WGS) has a lower risk of sequencing bias
than Whole Exome Sequencing (WES) and targeted panels, because it generally does
not require a capture or amplification step for sequences of interest. Genome-wide approaches (WES or WGS) offer greater versatility, enabling frequent updates of in silico
panel gene lists, customization of analysis based on patient phenotype (ad hoc panels),
re-evaluation of clinical cases over time and standardization of sample trajectory. The
massive amount of data generated, the complexity of analyses and the cost are currently
the main disadvantages of WGS compared with WES and targeted NGS’. (#2 ANALYTICAL CHARACTERISTICS): WGS stands out for its ability to interrogate the entire nuclear and mitochondrial genome.
It is also less influenced by GC content (cytosines and guanines) and low-complexity
DNA sequences, and provides more uniform and complete coverage of the exome than
WES itself. It is therefore considered an unbiased approach, and requires a lower
average read depth (30X to 60X) than WES (100X to 150X) for clinical use. Targeted
panels, on the other hand, can achieve high read depths (500X to 1,000X), improving
sensitivity for detecting certain types of variants, particularly those of low allelic
frequency, provided that the genes and genomic regions of interest are known and
included in the panel. (#3 EMPIRICAL SENSITIVITY OF VARIANT DETECTION): The ability to detect single nucleotide variants (SNVs) and short insertions and deletions
(indels) is similar for all three approaches. WGS stands out and generally outperforms
WES and targeted panels in the detection of copy number variants (CNVs), structural
variants (SVs), repeat expansions and loss of heterozygosity (LOH). Given its coverage
of the nuclear and mitochondrial genomes, it can also detect deep intronic variants and
mitochondrial DNA (mtDNA) variants. Targeted panels are more effective at detecting
low-frequency variants and mosaicism. Finally, the diagnostic yield of the different NGS
approaches may vary according to the clinical context, the coverage and quality of the
sequences produced, the types of variants analyzed and the state of knowledge of the
regions analyzed (#4 ETHICAL ISSUES): Variants of uncertain significance (VUS) and the risk of incidental findings (pathogenic
variants not associated with the phenotype under investigation) are ethical issues
frequently addressed in the literature. These are generally proportional to the size of the
region analyzed, and the risk is therefore increased with genome-wide approaches.
However, the use of filters and in silico or ad hoc panels can reduce these risks in the
context of genome-wide NGS.
Targeted panels are not affected by the risk of incidental findings, since the genes and
genomic regions analyzed are specific to a given disease or group of diseases. (#5 DIAGNOSTIC PERFORMANCE): Genome-wide approaches generally demonstrate a higher diagnostic yield than targeted
panels, particularly when the genes or regions potentially involved are difficult to
circumscribe and in the context of conditions with moderate to high phenotypic and genotypic heterogeneity. According to subgroup analyses of recent meta-analyses, in
general, the diagnostic yield of genome-wide approaches is significantly higher in
pediatric populations than in adult populations. Diagnostic yield was also higher in studies
with neurological indications. However, overall, the diagnostic yield of WGS does not
differ significantly from that of WES according to recent meta-analyses, except in infants
with acute conditions. CONCLUSION: The present state of the art has made it possible to compile the available and relevant
literature on the principles and criteria guiding the choice of proceeding with a genomewide sequencing compared to a targeted NGS of a limited number of genes for the
molecular diagnosis of diseases in constitutional genetics.
The literature analyzed has helped to meet the main objective of this work, which is to
inform the MSSS about best practices in the use of different NGS approaches in clinical
settings. Finally, the findings presented in this report should support the MSSS in its
guidance of clinicians and laboratories in the network wishing to develop NGS analyses,
in particular to determine in which contexts genome-wide or targeted NGS analyses
should be carried out to search for germline variants.
Authors' methods:
The present state of knowledge is a synthesis of the results of a quick review of the
scientific literature carried out by INESSS on the principles and criteria guiding the choice
of genome-wide sequencing versus targeted sequencing of a limited number of genes for
germline variants. Publications were selected according to previously established PIPOH2
criteria. These documents include technology and health intervention assessment
reports, systematic reviews, guidelines, clinical practice guides and recommendations or
positions of learned societies dealing with the subject.
Details
Project Status:
Completed
Year Published:
2024
English language abstract:
An English language summary is available
Publication Type:
Not Assigned
Country:
Canada
Province:
Quebec
MeSH Terms
- Molecular Diagnostic Techniques
- Whole Genome Sequencing
- Exome Sequencing
- Genetic Testing
- Congenital, Hereditary, and Neonatal Diseases and Abnormalities
- Neoplasms
Contact
Organisation Name:
Institut national d'excellence en sante et en services sociaux
Contact Address:
L'Institut national d'excellence en sante et en services sociaux (INESSS) , 2021, avenue Union, bureau 10.083, Montreal, Quebec, Canada, H3A 2S9;Tel: 1+514-873-2563, Fax: 1+514-873-1369
Contact Name:
demande@inesss.qc.ca
Contact Email:
demande@inesss.qc.ca
Copyright:
L'Institut national d'excellence en sante et en services sociaux (INESSS)
This is a bibliographic record of a published health technology assessment from a member of INAHTA or other HTA producer. No evaluation of the quality of this assessment has been made for the HTA database.