Genome sequencing after negative exome sequencing: Results in a rare disease cohort
Clinical Genetics and Therapeutics
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Primary Categories:
- Clinical- Pediatric
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Secondary Categories:
- Clinical- Pediatric
Introduction:
In this study, we aim to examine the diagnostic rate of genome sequencing (GS) in individuals with rare disorders with a history of negative exome sequencing (ES). The Center for Rare Childhood Disorders (C4RCD) at TGen has performed ES/GS in over 750 individuals (diagnostic rate of around 40%). A goal of the C4RCD is to explore techniques to increase the genetic diagnosis in rare disease patients, many of whom have a neurological component to their phenotype.
Methods:
We performed GS on 203 cases (167 exome-negative (EN), 20 exome-positive (EP) cases, and 16 research genome-negative (GN) cases). Genome Sequencing was performed by the Illumina Laboratory Services using TruSeq PCR-free kit on a HiSeqX or NovaSeq with 150bp paired-end reads, yielding a minimum mean sequencing depth of 30-40X. The data was aligned to the GRCh37/hg19 genome assembly and was processed and analyzed either through the DRAGENTM Bio-IT Platform, or using Strelka caller for SNVs or Canvas caller for CNVs, and variant annotation by Nirvana. A subset of the cases were also analyzed using Illumina’s Emedgene Software, leading to three of the new diagnoses.
Results:
GS diagnosed 15.6% (26/167) of EN cases and 6.3% (1/16) GN cases. The reason for a new diagnosis included: 42.3% (11/26) new gene-disease associations, 11.5% (3/26) technical limitations of ES (such as insufficient exon coverage, intronic, non-coding, etc.), 15.4% (4/26) upgrade in variant classification, 7.7% (2/26) variant identification (not called by previous software but not due to limitations of ES), 11.5% (3/26) copy number variant detection, 11.5% (3/26) short tandem repeats (STR). 9.6% (16/167) of cases would have been solved by reanalysis of ES, leading to a diagnostic yield of 6.0% (10/167) for GS. Diagnoses were confirmed in all 20 EP cases.
Conclusion:
GS detected SNVs, CNVs, and STRs in 15.6% of families with a previous negative ES, which supports the use of GS as a first-tier test, especially for children with medical complexity, compared to standard genetic testing. Many of the new diagnoses were due to changes in understanding of the genome over time, advancements in software analysis, and the discovery of new gene-disease associations because of sequencing technology.
In this study, we aim to examine the diagnostic rate of genome sequencing (GS) in individuals with rare disorders with a history of negative exome sequencing (ES). The Center for Rare Childhood Disorders (C4RCD) at TGen has performed ES/GS in over 750 individuals (diagnostic rate of around 40%). A goal of the C4RCD is to explore techniques to increase the genetic diagnosis in rare disease patients, many of whom have a neurological component to their phenotype.
Methods:
We performed GS on 203 cases (167 exome-negative (EN), 20 exome-positive (EP) cases, and 16 research genome-negative (GN) cases). Genome Sequencing was performed by the Illumina Laboratory Services using TruSeq PCR-free kit on a HiSeqX or NovaSeq with 150bp paired-end reads, yielding a minimum mean sequencing depth of 30-40X. The data was aligned to the GRCh37/hg19 genome assembly and was processed and analyzed either through the DRAGENTM Bio-IT Platform, or using Strelka caller for SNVs or Canvas caller for CNVs, and variant annotation by Nirvana. A subset of the cases were also analyzed using Illumina’s Emedgene Software, leading to three of the new diagnoses.
Results:
GS diagnosed 15.6% (26/167) of EN cases and 6.3% (1/16) GN cases. The reason for a new diagnosis included: 42.3% (11/26) new gene-disease associations, 11.5% (3/26) technical limitations of ES (such as insufficient exon coverage, intronic, non-coding, etc.), 15.4% (4/26) upgrade in variant classification, 7.7% (2/26) variant identification (not called by previous software but not due to limitations of ES), 11.5% (3/26) copy number variant detection, 11.5% (3/26) short tandem repeats (STR). 9.6% (16/167) of cases would have been solved by reanalysis of ES, leading to a diagnostic yield of 6.0% (10/167) for GS. Diagnoses were confirmed in all 20 EP cases.
Conclusion:
GS detected SNVs, CNVs, and STRs in 15.6% of families with a previous negative ES, which supports the use of GS as a first-tier test, especially for children with medical complexity, compared to standard genetic testing. Many of the new diagnoses were due to changes in understanding of the genome over time, advancements in software analysis, and the discovery of new gene-disease associations because of sequencing technology.
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