Journal Article

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

Wedell, Anna, Grigelioniene, Giedre, Stranneheim, Henrik, Nordgren, Ann, Georgii-Hemming, Patrik, Lindstrand, Anna, Magnusson, Måns, Martin, Marcel, Nilsson, Daniel, Norling, Ameli, Eisfeldt, Jesper, Pettersson, Maria, Anderlid, Britt-Marie, Lundin, Johanna, Carvalho, Claudia M. B., Kvarnung, Malin, Lagerstedt-Robinson, Kristina, Wincent, Josephine, Wirta, Valtteri, Tham, Emma, Lieden, Agne, Malmgren, Helena, Nordenskjöld, Magnus, Iwarsson, Erik, Johansson-Soller, Maria, Bjerin, Olof, Ygberg, Sofia, Sahlin, Ellika, Hammarsjö, Anna, Gustavsson, Peter

2019

Overview

Background Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test. Methods We analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n  = 68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n  = 156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure. Results First, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850 kb (min 500 bp, max 155 Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (> 10 kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7 . Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data. Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively. Conclusion The overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Bioinformatics / Biomedical and Life Sciences / Biomedicine / Cancer Research / Child / Chromosome Aberrations / Copy number variation / Cytogenetic Analysis - methods / Cytogenetics / Diagnosis / Diagnostic equipment (Medical) / Diagnostic Tests, Routine / Disabilities / DNA Copy Number Variations / DNA microarrays / DNA sequencing / Female / Genes / Genetic aspects / Genetic Markers / Genetic testing / Genetic variation / Genome, Human / Genomes / Genomics / Health aspects / Human Genetics / Humans / Identification and classification / Intellectual disabilities / Intellectual disability / Intellectual Disability - diagnosis / Intellectual Disability - genetics / Male / Medical tests / Medicine/Public Health / Metabolomics / Methods / Monogenic disease / Phenotypes / Pilot Projects / Polymorphism, Single Nucleotide / Prader-Willi syndrome / Prospective Studies / Repeat expansion / Retrospective Studies / Single nucleotide variant / Structural variation / Systems Biology / Uniparental disomy / Whole Genome Sequencing - methods / Whole-genome sequencing