Chromosomal microarray, exome and genome sequencing

Overview & Definition

Genomic diagnostics is the laboratory arm of clinical genetics, and the choice of test is the single most important decision a clinician makes after completing the clinical assessment. The four platforms are not interchangeable: they interrogate the genome at different resolutions and answer different questions, and ordering the wrong test wastes time, money and the family's trust. The fellowship candidate must be able to defend each choice against the clinical phenotype and the published evidence. [1] [2]

A karyotype is the light-microscope view of whole chromosomes, resolving changes larger than roughly five to ten megabases; it remains the test of choice for a suspected balanced rearrangement such as a translocation or inversion, which the newer platforms cannot see. Chromosomal microarray (CMA) uses array comparative genomic hybridisation (aCGH) and single-nucleotide-polymorphism (SNP) arrays to detect copy-number variants — deletions and duplications — down to tens of kilobases, and it can flag regions of homozygosity suggestive of uniparental disomy or consanguinity. It cannot detect single-nucleotide variants or balanced rearrangements. [1]

Whole-exome sequencing (WES) captures and sequences the protein-coding exons, which make up about one and a half percent of the genome but harbour roughly eighty-five percent of disease-causing variants. It detects single-nucleotide variants and small insertions or deletions in coding regions and canonical splice sites, but it misses deep intronic, regulatory and most structural variants, and it does not reliably detect repeat expansions. Whole-genome sequencing (WGS) sequences the entire genome and therefore captures the coding variants, the non-coding and regulatory variants, and the structural and copy-number variants in a single assay — at the cost of generating vastly more data and more variants of uncertain significance. [2] [3]

The clinical decision is which platform matches the phenotype, the acuity, and the locally funded pathway. In the well child with unexplained developmental delay or congenital anomalies, testing proceeds in a tier. In the critically ill infant in the intensive care unit, the tier collapses and rapid whole-genome sequencing becomes the first and sometimes only test, because a molecular diagnosis within days can change acute management, withdraw or escalate life-sustaining treatment, or redirect care. [7] [8]

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1. [1]Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. American Journal of Human Genetics, 2010.PMID 20466091
2. [2]Manickam K, McClain MR, Demmer LA, Biswas S, Kearney HM, Malinowski J Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genetics in Medicine, 2021.PMID 34211152
3. [3]Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genetics in Medicine, 2019.PMID 31182824
4. [4]Moeschler JB, Shevell M Comprehensive evaluation of the child with intellectual disability or global developmental delays. Pediatrics, 2014.PMID 25157020
5. [5]Moeschler JB, Shevell M Clinical genetic evaluation of the child with mental retardation or developmental delays. Pediatrics, 2006.PMID 16740881
6. [6]Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine, 2015.PMID 25741868
7. [7]Petrikin JE, Cakici JA, Smith MJ, Kingsmore SF The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants. NPJ Genomic Medicine, 2018.PMID 29449963
8. [8]Farnaes L, Hildreth A, Sweeney NM, Clark MM, Chowdhury S, Nahas S Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization. NPJ Genomic Medicine, 2018.PMID 29644095
9. [9]Sanford EF, Clark MM, Farnaes L, et al. Rapid whole genome sequencing has clinical utility in children in the PICU. Pediatric Critical Care Medicine, 2019.PMID 31246743
10. [10]Miller DT, Lee K, Abul-Husn NS, et al. ACMG SF v3.2 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genetics in Medicine, 2023.PMID 37347242