Low-Pass Genome Sequencing: Validation and Diagnostic Utility from 409 Clinical Cases of Low-Pass Genome Sequencing for the Detection of Copy Number Variants to Replace Constitutional Microarray

J Mol Diagn. 2020 Jun;22(6):823-840. doi: 10.1016/j.jmoldx.2020.03.008. Epub 2020 Apr 25.


DNA copy number variants (CNVs) account for approximately 300 Mb of sequence variation in the normal human genome. Significant numbers of pathogenic CNVs contribute toward human genetic disorders. Recent studies suggest a higher diagnostic and clinical significance of low-pass genome sequencing (LP-GS) compared with chromosomal microarrays (CMAs). The performance metrics of the 5X LP-GS was compared with CMA to validate a low-cost and high-throughput method. LP-GS test performed on 409 samples (including 78 validation and 331 clinical) was evaluated using American College of Medical Genetics and Genomics guidelines. The CNV accuracy, precision, specificity, and sensitivity were calculated to be 100% for all previously characterized CNVs by CMA. Samples (n = 6) run at both approximately 30X GS and approximately 5X GS (LP-GS) average depth detected a concordance of 89.43% to 91.8% and 77.42% to 89.86% for overall single-nucleotide variants and insertions/deletions, respectively. In the 331 clinical samples, 17.2% each were classified as pathogenic/likely pathogenic and uncertain clinical significance. In addition, several cases with pathogenic CNVs were detected that were missed by CMA. This study demonstrates that LP-GS (5X GS) was able to reliably detect absence of heterozygosity, microdeletion/microduplication syndromes, and intragenic CNVs with higher coverage and resolution over the genome. Because of lower cost, higher resolution, and greater sensitivity of this test, our study in combination with other reports could be used in an evidence-based review by professional societies to recommend replacing CMAs.

Publication types

  • Case Reports
  • Comparative Study
  • Validation Study

MeSH terms

  • Adolescent
  • Base Sequence
  • Child
  • Chromosome Mapping / methods*
  • DNA Copy Number Variations*
  • Data Accuracy
  • Gene Deletion
  • Genetic Testing / methods*
  • Genome, Human*
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Infant
  • Male
  • Microarray Analysis / methods*
  • Mutagenesis, Insertional
  • Polymorphism, Single Nucleotide
  • Sensitivity and Specificity
  • Whole Genome Sequencing / methods*