Osteogenesis Imperfecta Genetic Panel

Use: Diagnostic testing

Limitations: This assay will not consistently detect germline mosaicism below 50% or rule out the presence of large chromosomal aberrations, including rearrangements and inversions that do not change copy number of genomic regions. The assay does not detect repeat expansions. Possible intergenic variant interactions are not commented on. False positive or false negative results may occur for reasons that include: insufficient information available about rare genetic variants, sex chromosome abnormalities, pseudogene interference, homologous regions, blood transfusions, bone marrow transplantation, somatic or tissue-specific mosaicism, mislabeled samples, or erroneous representation of family relationships. Variants that do not alter an amino acid composition of a protein may be difficult to assess for pathogenicity since they may produce abnormalities in structures not assessed by conventional analysis paradigms (eg mRNA expression and processing).1 For mitochondrial DNA variants, low levels of heteroplasmy (<1%) may not be reliably detected by this technique. Mitochondrial variants may be tissue-specific. Interpretation of the clinical significance of gene variations is limited by information about the variant that is available at the time of reporting, and by the quality and quantity of clinical information provided with the sample. As the understanding of human genetic diversity improves, the interpretation of the clinical significance of variants may change.

This test was developed and its performance characteristics determined by Labcorp. It has not been cleared or approved by the Food and Drug Administration.

Methodology: Nuclear Gene Single Nucleotide Variant and Small Indel Sequencing Assessment: Genomic regions of interest are selected using a custom capture reagent for target enrichment (Twist Bioscience) and sequenced via the Illumina® Novaseq 6000 Next Generation Sequencing platform. Sequencing reads are aligned with the human genome reference GRCh37/hg19 build. Regions of interest include all exons and intron/exon junctions (+/-20 nucleotides) for each gene analyzed. A minimum of 99% of bases in targeted regions are covered at >15X. Analytical sensitivity is estimated to be >99% for single nucleotide variants, >97% for insertions/deletions less than six base pairs, and >95% for insertions/deletions between six and 15 base pairs. Uncovered regions with known pathogenic variants are sequenced in a targeted manner (list based on ClinVar Database: July 22, 2019, release).

Nuclear Gene Copy Number Variant Assessment: Next Generation Sequencing data used to call SNPs and small indels are assessed with Illumina’s DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform. Genes listed in ClinVar with intragenic pathogenic deletions are padded with additional intronic probes to allow single exon resolution CNV detection (list based on ClinVar Deletion Database: January 2019 release). For other genes, large deletions (>10 exons) can be detected. The resolution of this analysis can vary depending on region-specific features. Analytical sensitivity is estimated to be >95%.

Results Interpretation: Results should be used in the context of available clinical information and should not be used as the sole basis for patient management or treatment. Genetic counseling is recommended. Variants are assessed according to ACMG criteria.2 This report contains interpretation of pathogenic and likely pathogenic variants (by ACMG Criteria) as well as variants of uncertain significance (VUS) with pathogenic predictions related to the clinical information provided. Variants not reported: (1) Variants classified as benign or likely benign by ACMG Criteria; (2) VUS with benign or likely benign predictions; (3) variants related to carrier status; (4) polymorphisms with implications in drug response (pharmacogenomics variants). We will reanalyze the data periodically at the clinician’s request to allow potential reinterpretation based on new research or evidence. GnomAD abbreviations for population frequency data: African/African American (AFR), Latino (AMR), Ashkenazi Jewish (ASJ), East Asian (EAS), Finnish (FIN), Non-Finnish European (NFE), South Asian (SAS), Other (OTH).

Footnotes

1. Nackley AG, Shabalina SA, Tchivileva IE, et al. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science. 2006 Dec 22;314(5807):1930-1933. PubMed 17185601

2. Richards S, Nazneen A, Bale S, et al. 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. Genet Med. 2015 May;17(5):405-424. PubMed 25741868