Hereditary Bone Marrow Failure Panel, Sequencing and Deletion/Duplication

Bone marrow failure (BMF) encompasses a heterogenous array of acquired and germline conditions characterized by qualitative or quantitative defects in one or more hematopoietic lineages resulting in cytopenias and hypocellular bone marrow. These include inherited syndromes such as Fanconi anemia (FA), telomere biology disorders (TBD) such as dyskeratosis congenita (DC), Schwachman-Diamond syndrome (SDS), Diamond-Blackfan anemia (DBA), congenital amegakaryocytic thrombocytopenia (CAMT), severe congenital neutropenia (SCN), aplastic anemia, and others.

This panel includes genes causative for hereditary BMF syndromes as well genes associated with hereditary predisposition to myeloid neoplasms, as there is often clinical overlap between these two entities.

Disease Overview

Hereditary BMF syndromes are caused by germline pathogenic variants that disrupt DNA repair, telomere maintenance, ribosome biogenesis, and structural protein pathways. In addition to BMF, these conditions may also be accompanied by syndromic physical findings and predisposition to hematologic and other malignancies. While most patients with hereditary BMF present in childhood, these conditions may manifest at any age.

Genetics

Genes

For a list of genes tested, associated disorders, and inheritance, refer to the Genes Tested table.

Refer to Limitations for exons not covered by sequencing and genes for which deletion and/or duplication is not available.

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

• Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
• Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing, or NGS) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for the detection of large deletions and duplications.
• Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
• Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Analytic Sensitivity/Specificity

Limitations

• A negative result does not exclude a diagnosis of bone marrow failure.
• Diagnostic errors can occur due to rare sequence variations.
• Interpretation of this test result may be impacted if this patient received an allogeneic stem cell transplant unless the sample analyzed is definitively from the recipient, such as cultured skin fibroblasts.
• The germline or somatic status of a detected variant cannot be definitively determined in patients with hematologic malignancy if the assay is performed on blood or other tissue that may be contaminated by clonal or malignant cells; testing a definitively germline specimen such as cultured fibroblasts may be recommended in such cases.
• The following will not be evaluated:
  • Variants outside the coding regions and intron-exon boundaries of targeted genes
  • SBDS gene associated with Schwachman-Diamond syndrome
  • Regulatory region and deep intronic variants
  • SNVs and small insertions/deletions will not be called in the following exons due to technical limitations of the assay:
    • CXCR4 (NM_001348056) exon 2
    • CXCR4 (NM_001348059) exon 2
    • DNAJC21 (NM_001348420) partial exon 9 (Chr5:34945827-34945845)
    • ERCC6L2 (NM_001375291) exon 19
    • ERCC6L2 (NM_001375292) exon 19
    • ERCC6L2 (NM_001375293) exon 18
    • ERCC6L2 (NM_001375294) exon 18
    • FANCA (NM_001018112) exon 11
    • FANCA (NM_001351830) exon 10
    • FANCD2 (NM_033084) exons 14, 17, 21, 22
    • FANCD2 (NM_001018115) exons 14, 17, 21, 22
    • FANCD2 (NM_001319984) exons 14, 17, 21, 22
    • FANCD2 (NM_001374253) exons 14, 17, 20, 21
    • FANCD2 (NM_001374254) exons 14, 17, 21, 22
    • FANCD2 (NM_001374255) exon 10
    • FANCL (NM_001374615) exon 8
  • Deletions/duplications in CEBPA, NOP10, RMRP, and RPL15 genes
  • Duplications in the TERC gene
  • Breakpoints of large deletions/duplications
• The following may not be detected:
  • Deletions/duplications/insertions of any size by massively parallel sequencing
  • Large duplications less than 3 exons in size
  • Noncoding transcripts
  • Some variants due to technical limitations in the presence of pseudogenes and/or repetitive/homologous regions
  • Low-level somatic variants

Genes Tested