Background:
Inherited bone marrow failure syndromes are a group of disorders characterized by the inability to sufficiently produce red blood cells, white blood cells or platelets. These conditions are caused by mutations in genes involved in ribosome assembly, DNA repair, and telomere maintenance and are associated with Fanconi anemias, Diamond Blackfan anemia, Shwachman Diamond syndrome, dyskeratosis congentia, aplastic anemias, and myelodysplastic anemia syndromes. This next-generation sequencing tests the coding regions for 117 genes that are associated with these conditions. These may be inherited as autosomal recessive, dominant or X-linked pattern.
Reasons for Referral:
- Genetic diagnosis for patients with bone marrow failure
- Carrier testing
Methodology:
Next generation sequencing will analyze the exons or coding regions of 117 Bone Marrow Failure-associated genes using Illumina NextSeq 500/550 technology. Samples are prepared using hybridization probes to enrich exonic regions. This assay does not assess regions of insufficient coverage, introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and regions of high GC or polynucleotide repeats, but may contain variants that impact gene function.
Exon-level deletion/duplication analysis is performed by running the same NGS data through the Genome Analysis Toolkit (GATK) Germline CNV best practices pipeline from a GATK version. The pipeline has been validated to detect deletion and duplication events as large as full chromosomes and as small as three exons. Detection of events involving one or two exons may occur but are not guaranteed within our validated parameters. If deemed reportable, deletions and duplications of <3 exons or with lower quality scores may be confirmed by orthogonal methods.
The 117 Bone Marrow Failure-associated genes are listed below:
ABCB7, ACD, AK2, ALAS2, ANKRD26, ATM, ATR, BLM, BRCA1, BRCA2, BRIP1, c6orf25 (MPIG6B), CBL, CDAN1, CECR1 (ADA2), CLPB, CSF3R, CTC1, CXCR4, DDX41, DKC1, DNAJC21, EFTUD1 (EFL1), ELANE, EPO, ERCC4, ERCC6L2, ETV6, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, G6PC3, GATA1, GATA2, GFI1, HAX1, HOXA11, ITK, JAGN1, KLF1, KRAS, LIG4, LYST, MAD2L2, MECOM, MPL, MYSM1, NBN, NHP2, NOP10, NRAS, PALB2, PARN, PRF1, PTPN11, PUS1, RAB27A, RAC2, RAD51, RAD51C, RBM8A, RFWD3, RPL11, RPL15, RPL18, RPL26, RPL27, RPL31, RPL35, RPL35A, RPL5, RPL9, RPS10, RPS15, RPS15A, RPS19, RPS24, RPS26, RPS27, RPS27A, RPS28, RPS29, RPS7, RTEL1, RUNX1, SAMD9, SAMD9L, SBDS, SLC37A4, SLX4, SMARCD2, SRP54, SRP72, TBXAS1, TCN2, TERC, TERT, THPO, TINF2, TP53, TSR2, UBE2T, USB1, VPS45, WAS, WDR1, WIPF1, WRAP53, XRCC2, ZCCHC8
Specimen Requirements:
Blood: EDTA or ACD (Solution A or B):
- Adult: 5 mL
- Child: 5 mL
- Infant: 2-3 mL
Saliva: 2 ORAgene™ Saliva Collection Kit(s) (OGR-500) used according to manufacturer instructions. Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.
Skin Fibroblast: Punch Biopsy (Cell cultures will be prepared at KDL and used for testing), or 2 T-25 confluent flasks.
DNA: 7-10 µg at a minimum of 60-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS)
Important note on specimen type: This test is designed for detecting germline variants. As such, results may be compromised for blood, bone marrow, or saliva from patients with certain hematological conditions that are in an active disease state. In such cases, skin fibroblasts are highly recommended.
For routine testing of blood and saliva (or DNA extracted from them), KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed outside of the above windows, please contact our lab. For patients with bone marrow transplants, the only acceptable specimen type is a skin biopsy (Cell cultures will be prepared at KDL before testing)
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information, including ethnicity, clinical history, and family history.
Test Performed (Days):
Weekly
Turn Around Time:
3-4 weeks
Shipment Sensitivity Requirements:
- Package and ship specimen to remain cold, but not frozen.
- Ship via overnight express, using the FedEx priority overnight label provided.
- Contact Client Services for shipping kits and instructions at (855) 535-1522.
References:
- Haematologica. 2010 Aug; 95(8): 1236–1240
Additional Info: