Background:
Heterotaxy is a congenital condition diagnosed by abnormal arrangement of organs in the chest and abdomen. The arrangements of the organs are flipped where they are typically seen, a condition called situs inversus or situs amiguus. This mis-orientation may cause structural abnormalities of the organs. The prevalence of these conditions is about 1:10,000 worldwide. These conditions may be sporadic or follow an autosomal dominant, recessive or X-linked pattern. This next-generation sequencing test assesses the coding regions of 42 genes associated with heterotaxy syndrome.
Reasons for Referral:
- Confirm a clinical diagnosis for a genetic etiology for heterotaxia
- Carrier testing
- Positive family history
Methodology:
Next generation sequencing (NGS) will analyze the exons or coding regions of the genes using Illumina NextSeq 500/550 technology and preparing samples 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 NGS data through the Genome Analysis Toolkit (GATK) Germline Copy Number Variation best practices pipeline from GATK, version 4.1.4.1. A Bayesian model was validated clinically in our lab. The model can detect copy changes at a resolution of three (3) or more probe targets (exons) for deletions and duplications in genes that do not have pseudogenes, and is not designed to detect low-level mosaicism or balanced alterations.
The 42 Heterotaxia-associated genes are listed below:
ACVR2B, ARMC4, C21ORF59, CCDC103, CCDC114, CCDC151, CCDC39, CCDC40, CCDC65, CCNO, CENPF, CITED2, CRELD1, DNAAF1, DNAAF2, DNAAF3, DNAH11, DNAH5, DNAI1, DNAI2, DNAJB13, DRC1, DYX1C1, FOXH1, GAS8, GATA4, GDF1, HEATR2, LEFTY2, LRRC6, NKX2-5, NODAL, PIH1D3, RSPH1, RSPH3, RSPH4A, RSPH9, SHROOM3, SMAD2, SPAG1, ZIC3, ZMYND10
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). Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.
Assisted Saliva: 4 ORAgene™ Assisted Saliva Collection Kit(s) (OGR-575) 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.
Prenatal:
Direct Amniotic Fluid (10-20mL)
Direct CVS
Direct POC
Cultured Amniocytes (2 T-25 flasks)
Cultured CVS (2 T-25 flasks)
Cultured Fetal Tissue: Product of Conception (2 T-25 flasks)
Cord Blood (1-2mL)
DNA: 10µg 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)
Notice Regarding Molecular Genetic Testing on Prenatal Specimens:
- Maternal cell rule-out testing will be performed on all prenatal specimens received. Please provide maternal blood (or saliva) in addition to the fetal specimen. Additional charges apply for the maternal cell rule-out test.
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.
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:
8 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:
- Genetics Home Reference: Heterotaxy Syndrome https://ghr.nlm.nih.gov/condition/heterotaxy-syndrome#
Additional Info: