Achalasia Panel: Sequencing and CNV Analysis

Condition Description

Achalasia is a disorder of the esophagus, in which the esophagus has abnormal muscle activity and does not possess the ability to move food into the stomach. The major symptom is usually difficulty with swallowing. Complications may include regurgitation, gastroesophageal reflux, pulmonary aspiration, and perforation of the esophagus. Achalasia affects approximately 1 in every 100,000 people in the United States.

The etiology of achalasia remains largely unknown; however, the occurrence of familial achalasia and its association with defined genetic syndromes have indicated that in some cases achalasia can be caused by genetic anomalies. EGL tests for genes known to cause the following achalasia-associated syndromes:

  • Triple A syndrome (Achalasia-Addisonianism-Alacrima) or Allgrove syndrome
  • Moyamoya diesase-6 with achalasia
  • Alacrima, achalasia, and mental retardation syndrome
  • Baraister-Winter Cerebrofrontofacial syndrome
  • Autoimmune Polyendocrine syndrome type with or without Reversible Metaphyseal dysplasia
  • Ataxia, posterior column, with retinitis pigmentosa (PCARP)


  1. MedlinePlus:
  2. Dumic M et al. Long-term clinical follow-up and molecular genetic findings in eight patients with triple A syndrome. Eur J Pediatr. 2012 Oct;171(10):1453-9. Epub 2012 Apr 28.
  3. OMIM.

Genes (6)

Your search may have returned a result for a gene alias. Click here for a full list of genes and their aliases.


The test is indicated for:

  • Individuals with a clinical diagnosis of achalasia.


Next Generation Sequencing: In-solution hybridization of all coding exons is performed on the patient's genomic DNA. Although some deep intronic regions may also be analyzed, this assay is not meant to interrogate most promoter regions, deep intronic regions, or other regulatory elements, and does not detect single or multi-exon deletions or duplications. Direct sequencing of the captured regions is performed using next generation sequencing. The patient's gene sequences are then compared to a standard reference sequence. Potentially causative variants and areas of low coverage are Sanger-sequenced. Sequence variations are classified as pathogenic, likely pathogenic, benign, likely benign, or variants of unknown significance. Variants of unknown significance may require further studies of the patient and/or family members.

Copy Number Analysis: Comparative analysis of the NGS read depth (coverage) of the targeted regions of genes on this panel was performed to detect copy number variants (CNV). The accuracy of the detected variants is highly dependent on the size of the event, the sequence context and the coverage obtained for the targeted region. Due to these variables and limitations a minimum validated CNV size cannot be determined; however, single exon deletions and duplications are expected to be below the detection limit of this analysis.


Next Generation Sequencing: Clinical Sensitivity: Unknown. Mutations in the promoter region, some mutations in the introns and other regulatory element mutations cannot be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient's clinical/biochemical phenotype.

Analytical sensitivity for sequence variant detection is ~99%.

Copy Number Analysis: The sensitivity and specificity of this method for CNV detection is highly dependent on the size of the event, sequence context and depth of coverage for the region involved. The assay is highly sensitive for CNVs of 500 base pairs or larger and those containing at least 3 exons. Smaller (< 500 base pairs) CNVs and those that involving only 1 or 2 exons may or may not be detected depending on the sequence context, size of exon(s) involved and depth of coverage.

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (
Submit only 1 of the following specimen types
Whole Blood (EDTA)

EDTA (Purple Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 72 hours of collection. Do not freeze.

Oragene™ Saliva Collection Kit
Orangene™ Saliva Collection Kit used according to manufacturer instructions. Please contact EGL for a Saliva Collection Kit for patients that cannot provide a blood sample.
Collection and Shipping
Please do not refrigerate or freeze saliva sample. Please store and ship at room temperature.
DNA, Isolated

Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Collection and Shipping
Refrigerate until time of shipment in 100 ng/µL in TE buffer. Ship sample at room temperature with overnight delivery.

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