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  • Test code: 04743
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit
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Invitae CHOPS Syndrome Test

Test description

The Invitae CHOPS Syndrome Test analyzes the AFF4 gene which is associated with cognitive impairment, coarse facies, heart defects, obesity, pulmonary involvement, short stature, and skeletal dysplasia (CHOPS).

Genetic testing of this gene may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant can inform recurrence-risk assessment and genetic counseling.

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Primary panel (1 gene)

Alternative tests to consider

Given the significant phenotypic overlap between Cornelia de Lange syndrome (CdLS) and CHOPS syndrome and the difficulty in differentiating between these syndromes early in life, analyzing the genes associated with Cornelia de Lange syndrome may be appropriate. These genes can be ordered with this test at no additional charge.

  • CHOPS syndrome

CHOPS syndrome is a congenital disorder with features including microcephaly, cognitive impairment, cataracts, hearing loss, obstructive sleep apnea, congenital heart defects, and genitourinary and skeletal anomalies. Most affected individuals have short stature, obesity, and distinctive coarse facial features.

AFF4 is the only gene known to be associated with CHOPS syndrome. However, due to the rarity of this condition, the percent of CHOPS syndrome attributed to pathogenic variants in AFF4 is currently unknown.

CHOPS syndrome is inherited in an autosomal dominant manner.

CHOPS syndrome is very rare and the penetrance is not clearly established.

The prevalence of CHOPS syndrome is not clearly established.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
AFF4 NM_014423.3