Test Background

Hemophagocytic lymphohistiocytosis (HLH) includes a wide array of related diseases that also encompasses some types of autoimmune-associated macrophage activation syndrome (MAS). 

The Hemophagocytic Lymphohistiocytosis (HLH) Region of Interest analysis was designed in collaboration with immunology, rheumatology and oncology experts at Boston Children’s Hospital and evaluates 20 genes related to HLH and HLH-associated MAS. The HLH Region of Interest Report includes orthogonally-confirmed variants identified by Next Generation Sequencing and the results of the companion deletion/duplication analysis, if ordered.

This study can be ordered for the proband alone by submitting a sample from the affected individual or as a trio with parental samples included in the analysis.

In the case of a non-diagnostic finding, ordering providers have the option to go beyond the Region of Interest test by ordering an expansion to the Claritas Clinical Exome (Test Code N0527). A new sample will not need to be submitted. Interpretation will be provided in a new report that will be available in 12-14 weeks.

Clinical Features and Causes of HLH

HLH results when the body over-produces certain immune cells resulting in an uncontrolled hyperinflammatory response. Symptoms of HLH often present within the first months of life with 70% of familial cases due to genetic factors occurring before one year of age. Symptoms include fever, enlarged liver or spleen, skin rash, lymph node enlargement, breathing problems, easy bruising, abnormal bleeding, kidney or heart problems, neurologic abnormalities and an increased risk for leukemia or lymphoma. Laboratory findings may include cytopenia (low blood cell count), elevated triglycerides or low levels of fibrinogen, hemophagocytosis, decreased or absent natural killer (NK) cell activity, high levels of ferritin in the blood and/or elevated soluble CD25 (IL-2r) blood levels.

HLH is believed to be an under-recognized disorder, which may be a factor contributing to its high morbidity and mortality. Early recognition is crucial in order to begin potentially curative therapy.

HLH may be genetic (sometimes referred to as familial HLH [FHLH] or “primary HLH”) or acquired (“secondary HLH”). This assay is designed to assess genes that may cause autosomal recessive or X-linked recessive forms of primary HLH. While MAS is often considered to be a form of secondary HLH associated with autoimmune disorders, it is now recognized that there are a number of genetic factors that can predispose or cause this disorder. This assay includes genes with known Mendelian inheritance that are associated with HLH and HLH-associated MAS.

Acquired causes of HLH include: infection, autoimmune disorders, immune suppression drugs, other immunodeficiencies, specific forms of cancer, and/or metabolic diseases. This assay does not detect these acquired causes of HLH.

Test Characteristics

  • Assessment of 20 genes related to HLH and HLH-associated MAS; protein coding sequences and 10 bp of adjacent intronic sequences are analyzed
  • Orthogonal approach using Illumina NextSeq™ with simultaneous confirmation of 95% of variants on the Thermo Fisher (formerly Life Technologies) Ion Proton™; reported variants that are not orthogonally confirmed are confirmed with Sanger sequencing
  • Mean coverage of >100x for the combined Illumina NextSeq™ and Thermo Fisher Ion Proton™ platforms; >98% at 20x**
  • This assay can detect SNVs, insertions, and deletions less than 10 bp
  • Two intronic variants in the UNC13D gene are assessed by Sanger sequencing: c.118-308C>T and c.118-307G>A
  • Adding the companion deletion/duplication analysis (Test Code N0659) can increase detection rate for copy number variants and larger indels.

**Data for the Claritas Clinical Exome

Indications for Testing

Symptoms of HLH due to genetic factors can be difficult to distinguish from acquired HLH. Molecular testing has value in making a diagnosis of HLH and detecting cases due to genetic factors which can also have implications for other family members.

  • Patient with suspected HLH (multiple symptoms consistent with the disorder)
  • More than one family member with HLH symptoms that are not explainable by acquired factors, or MAS is suspected and symptoms are consistent.

Increase the Power of the Assay

  • Add companion deletion/duplication testing (Test Code N0659)
  • If no diagnostic findings are reported in the ROI, providers can order an expanded interpretation of the whole clinical exome (Test Code N0527)

Additional Service Highlights

  1. Providers may request a review of variant classification at any time.
  2. Providers may access the Interpretative Genomics Service at Boston Children’s Hospital, which provides consultation with experts in genes and/or phenotypes. Please contact [email protected] for more information.
  3. Claritas Genomics will release raw data files or provide access to exome data via NextCODE to authorized health care providers. Review Data Return Program details here.



*Deletion/duplication analysis for this gene is not included or coverage is limited