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Test Code LUCSF LiquidHALLMARK CSF


Shipping Instructions


Freeze the specimen immediately following collection. It is critical that the specimen remains frozen throughout the shipping process and is never thawed.

 

The collected specimen is stable for up to 30 days if stored frozen at the collection site.



Necessary Information


1. Order questions are required for testing to proceed.

If not ordering electronically, submit LiquidHALLMARK Patient Information with the specimen.

2. A pathology report is recommended. Testing may proceed without this information; however, it aids in providing a more thorough and accurate interpretation of results. Ordering healthcare professionals are strongly encouraged to provide the information and send it with the specimen.



Specimen Required


Supplies: Sterile Specimen Tube, 6 mL (T485)

Container/Tube: Sterile tube

Specimen Volume: 5 mL

Collection Instructions:

1. Perform lumbar puncture and discard the first 1 mL to 2 mL of cerebrospinal fluid (CSF).

2. Collect CSF directly into a sterile tube.

3. Inspect specimen for visible discoloration. Specimen must be clear and colorless to perform testing.

4. Freeze sample upright prior to placing in transport container.

5. Send frozen.


Forms

If not ordering electronically, complete, print, and send a LiquidHALLMARK Patient Information with the specimen.

Secondary ID

622814

Useful For

Genomic profiling of suspected primary brain tumors or brain or leptomeningeal metastases for predicting prognosis and identifying matched targeted therapies or emerging resistance mechanisms

 

This test is not useful for prenatal screening.

Highlights

LiquidHALLMARK CSF is a sensitive next-generation sequencing assay that targets circulating tumor DNA in cerebrospinal fluid (CSF) in patients with suspected brain or leptomeningeal metastases. It can detect driver mutations and emerging mutations of therapeutic resistance to inform physicians of the appropriate targeted treatment selection.

Method Name

Amplicon-Based Next-Generation Sequencing

Reporting Name

LiquidHALLMARK CSF

Specimen Type

CSF

Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time
CSF Frozen 30 days

Reject Due To

Hemolysis Reject

Clinical Information

LiquidHALLMARK CSF enables genomic profiling of cerebrospinal fluid (CSF) cell-free DNA to detect clinically relevant and actionable alterations associated with FDA-approved and emerging therapies, including key biomarkers such as EGFR, BRAF, KRAS, ERBB2, and H3 (histone) gene mutations, as well as other guideline-recommended targets.

 

In patients with suspected or confirmed CNS or leptomeningeal metastases, CSF-based analysis can complement tissue and plasma testing by improving detection of tumor-derived alterations within the central nervous system. Results may support therapy selection and provide insight into molecular evolution and treatment response over time.

 

This test is intended as an adjunct to standard diagnostic approaches and is not a substitute for primary diagnosis.

Reference Values

An interpretive report will be provided

Interpretation

The interpretation of molecular biomarker analysis includes an overview of the results and the associated prognostic and therapeutic implications.

Method Description

Nucleic acid (cfDNA) is extracted from the cerebrospinal fluid (CSF) sample. The extracted DNA undergoes sequencing library construction for genes targeted in the LiquidHALLMARK CSF assay. Quality and concentration of constructed libraries are determined and then sequenced on an Illumina NextSeq/NovaSeq instrument with 2x150 pair-end reads. Targeted regions listed in the LiquidHALLMARK Targets by Cancer Type (ctDNA) or a relevant subset of the list, selected to maximize detections of known hotspot mutations, are analyzed for sequence variants. Six microsatellite loci (BAT25, BAT26, NR21, NR24, NR27, MONO27) are analyzed for deletions-insertions in homopolymeric regions. Samples with microsatellite instability (MSI) detected in two or more of six sites are considered MSI-High (MSI-H) and those with MSI detected in one of six sites are considered MSI-Low (MSI-L). Sequences are aligned to reference sequences based on human genome build GRCh37/UCSC hg19. Data is analyzed using in-house bioinformatics pipelines, and proprietary sequencing error-correction methodology is applied on raw sequencing data. Copy number changes are calculated based on adjusted read count, and its variation from normalized baseline read count determined across control samples. All sequence alterations are described according to the Human Genome Variation Society (HGVS) nomenclature guidelines as published.(1) Clinical actionability of genomic findings is determined based on curated databases from publicly available data sources, including peer-reviewed publications of genomic alterations and biomarkers and associated drugs. Tiering of clinical actionability is based on Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists consensus recommendation (2,3) where clinical actionability are based on Tier 1 evidence level (US Food and Drug Administration [FDA], guidelines, Phase III trials, well-powered studies with expert consensus). Drug and clinical trial information are obtained from curated databases including NCI thesaurus and ClinicalTrials.gov.

 

1. den Dunnen JT, Dalgleish R, Maglott DR, et al. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016;37(6):564-569. doi:10.1002/humu.22981

2. Li MM, Datto M, Duncavage EJ, et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017;19(1):4-23. doi:10.1016/j.jmoldx.2016.10.002

3. Wagner AH, Walsh B, Mayfield G, et al. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet. 2020;52(4):448-457. doi:10.1038/s41588-020-0603-8

Day(s) Performed

Monday through Friday

Performing Laboratory

Lucence Health, Inc.

Test Classification

This clinical test was developed and its performance characteristics determined by Lucence Health Inc. It has not been cleared or approved by the US Food and Drug Administration (FDA). The FDA does not require this test to go through premarket FDA review. This test is used for clinical purposes and should not be regarded as investigational or for research, unless otherwise stated in the report. Lucence Health Inc. is a Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory (CLIA ID Number: 05D2200843) and is accredited to College of American Pathologists (CAP) laboratory quality standards.

CPT Code Information

81455

LOINC Code Information

Test ID Test Order Name Order LOINC Value
LUCSF LiquidHALLMARK CSF Not Provided

 

Result ID Test Result Name Result LOINC Value
LU003 LiquidHALLMARK CSF Not Provided