Glossary

The language of the modern lab.

Plain-English definitions of the LIS/LIMS, genomics, pharmacogenomics, compliance, and billing terms genetic and molecular labs work in every day. Built by people who speak it.

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Operations & informatics

LIS (Laboratory Information System): Software that runs the clinical workflow of a lab — patient and order management, accessioning, result entry and reporting, and instrument/EHR interfacing. A LIS is patient- and result-centric and is the regulated system of record in clinical (CLIA/CAP) labs.
LIMS (Laboratory Information Management System): Software that manages samples and operational data — sample tracking, batches and plates, reagent and inventory management, workflow orchestration, and QC. A LIMS is sample- and process-centric, with roots in research and high-throughput labs.
LIS vs LIMS: The practical difference is patient-centric versus sample-centric. A LIS (Laboratory Information System) is built around a patient and an ordered test: it carries protected health information, manages orders, results, and clinical reports, and is the regulated system of record in clinical (CLIA/CAP) labs. A LIMS (Laboratory Information Management System) is built around samples, plates, batches, reagents, and workflows, and excels at high-volume operational tracking; it originated in research and industrial labs. There is no governing standard enforcing the line, and vendors use the labels loosely. Genetic, molecular, and NGS labs typically need both capabilities at once — clinical reporting and sign-out plus deep specimen-lineage and batch tracking — which is why many modern platforms, including Labrynix, span both rather than forcing a lab to choose.
Accessioning: The intake event where a received specimen is logged, assigned a unique accession ID, linked to its order and patient, and checked against acceptance criteria. It anchors everything downstream.
Chain of custody: A documented, unbroken record of everyone who handled, transferred, or stored a specimen, with timestamps, from collection to disposal — required where results carry legal or regulatory weight.
Specimen / sample lineage: The tracked genealogy linking an original specimen to everything derived from it — aliquots, extractions, and sequencing libraries — as parent→child relationships. Essential in molecular/NGS labs so any library result traces back to the patient specimen for QC and audit.
Turnaround time (TAT): The elapsed time between defined start and end points of testing — commonly order/receipt to result/report release. A core operational and regulatory KPI; labs often track multiple TAT segments separately.
QC (quality control): Running control materials with known expected results alongside patient samples to confirm an assay or instrument is performing within limits before results are released. Distinct from the broader quality-management system (QA).
Audit trail: A secure, time-stamped, attributable record of who did what and when to data — creations, changes, deletions — that can't be altered without itself being logged. Central to data integrity.

Integration & interoperability

HL7 v2: The long-established Health Level Seven messaging standard (e.g., ORM orders, ORU results) used for most lab–EHR interfaces today. Widely deployed but loosely constrained, so implementations usually need per-interface mapping.
FHIR: HL7's modern interoperability standard that models healthcare data as discrete resources (Patient, Observation, DiagnosticReport) exchanged over RESTful APIs. Increasingly the basis for app- and API-driven EHR integration, including genomics.
FHIR Genomics Reporting IG: An HL7 FHIR implementation guide that standardizes how genomic results — variants, haplotypes/genotypes, annotations — are structured in FHIR, so genomic reports are consistent and computable across systems.
CDS Hooks: An HL7 spec that lets an EHR call out to external decision-support services at specific moments (opening a chart, signing an order) and show the response as cards. In PGx, it's how a real-time gene–drug alert surfaces in the prescriber's workflow.
EHR/EMR integration: The connection between lab software and a clinical record system so orders flow in and results/reports flow back — via HL7 v2 today and increasingly FHIR. (EHR implies a broader, cross-organization record than EMR, but the terms are used interchangeably in practice.)
Interface engine: Middleware that routes, translates, and reformats messages between systems (e.g., normalizing one EHR's HL7 dialect to your LIS's expected format) so a lab can maintain many client interfaces without custom point-to-point code.

Genomics & testing

NGS (next-generation sequencing): High-throughput, massively parallel DNA/RNA sequencing that reads many sequences at once, enabling panels, exomes, and genomes at a scale and cost impractical with older Sanger sequencing. The data backbone of modern molecular testing.
Variant interpretation: Determining the clinical meaning of an observed genetic variant — its likely effect and significance for disease, drug response, or cancer — using population data, functional evidence, databases, and published guidelines.
ACMG/AMP classification (5 tiers): The 2015 ACMG–AMP framework for classifying germline sequence variants by combining weighted evidence into one of five tiers: Pathogenic, Likely pathogenic, Variant of uncertain significance (VUS), Likely benign, and Benign. The dominant standard for germline classification.
VUS (variant of uncertain significance): A variant with insufficient or conflicting evidence to classify as pathogenic or benign. It generally shouldn't drive medical decisions, and may be reclassified as more evidence accumulates.
Tier I/II (somatic — AMP/ASCO/CAP): From the 2017 AMP/ASCO/CAP four-tier system for somatic (tumor) variants by clinical actionability: Tier I = strong clinical significance; Tier II = potential clinical significance. A separate framework from ACMG/AMP germline classification — don't conflate the two.

Pharmacogenomics (PGx)

Pharmacogenomics (PGx): The study and clinical application of how an individual's genetic variation affects their response to drugs — efficacy, dosing, and the risk of adverse reactions — used to guide drug and dose selection. In practice, a PGx test genotypes a panel of drug-metabolizing genes (such as CYP2D6, CYP2C19, and SLCO1B1), translates the genotype into a predicted metabolizer phenotype, and maps that phenotype to evidence-based prescribing guidance from sources like CPIC, FDA drug labeling, and PharmGKB. The output is a clinician-facing report describing gene–drug interactions and prescribing considerations. PGx does not diagnose disease; it informs medication decisions. In the lab, qualified staff validate the interpretation and sign out the report — software and AI assist the workflow, but the clinical decision stays with the prescriber and the lab.
CPIC: The Clinical Pharmacogenetics Implementation Consortium is an international body, associated with the NIH and PharmGKB, that publishes peer-reviewed, freely available, evidence-based gene–drug clinical practice guidelines. CPIC guidelines answer a specific question: given a genetic test result that is already available, how should a clinician act on it — that is, how to translate a patient's genotype and predicted phenotype into concrete prescribing or dosing guidance. They deliberately do not advise whether to order testing in the first place. CPIC assigns standardized terms for metabolizer phenotypes and grades the strength of each recommendation. PGx reporting workflows commonly reference CPIC guidance, applied under each lab's own validated interpretation rules, to produce consistent, defensible drug–gene recommendations.
PharmGKB: The Pharmacogenomics Knowledgebase — a publicly available, expertly curated resource of gene–drug–phenotype relationships, annotations, and dosing guidelines. NIH-funded, managed at Stanford, and a close partner of CPIC.
DPWG: The Dutch Pharmacogenetics Working Group develops evidence-based pharmacogenetic therapeutic recommendations and integrates them into prescribing decision-support. The main European counterpart to CPIC; the two sometimes differ.
Star allele (e.g., *1/*2): Standardized nomenclature for naming haplotype variants of a pharmacogene. *1 conventionally denotes the reference/normal-function allele; other numbers denote variant alleles with known functional consequence.
Diplotype: The pair of star alleles a person carries for a gene — one from each parent (e.g., CYP2C19 *1/*2). The diplotype is translated into a predicted metabolizer phenotype.
Metabolizer phenotype: The functional interpretation of a person's diplotype (their pair of star alleles for a gene), describing the predicted activity of a drug-metabolizing enzyme. CPIC defines standardized categories: Poor Metabolizer (little or no enzyme activity), Intermediate Metabolizer, Normal Metabolizer, Rapid Metabolizer, and Ultrarapid Metabolizer. This predicted phenotype — not the raw genotype — is what typically drives the prescribing recommendation: a poor metabolizer may accumulate a standard-dose drug toward toxic levels, while an ultrarapid metabolizer may clear it too quickly to work, or activate a prodrug too aggressively. The term Normal Metabolizer replaced the older Extensive Metabolizer. A PGx report translates each gene's diplotype into its phenotype and pairs it with CPIC-informed guidance for the affected medications.

Compliance & validation

CLIA: The Clinical Laboratory Improvement Amendments of 1988 (42 CFR Part 493), administered by CMS, govern all U.S. labs testing human specimens for health assessment or diagnosis. A lab needs the appropriate CLIA certificate before accepting clinical samples.
CAP accreditation: A voluntary College of American Pathologists program built on peer inspection, with requirements meeting or exceeding CLIA. CAP holds CLIA deeming authority, so a CAP-accredited lab is deemed to meet corresponding CLIA requirements. A rigorous quality benchmark.
21 CFR Part 11: The FDA regulation for when electronic records and signatures are considered trustworthy and equivalent to paper — driving system validation, secure audit trails, access controls, and attributable e-signatures. It applies to FDA-regulated activities; routine CLIA testing is governed by CLIA/CAP, though Part 11-style controls are common best practice.
IQ/OQ/PQ: Staged qualification that a system or instrument is fit for use. IQ: installed and configured per spec. OQ: functions correctly across intended ranges. PQ: performs reliably under real-world workflows. Together they form the documented qualification evidence.
Validation vs verification: Validation asks 'did we build the right thing?' (meets intended use — e.g., establishing performance of a lab-developed test). Verification asks 'did we build it right?' (meets specs — e.g., confirming an FDA-cleared assay performs as claimed in your hands). CLIA labs typically verify cleared tests and validate modified/LDT tests.

Billing & revenue cycle (RCM)

RCM (revenue cycle management): The end-to-end financial process of a lab's testing business — eligibility, coding, claim submission, payment posting, denials, and patient billing — managing a claim from order to final payment.
DEX Z-Code: A unique five-character alphanumeric identifier issued through the Palmetto GBA DEX Diagnostics Exchange registry that pins a non-specific molecular CPT code to one laboratory's specific molecular or lab-developed test. Because molecular CPT codes often can't distinguish one proprietary assay from another, the MolDX program — and, as of 2026, a growing number of commercial and Medicare Advantage payers including UnitedHealthcare, Optum, and Humana — require the Z-code to be submitted alongside the CPT code so the payer knows exactly which test was performed, and routinely deny claims that arrive without it. A viable reimbursement pathway generally requires three things to align: the CPT code as registered in DEX, the correct Z-code, and an approved Technical Assessment. Changing any one piece unilaterally — especially the CPT code — tends to trigger denials.
CPT code: The AMA-maintained standard codes identifying the procedure/service billed. Molecular CPT codes are often not specific enough to distinguish proprietary tests — which is precisely why DEX Z-Codes exist as an adjunct.
Prior authorization: A payer requirement that approval be obtained before a test is performed (or covered), based on documented clinical justification. Missing required prior auth is a common — and often non-appealable — cause of denial.
Medical necessity: The payer standard that a test be reasonable and necessary for the diagnosis or treatment of the patient's condition (evidenced by appropriate diagnosis/ICD-10 codes and coverage policy) to be covered.
Clean claim: A claim submitted with all required, accurate information — correct patient, coverage, codes, and documentation — so the payer can adjudicate it without needing more. Clean claims are paid faster and are the core efficiency metric of RCM.
Denial / denial management: A denial is a payer's refusal to pay a claim (missing prior auth, lack of medical necessity, coding errors, non-coverage). Denial management is the systematic process of analyzing, correcting, appealing, and preventing denials to recover revenue.

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