Esoteric assays
The anchor question: which laboratory runs the assay the care map calls for, at a price the patient sees first, on a sample that survives the trip from Colorado? Most care maps turn on one or two tests that sit outside a standard reference-lab menu: quantitative amino acids, an enzyme activity, a repeat sizing, a genome with reanalysis built in. This roster is where those laboratories live.
What the care maps need
| Assay | Serves | What the lab has to get right |
|---|---|---|
| Genome or exome sequencing, with mitochondrial DNA where the map asks for it, and reanalysis on request | Neurogenetic, nonspecific symptoms, connective tissue, comprehensive genetic risk, specific signs | A written reanalysis policy the lab shares with the ordering physician, and a timely answer to a reanalysis request.1 The secondary-findings choice recorded on the requisition, as the comprehensive genetic risk map asks. |
| Multigene panels with deletion and duplication analysis; known-variant testing for relatives | Hereditary cancer risk, connective tissue, transthyretin amyloidosis | Deletion and duplication analysis included, as the hereditary cancer map specifies. TTR sequencing for every confirmed ATTR patient. A published price for single-site testing in relatives, so cascade testing stays affordable. |
| Biochemical genetics: plasma amino acids, acylcarnitines, urine organic acids, lactate | Neurogenetic, inherited metabolic disease, specific signs | Quantitative amino acids by a separation method; the flow-injection tandem mass spectrometry used for newborn screening is not adequate for diagnosis.2 An interpretation signed by a biochemical geneticist, not a bare reference range. |
| Targeted metabolic tests: urine orotic acid, total homocysteine, cholestanol, porphyrin precursors, copper studies, AAT phenotyping | Inherited metabolic disease | The first test in the inherited metabolic map's table for each suspected disorder, then the confirming gene, ideally from the same lab. The treat-to-target levels that map sets (phenylalanine, total homocysteine, cholestanol, copper) need the same assay each time so results trend. |
| Repeat expansion and copy number: FXN GAA sizing, SMN1 dosage with SMN2 copy number | Neurogenetic | Run the way the neurogenetic map orders them: repeat sizing together with FXN sequencing for the compound heterozygotes, and SMN2 copy number reported with SMN1, which the map uses to confirm therapy eligibility. |
| Paraprotein studies: serum and urine immunofixation with free light chains | Transthyretin amyloidosis | Resulted on the same timeline as the bone scintigraphy, because the ATTR map reads the scan only with the paraprotein studies in hand. |
| Specialty immunology: paired serum tryptase | Connective tissue, nonspecific symptoms | Only when the maps' criteria for a mast cell workup are met. A baseline draw and a second draw 1 to 4 hours after a flare; a rise of 20% above baseline plus 2 ng/mL is the threshold the AGA update uses.3 The lab has to accept a sample drawn on the patient's schedule. |
| Enzyme activity on leukocytes or dried blood spot; lysosomal gene panels | Lysosomal storage disorders | The lysosomal map treats a low dried-blood-spot activity as a screen and confirms it molecularly, so the gene panel comes from the same lab on the same workup. Sample type, temperature and shipping day stated before the draw. |
| Alkaline phosphatase, pyridoxal 5'-phosphate, ALPL sequencing; hypophosphatemia gene panels and FGF23 | Hypophosphatasia, specific signs | Alkaline phosphatase read against age- and sex-specific ranges, since the workup starts from a persistently low value. Vitamin B6 measured after pyridoxine supplements have been stopped for a week. No EDTA or citrate tubes, which lower the result.4 |
| Pharmacogenomic panel | Pharmacogenomic profile | Covers the gene-drug pairs that have CPIC guidelines,5 calls CYP2D6 copy number, including the *5 deletion and duplications, as the pharmacogenomic map specifies, and puts the genotype on the report so it can be reread as the guidelines are updated. |
| Expanded carrier screening | Preconception carrier screening | Covers the ACMG tier-3 list and runs the FMR1 and SMN1 assays, as the carrier screening map asks. Partner testing at a published price. |
| Polygenic risk scores | Polygenic risk score | Reports the ancestry the score was developed in and calibrates to it, as the polygenic map asks. |
Vetting criteria
Every entry is checked against these before listing and reviewed yearly.
- CLIA-certified for every test listed, and accredited by CAP or another deemed accreditor; CAP inspection is one of the deemed routes to CLIA certification.6 According to a 2026 review, the FDA rescinded its 2024 rule on laboratory-developed tests in 2025 after a federal court ruling, leaving CLIA as their primary oversight.7
- Sequencing results signed out by a board-certified clinical molecular geneticist or molecular genetic pathologist, with variants classified on the five-tier ACMG-AMP scale.8
- Publishes cash prices, including reanalysis and known-variant testing for relatives, and runs the assay the physician ordered rather than substituting a panel.
- Sample logistics from Colorado in writing: tube, volume, temperature, stability, shipping days, and a kit or courier that gets a frozen sample there intact.
- States a turnaround and meets it. Calls the ordering physician directly with an unexpected or critical result.
- A reanalysis and reclassification policy shared on request, with amended reports sent to the ordering physician and a stated plan for when that physician is no longer involved.1
How the roster is built
- Year one: one laboratory per row, starting with genome sequencing with reanalysis and biochemical genetics, because the neurogenetic and comprehensive genetic risk maps can't start without them. A one-page shipping sheet per assay, written for a Colorado office.
- Year two: a second laboratory per row, plus the rows the newer care maps add. Requisition templates that carry the clinical question, so the interpretation answers it.
- Year three: track quoted against actual turnaround, price changes, and whether amended reports reached the anchor. Prune and add.
Roster
No entries yet. The convener drafted this roster and it's looking for a member to lead it. Members propose laboratories in the cohort channel; the convener and one member check the criteria before listing. Each entry will show the laboratory, the assays it covers from the table above, CLIA and accreditation status, the cash price list, sample and shipping requirements from Colorado, quoted turnaround, and the member who vouched for it.
References
- Deignan JL, Chung WK, Kearney HM, et al. Points to consider in the reevaluation and reanalysis of genomic test results: a statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2019;21(6):1267-1270. doi:10.1038/s41436-019-0478-1
- Sharer JD, De Biase I, Matern D, et al. Laboratory analysis of amino acids, 2018 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2018;20(12):1499-1507. doi:10.1038/s41436-018-0328-6
- Aziz Q, Harris LA, Goodman BP, Simrén M, Shin A. AGA clinical practice update on GI manifestations and autonomic or immune dysfunction in hypermobile Ehlers-Danlos syndrome: expert review. Clin Gastroenterol Hepatol. 2025;23(8):1291-1302. doi:10.1016/j.cgh.2025.02.015
- Khan AA, Brandi ML, Rush ET, et al. Hypophosphatasia diagnosis: current state of the art and proposed diagnostic criteria for children and adults. Osteoporos Int. 2024;35(3):431-438. doi:10.1007/s00198-023-06844-1
- Relling MV, Klein TE. CPIC: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network. Clin Pharmacol Ther. 2011;89(3):464-467. doi:10.1038/clpt.2010.279
- Kaul KL, Sabatini LM, Tsongalis GJ, et al. The case for laboratory developed procedures: quality and positive impact on patient care. Acad Pathol. 2017;4:2374289517708309. doi:10.1177/2374289517708309
- Choi J, Jeon S, Jung J, et al. Comparative analysis of in vitro diagnostic medical devices and laboratory-developed tests: insights from global regulation. Health Policy. 2026;172:105694. doi:10.1016/j.healthpol.2026.105694
- Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-424. doi:10.1038/gim.2015.30
References retrieved from PubMed on 2026-10-30. Rosters are reviewed at each yearly cycle.
Colorado Care Network. Esoteric assays. Version 2026-10-30.