Rapid Whole Genome Sequencing PLA Codes: Proband vs Comparator Billing
Short answer: Rapid and ultrarapid whole genome sequencing is billed with lab-specific PLA codes, not a generic molecular code. GeneDx uses 0658U or 0659U for the proband, and 0657U or 0713U for comparator samples reported with it. Phoenix Children's 0699U and Rady's 0094U share one descriptor. Labs must match code, lab name, and effective date.
Why this matters now
The AMA's PLA code list, updated October 1, 2026, shows 17 additions (0699U to 0715U), 5 revisions and 11 deletions accepted by the CPT Editorial Panel, with most new codes released October 1, 2026. Several are rare disease genome codes. For labs that run rapid genome sequencing for NICU and PICU patients, the details of which code pairs with which, and from what date, now drive clean claims.
PLA codes are released quarterly on the AMA CPT website and distributed through quarterly CPT data files, and they appear in the printed codebook at least annually. That cadence means a code can be valid on a payer's schedule weeks after it appears on the AMA list, or the reverse. Build an effective-date check into claim scrubbing rather than relying on a yearly code update.
The proband and comparator structure
For GeneDx products, the AMA list separates the proband test from the comparator test. 0658U (GenomeDx Rapid, Proband) and 0659U (GenomeDx ultraRapid, Proband) were both listed with a July 1, 2026 effective date. The comparator codes are add-ons: 0657U (Rapid, Comparator) carries a revision effective January 1, 2027, and 0713U (ultraRapid, Comparator) is effective January 1, 2027.
The pairing rules are explicit in the list. 0657U is used with 0658U. 0713U is used with 0659U and should not be reported with 81425, 81426, 0657U or 0658U. In practice, a lab that mixes a rapid proband with an ultrarapid comparator, or that reports a CPT genome code alongside a PLA genome code, creates a bundling edit the payer did not need to invent.
Same descriptor, different codes
0699U (Phoenix Children's Rapid Whole Genome Sequencing) and 0094U (Rady Children's Institute for Genomic Medicine rWGS) carry an identical descriptor: genome sequence analysis, rapid, for an unexplained constitutional or heritable disorder or syndrome. Both appear with a January 1, 2027 date in the AMA list. The proprietary name and the performing laboratory are what distinguish them.
That has a billing consequence. PLA codes are tied to a specific proprietary test and laboratory. Confirm which laboratory performs the test and holds the code, and see our guide on unlisted molecular code denials for what happens when a code does not fit.
Variantyx's Genomic Unity 2.0 Duo (0670U, effective October 1, 2026) is a related example. It combines short and long reads for rare disease genome analysis and should not be reported with 81425, 81426, 0212U, 0213U or 0671U.
The clinical evidence payers will be shown
The ACMG evidence-based guideline, published in 2021 in Genetics in Medicine, strongly recommends exome or genome sequencing as a first- or second-tier test for pediatric patients with congenital anomalies, developmental delay or intellectual disability. Medical directors should cite it in appeal letters alongside the lab's own validation data. Our post on exome sequencing coverage gaps covers the policy side of that gap.
For the acute setting, the best-known payer-facing evidence is California's Project Baby Bear. In a final report to the California Department of Health Care Services released by Rady Children's, 178 Medi-Cal infants across five hospital sites were enrolled. Diagnoses were provided for 76 (43%), management changed for 55 (31%), and 513 hospital days were avoided. Reported savings were $2.5 million against a $2 million pilot budget. Average turnaround for rare condition diagnoses was about three days, against four to six weeks with standard genetic testing.
These are pilot figures reported by the sponsoring institution, not a randomized trial, and payers know it. Use them as context for the clinical case, not as a guarantee of coverage.
Medicaid coverage is state by state
As of a June 20, 2023 GeneDx release, eight state Medicaid programs covered rapid whole genome sequencing in the pediatric inpatient setting: Florida, Arizona, California, Louisiana, Maryland, Michigan, Minnesota and Oregon, with bills pending in three more states. That count is more than three years old, so verify each state's current policy before building a billing workflow around it. Coverage criteria in those programs apply to NICU and PICU children who meet clinical criteria, which is why order-form documentation of the clinical indication matters as much as the code.
Practical checklist for labs
First, map each rWGS offering to its exact PLA code and effective date, and block claims for dates of service before it. Second, build proband and comparator pairs as linked line items so a comparator is never billed without its proband. Third, add edits that stop co-reporting with the excluded CPT and PLA codes named in the AMA list. Fourth, capture the clinical indication, the ordering clinician and the care setting on the requisition. Fifth, track payer-specific pricing: a PLA code on the AMA list does not set a Medicare rate, and our October 2026 CLFS quarterly update post explains how new codes are priced. For workflow support, see the ScreenMyGene homepage.
Frequently asked questions
Can a lab bill 0713U on its own?
No. 0713U is a comparator add-on reported with the 0659U proband code. It describes comparator DNA analysis relevant to the proband result, so billing it without a proband claim invites a denial and may be treated as a mismatched submission.
Are 0699U and 0094U the same test?
No. They share a descriptor for rapid genome sequence analysis in unexplained constitutional or heritable disorders, but belong to different laboratories: Phoenix Children's and Rady Children's Institute for Genomic Medicine. Report the code that matches the laboratory performing the test.
When do the new PLA codes take effect?
Dates vary by code. 0658U and 0659U were listed for July 1, 2026, 0670U and 0691U for October 1, 2026, and 0699U, 0713U and 0094U for January 1, 2027. The AMA notes some listing dates are ambiguous, so confirm each against the current AMA list.
Does a PLA code guarantee payment?
No. A PLA code identifies a test for reporting. Coverage and rate are set separately by each payer, and Medicare pricing for new codes follows the CLFS process. Verify payer policy and prior authorization rules for each plan before submitting claims.
What evidence supports genome sequencing in children?
The 2021 ACMG guideline strongly recommends exome or genome sequencing as a first- or second-tier test for congenital anomalies, developmental delay and intellectual disability. Project Baby Bear reported a 43% diagnosis rate and 31% management change among 178 Medi-Cal infants.
Educational disclaimer: This article is for educational purposes only and does not constitute legal, coding, billing, reimbursement, or medical advice. Payer policies and code effective dates change; verify with the AMA, CMS, and each payer before acting.
Sources: AMA CPT PLA Codes list (updated October 1, 2026), ama-assn.org; Inside Precision Medicine, Rady Children's and California's Project Baby Bear; GeneDx press release, June 20, 2023; ACMG evidence-based clinical guideline on exome and genome sequencing, 2021, acmg.net.