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The firm said it will dispute the claim of overpayment and will separately negotiate with the undisclosed payor for in-network status.
From 2009 to 2012, the laboratory allegedly billed Medicare for testing on hospital inpatients that should have been billed to the hospitals.
Along with the federal settlement, the company will also pay an additional $13.2 million to settle civil claims by different state attorneys general.
The US DOJ alleged that the company conspired to "artificially delay" ordering its MammaPrint test in order to circumvent Medicare's 14-day rule.
The May 8 settlement resolves all claims and counterclaims relating to noninvasive prenatal testing and pre-implantation genetic screening and diagnosis.
The US DOJ had alleged Boston Heart Diagnostics conspired to pay doctors kickbacks that were disguised as investment returns.
The company decided to settle the complaint in order to avoid "lengthy and distracting litigation," but denies any wrongdoing.
The federal government said GenomeDx billed Medicare for its Decipher Biopsy prostate cancer genome classifier on behalf of patients who didn't need the test.
As part of the legal settlement, Akers Bio will pay $930,000 to Pulse Health, and it has agreed to a permanent injunction against selling a disposable breath test.
The judgment settles charges that Calloway Laboratories provided free testing supplies to physicians in exchange for urine test referrals.