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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.
The company is developing tests based on the analysis of the spatial patterns of chromosomes by tagging and imaging their telomeres.
The company launched in 2013 as a spinout from Boston Children's Hospital to provide genetic diagnostic tests.
The company said the layoffs are part of a cost-reduction plan that aims to initially cut annual operating expenses by $1.7 million.
The restructuring and job cuts are expected to save the firm more than $70 million annually.
The decisions are part of the company's restructuring efforts after it was unable to extend deferral of its debt payment with its senior lender.
The moves are part of an effort to consolidate and reduce costs related to administrative, finance, and operational support functions.
The embattled company is laying off 155 employees leaving it with 220.
The firm said that it planned to lay off its oncology sales team in order to focus on women's health, despite launching an oncology business unit last spring.
In October, Roche reported the tissue diagnostics business contributed 8 percent to diagnostics sales in the first nine months of 2016.