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The Company has recognized the Excess Amounts as a reduction to operating expenses in the current year as the Company's repayment of the Excess Amounts to Janssen is contingent and would become payable only after the third profitable calendar quarter for the product under the collaboration. Further, the Excess Amounts shall be reimbursable only from the Company's share of future full calendar quarter pre-tax profits (if any) after the third profitable calendar quarter for the product under the collaboration.
For the calendar year ended December 31, 2012, the Company's total share of collaboration expenses under the Agreement was $68.1 million. As of December 31, 2012, total Excess Amounts totaled $18.1 million, of which during the quarter ended December 31, 2012, $17.3 million was recorded as a reduction to research and development expense and $0.8 million was recorded as a reduction to general and administrative expense.
GAAP operating expenses were $40.6 million for the six months ended December 31, 2012, compared to $30.6 million for the six months ended December 31, 2011. Included in operating expenses for the six months ended December 31, 2012 is the $18.1 million reduction to operating expenses for Excess Amounts.
GAAP operating expenses were $16.7 million for the quarter ended December 31, 2012, compared to $16.0 million for the quarter ended December 31, 2011 and $23.9 million for the quarter ended September 30, 2012. Included in operating expenses for the quarter ended December 31, 2012 is the $18.1 million reduction to operating expenses for the Excess Amounts.
At December 31, 2012, the Company had cash, cash equivalents and marketable securities of $317.1 million, compared with $203.6 million at June 30, 2012. In addition, as of December 31, 2012, the Company had $26.6 million receivable from Jansse
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