"How does the official (of patent office) substantiate his order? What is the evidence based on which he passed the order," Justice Sanjeev Sachdeva asked.
It also issued notice to the Centre and sought its reply by May 2.
The university, which claims to have invented the drug Xtandi, used in treatment for prostrate cancer, has claimed that it has been granted patent for its innovation in over 50 jurisdictions across the world since 2007.
Japan's Astellas Pharma, which has the rights for marketing the drug outside the US, sells the medicine in India at a price of Rs 3.35 lakh for a pack of 112 capsules for a month's dose.
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The university, represented by senior advocate P Chidambaram, has contended that its application filed in 2007 for a patent was rejected in November last year merely on the ground of opposition by some competitors.
It has sought that its patent application be remanded back to the authority for consideration of the evidence submitted by it in support of its claim.
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