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The money raised has been split between Royal Manchester Children's Hospital and the Cystic Fibrosis Trust.
BBC: Joe Geeling
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The Cystic Fibrosis Trust said not funding the drug in Scotland would cause "dismay and heartache".
BBC: Call for cystic fibrosis drug to be available in Scotland
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The Cystic Fibrosis Trust had warned patients in Wales could have been faced with a second class health service.
BBC: Cystic fibrosis x-ray
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The Cystic Fibrosis Trust has submitted evidence to a health committee inquiry.
BBC: NEWS | UK | Scotland | Sufferer's free prescription call
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But the Cystic Fibrosis Trust said the medicine was "transformational", had a "dramatic effect" and that experts say "no other medicine addresses the basic genetic defect in cystic fibrosis".
BBC: Cystic fibrosis: New drug Kalydeco refused for Welsh NHS
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Ed Owen, chief executive of the Cystic Fibrosis Trust, welcomed the Scottish government's decision to make "additional funding available to enable Kalydeco to be made available to those that need it".
BBC: Scottish 'orphan drugs' fund launched
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Kalydeco treats people who have the G551D cystic fibrosis mutation, which affects about 11% of people with cystic fibrosis in Scotland, compared with about 4% in the UK, according to the Cystic Fibrosis Trust.
BBC: Scottish 'orphan drugs' fund launched
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Ivacaftor treats people who have the G551D cystic fibrosis mutation, which affects about 11% of people with cystic fibrosis in Scotland, compared with about 4% in the UK, according to the Cystic Fibrosis Trust.
BBC: Kalydeco tablets
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The Joe Geeling Trust opened in 2007, a year after Joe, who had cystic fibrosis, was killed by a fellow pupil.
BBC: Joe Geeling
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The trust said funding of Kalydeco should not impact on the wider funding of cystic fibrosis care.
BBC: Cystic Fibrosis Trust in Kalydeco drug plea for Wales