Amgen Inc. has laid off 98 workers in Fremont as part of the close of its more than $2 billion acquisition of Abgenix Inc. this week. The Thousand Oaks biotech giant, which has a rapidly growing Bay Area presence, retained "substantially all of the manufacturing employees in Fremont," according to Amgen spokeswoman Mary Klem. Abgenix employed about 440 workers companywide, and 98 workers were given layoff notices, according to the Alameda County Workforce Investment Board. Klem said the company retained all the employees at its other site in Burnaby, British Columbia.