Through his lawyer, Van Dyke entered a not guilty plea in court.
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The charges were handed down last week by a grand jury following the request of the case's special prosecutor, Kane County Assistant State's Attorney Joseph McMahon, who was appointed in August of last year.
Thursday's indictment still included the six counts of first degree murder as well as one count of official misconduct that were filed against Van Dyke in November 2015.
The 38-year-old cop is accused of shooting 17-year-old Laquan McDonald 16 times in October of 2014. But he wasn't charged until a year later, when dashcam video of the incident was released and sparked protest across the city and the country.
Attorneys for Van Dyke filed a three-page motion in January seeking to dismiss the indictment, accusing investigators of taking statements their client made and improperly using them against him.
Last month, Van Dyke's defense attorneys filed a second motion to dismiss the murder charges, alleging the Cook County State's Attorney's Office misled a grand jury convened to hear about the 2014 shooting.
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Richard Kling, a law professor at the Chicago Kent College of Law - who is not involved in the case - says that, along with several other factors could be the reason for Thursday's new indictment.
"I can't guess why the prosecutor from Kane County decided to introduce it. There could be strategic reasons, there could be legal reasons, There could be political reasons," said Kling.
Defense attorneys for Van Dyke said they plan on filing motions to get the new indictment dismissed.
Van Dyke is due back in court on April 20.
A spokesperson for Mayor Rahm Emanuel released this statement Thursday:
"We're not going to comment on pending court matters, but we respect the seriousness with which the special prosecutor is handling the matter."
WLS-TV contributed to this report.
Sun-Times Media Wire contributed to this report.