Lies in Bone by Natalie Symons

On Halloween 1963, 11-year-old Chuck Coolidge and his brother, Danny, are lost in a toxic smog covering the steel town of Slippery Elm, Pennsylvania. When the smog lifts, half the town is sick, and 20 people are dead. And Danny is missing. Now, more than 20 years later, Chuck's teenage daughter, Frank, Descriptions her escape from this "busted and disgusted" town.
When a murdered child is found in the river, investigators link the crime to the disappearance of Danny in '63, and Frank's life is turned upside down. In the face of her worst fears, she must uncover her family's dark past if she wants to keep her sister, Boots, from the hands of the state.
As she discovers the unimaginable truth about Danny's disappearance, Lies in Bone culminates in a shocking 11th-hour reveal and an emotionally charged finale.