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#!/usr/bin/env perl

...

    return \%data;
}

{
  Gene01 => { ColA => 5, ColB => 15 },
...
  Gene01 => [{ ColA => 5, ColB => 15 }, { ColA => 12, ColC => 3 }],
  Gene03 => [{ ColA => 25, ColB => 5 }, { ColA => 5, ColC => 20 }],
}