my %myArray; #my @myArray;
my $GeneID = shift @columns; $myArray{$GeneID} = \@columns; #push @myArray, \@columns;

# and how to calculate sum of each row
for my $GeneID (sort keys %myArray){ # optionally sort to have a consistent view
  my $sum = 0;
  for my $colItem (@{$myArray{$GeneID}}){
    $sum += $colItem;
  }
  print "sum for $GeneID: $sum\n";
}