Patent ID: 8313905

Claim:
A method of assessing biochip quality, the method comprising: providing a biochip comprising at least first full length polynucleotide probes and second truncated polynucleotide probes, each having first ends that are coupled to an immobilization layer, the first full length polynucleotide probes having a different number of nucleotide monomers than the second truncated polynucleotide probes; hybridizing Quality Control (QC) probes to the first full length polynucleotide probes and second truncated polynucleotide probes, each QC probe comprising: a template portion having a nucleotide sequence complementary to a nucleotide sequence of the first full length polynucleotide probes and second truncated polynucleotide probes; and a hairpin connected to a first end of the template portion; exposing the biochip to conditions suitable for ligation of polynucleotides; washing the biochip to de-hybridize the QC probes from the first full length polynucleotide probes and second truncated polynucleotide probes, thereby removing un-ligated QC probes; detecting a ratio of the amount of the first full length polynucleotide probes that are ligated to the QC probes to the amount of the second truncated polynucleotide probes that are ligated to the QC probes to assess biochip quality, wherein the quality of the biochip is a measure of the relative amounts of first full length polynucleotide probes and second truncated polynucleotide probes.