Multiplex Nucleic Acid Amplification and Library Preparation

A process for preparing a plurality of multiplex amplified nucleic acid products for targeted next generation-sequencing providing reduced background noise, comprising:

• (a) contacting one or more nucleic acids with at least two pairs of non-5′phosphorylated amplification primers and a DNA polymerase under amplification conditions to form a plurality of amplification products, each amplification primer comprising at least one and no more than four protecting groups in its 3′ region;
• and wherein the protecting groups are phosphorothioate bonds;
• (b) contacting the plurality of amplification products with a 5′ to 3′ exonuclease and either a 3′ to 5′ single strand-specific exonuclease or a proofreading polymerase to form a plurality of digested amplification products;
• wherein the plurality of digested amplification products has a reduced level of non-specific amplification artifacts as compared to a standard nucleic acid amplification reaction performed with primers devoid of protecting groups.