Compositions and methods for making controls for sequence-based genetic testing

A method of using a control in a nucleic acid detection test, the method comprising:

• providing a plurality of double-stranded template nucleic acids originating from a sample obtained from a subject, wherein the double-stranded template nucleic acids comprise a population of sizes and sequences similar to or identical to the sizes and sequences obtained from the subject;
• ligating a universal adapter to both ends and both strands of the template nucleic acids to form a plurality of adapter-template-adapter molecules comprising template nucleic acids flanked by the universal adapter, wherein the universal adapter comprises a region of double stranded nucleic acid and a restriction endonuclease recognition site;
• and
• amplifying the plurality of adapter-template-adapter molecules with a first universal primer and a second universal primer to result in amplified adapter-template-adapter molecules;
• removing at least a portion of the universal adapter from both ends of the amplified adapter-template-adapter molecules to result in removed universal adapters and a plurality of regenerated template nucleic acids (reDNAs), wherein the reDNAs comprise a population of template molecules of sizes and sequences similar to or identical to the sizes and sequences obtained from the subject;
• performing a nucleic acid detection test on a test sample and on the reDNAs;
• and
• analyzing results from the nucleic acid detection test using the reDNAs as a synthetic control.

A method of using a control in a nucleic acid detection test, the method comprising:

• providing a plurality of double-stranded template nucleic acids originating from a sample obtained from a subject, wherein the subject is a pregnant human, wherein the double-stranded template nucleic acids comprise a mixture of fetal and maternal nucleic acids, and wherein the double-stranded template nucleic acids comprise a population of sizes and sequences similar to or identical to the sizes and sequences obtained from the subject;
• ligating a universal adaptor to both ends of the template nucleic acids to form a plurality of adaptor-template-adaptor molecules comprising a template nucleic acid flanked by the universal adaptor, wherein the universal adaptor comprises a region of double stranded nucleic acid and a restriction endonuclease recognition site;
• and
• amplifying, such as by an exponential amplification reaction, the plurality of adaptor-template-adaptor molecules with a first universal primer and a second universal primer to result in amplified adaptor-template-adaptor molecules;
• removing at least a portion of the universal adaptor from both ends of the amplified adaptor-template-adaptor molecules to result in removed universal adaptors and a plurality of regenerated template nucleic acids (reDNAs), wherein the reDNAs comprise a population of template molecules of sizes and sequences similar to or identical to the sizes and sequences obtained from the subject;
• performing a nucleic acid detection test on a test sample and on the reDNAs;
• and
• analyzing results from the nucleic acid detection test using the reDNAs as a synthetic control.