Automatic Design Of Quantitative PCR Primers For Chromosome Aneuploidy Diagnosis

Chromosome aneuploidy is a kind of chromosome aberration resulting from single or several chromosome number change rather than whole chromosome duplication.Every year,the severe birth defect caused by chromosome aneuploidy bring tremendous pains and burdens to the newborns,the parents and the society.Prenatal testing is an active solution for detecting chromosome aneuploidy in advance.However,Traditional prenatal diagnosis like karyotyping is time consuming,work-intensive and sometimes affected by sample contamination.The recent emerged molecular diagnosis technology,like High Resolution Melting Curve Analysis(HRMCA),provide labor-free,cheap and fast testing ways by identifying chromosome unbalanced translocation,and thus can be an alternative solution to assist traditional methods.The primers used in HRMCA are usually designed in basis of the Segmental Duplications(SD).The primer design has several constrains like exclusive amplification of both the target sequence and reference sequence,nearly same lengths of ampl icons,proper thermodynamic attributes,and so on.So far as our surveillance,there is no software available in public that fulfills all these requirements for automatic primer design.Therefore,we developed a novel tool,the Chromosome Aneuploidy Primer Designer(ChAPDes),for aiding HRMCA primer design.The ChAPDes followed the design principle of software Primer-BLAST for primer search.It integrated the short sequence alignment tool Bowtie2,several empirical rules and BLAST for primer search,and then Primer3 for thermodynamic attributes checking.The software allows high-throughput search of primers in the target sequence by setting amplicon length range,primer length range and different aspects of primer attributes.In summary,the ChAPDes largely reduces the primer design time for chromosome aneuploidy molecular diagnosis.It makes primer design easier and more rational,enhances the primer stability of HRMCA.We believe that our work will prompt the development of molecular prenatal diagnosis methods in long term countermining chromosome aneuploidy.