Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: A base-calling algorithm for Tm-shifted melting curve SNP assay. | Liang et al. Journal of Clinical Bioinformatics 2011 1 3 http content 1 1 3 JOURNAL OF CLINICAL BIOINFORMATICS RESEARCH Open Access A base-calling algorithm for Tm-shifted melting curve SNP assay Kung-Hao Liang1 Jun-Jeng Fen1 2 Hsien-Hsun Chang1 3 Hsei-Wei Wang2 4 and Yuchi Hwang1 Abstract Background Tm-shifted melting curve SNP assays are a class of homogeneous low-cost genotyping assays. Alleles manifest themselves as signal peaks in the neighbourhood of theoretical allele-specific melting temperatures. Base calling for these assays has mostly relied on unsupervised algorithm or human visual inspection to date. However a practical clinical test needs to handle one or few individual samples at a time. This could pose a challenge for unsupervised algorithms which usually require a large number of samples to define alleles-representing signal clusters on the fly. Methods We presented a supervised base-calling algorithm and software for Tm-shifted melting curve SNP assays. The algorithm comprises a peak detection procedure and an ordinal regression model. The peak detection procedure is required for building models as well as handling new samples. Ordinal regression is proposed because signal intensities of alleles AA AB and BB usually follow an ordinal pattern with the heterozygous allele lie between two distinct homozygous alleles. Coefficients of the ordinal regression model are first trained and then used for base calling. Results A dataset of 12 SNPs of 44 unrelated persons was used for a demonstration purpose. The call rate is . Among the base calls are identical to those made by the sequencing method. A small fraction of the melting curve signals is declared as no call for further human inspection. A software was implemented using the Java language providing a graphical user interface for the visualization and handling of multiple melting curve signals. Conclusions Tm-shifted melting curve SNP assays together with the
