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MAPP and MAPP-MMR m ultivariate a nalysis of p rotein p olymorphisms - m is m atch r epair Helen Stuart, Cardiff. What is MAPP/MAPP-MMR?. In silico evaluation resources that help in determining pathogenicity of missense variants detected in sequencing.
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MAPP and MAPP-MMRmultivariate analysis of protein polymorphisms -mismatch repairHelen Stuart, Cardiff
What is MAPP/MAPP-MMR? • In silico evaluation resources that help in determining pathogenicity of missense variants detected in sequencing. • The MAPP-MMR site is specifically for the investigation of the MLH1 and MSH2 genes.
What does MAPP do? • MAPP considers the physicochemical variation present in a column of a protein sequence alignment and, on the basis of this variation, predicts the impact of all possible amino acid substitutions on the function of the protein.
How does MAPP work? MAPP is based on the comparison of the multiple sequence alignments of orthologs or closely related paralogs. Ortholog = genes in different species that evolved from a common ancestral gene; same function Paralog = genes related by duplication within a genome; evolve different functions.
Basic MAPP summary: Find orthologs or closely related paralogs of your protein of interest • Align multiple orthologs e.g. using ClustalW or ProbCons • Comparison of these sequences to determine which amino acid/s occur at each position. • This results in establishing which aa positions are restricted in terms of the aa that can be tolerated in this position. = determining physicochemical variation • Comparison of each aa in the seq of interest to this alignment • Each aa is given an impact score based on thedeviation of each aa from the variation. • 6 physicochemical properties are used to evaluate missense variants: (1) hydropathy (2) polarity (3) charge (4) side-chain volume (5) free energy in α-helical conformation and (6) free energy in β-sheet conformation. • A high impact score identifies a potentially deleterious variant by virtue of its physicochemical dissimilarity to the observed evolutionary variation, whereas low-scoring variants are less likely to compromise protein structure or function.
MAPP homepagehttp://mendel.stanford.edu/SidowLab/downloads/MAPP/index.html
MAPP output I MAPP produces an output table in which each row corresponds to a position (column) in the alignment. • Column score = median MAPP score for this alignment column Remember: the MAPP score estimates the impact of aa substitutions on protein function so a high MAPP score = variant is likely to compromise protein function • Column p-value = P-value interpretation of the column’s median MAPP score • Alignment = amino acids observed in that column • Hydropathy…free beta energy = P-values corresponding to the significance of each property A low p-value means that the column exhibits strong constraint for this property
Output: MLH1 p.Gly232ArgIf MAPP-MMR score >4.55 then the AA substitution is predicted to affect protein function.
Features/Limitations of MAPP • MAPP requires evolutionary variation. You cannot run MAPP without a reasonably large number of homologs, preferably orthologs. • Comparative analyses such as MAPP assume that function is conserved within the aligned set of homologs under study. • Does not take into account potential effects of other genetic factors or environment on disease. • MAPP focuses on single sites and single variants (not on averages of neighbouring sites). • MAPP allows you to select all 6 physicochemical properties or only a subset of these….but “dropping properties to go fishing for better results is statistically inappropriate”!
