Quality control test for sequence-phenotype assignments

• Published in: PloS one Vol. 10; no. 2; p. e0118288
• Main Authors: Ortiz, Maria Teresa Lara, Rosario, Pablo Benjamín Leon, Luna-Nevarez, Pablo, Gamez, Alba Savin, Martínez-del Campo, Ana, Del Rio, Gabriel
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20.02.2015; Public Library of Science (PLoS)
• Subjects: Biochemistry; Biology; Deoxyribonucleic acid; Dihydrofolate reductase; DNA; DNA - analysis; DNA sequencing; E coli; Escherichia coli; Experiments; Gene mutation; Genes; Genotype & phenotype; High-Throughput Nucleotide Sequencing - standards; Internet; Methods; Mutagenesis; Mutation; Nucleotide sequence; Phenotype; Phenotypes; Point mutation; Proteins; Proteins - chemistry; Proteins - genetics; Proteins - metabolism; Quality Control; Research methodology; Sequence Analysis, DNA - methods; Sequence Analysis, DNA - standards; Statistical analysis; Structure-function relationships; User-Computer Interface
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0118288

Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10-20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas.