Is reliance on an inaccurate genome sequence sabotaging your experiments?

Advances in genomics have made whole genome studies increasingly feasible across the life sciences.However, new technologies and algorithmic advances do not guarantee flawless genomic sequences or annotation.Bias, errors, and artifacts can enter at any stage of the process from library preparation to annotation.When planning an experiment that utilizes a genome sequence as the basis for the design, there are a few basic checks that, if performed, may better inform the experimental design and ideally help avoid a failed experiment or inconclusive result. All genome sequences have "issues"There are many factors that can affect the ultimate genome sequence and annotation that are produced, and both should be considered "works in progress."An awareness of these factors can inform experimental decisions that may depend upon the accuracy of a particular genome sequence, region, gene, or genes.This Pearl focuses on eukaryotic sequences, as they are still subject to greater challenges, but many factors are universal.The target audience for this Pearl is the wet-bench researcher who can use web-based genome resources, commercial genomics software, or has access to a member of the community with a small amount of genomics or bioinformatics experience.No coding is required to address the questions and solutions that are proposed. What is the origin of the sample used to generate the genome sequence?The origin matters.Did the sample originate from a clone, a mixed population (common with microbes), or possibly a hybrid?Differences between individuals can be single nucleotide polymorphisms (SNPs), but often they involve insertions or deletions (indels) of various sizes, copy number variations (CNV), and even small rearrangements.Hybrids can have dramatic differences between orthologous chromosomes [1].Genome sequences derived from a heterogenous population, especially when CNVs exist, complicate genome assembly, and often the sequence produced is a composite of the major alleles present in the sequenced sample.Genome sequences derived from clonal laboratory strains are often easier to assemble, but they may not be truly representative of circulating wildtype strains because they are adapted to culture and, if propagated for a long time, may have lost genes or accumulated mutations [2].