False Alarms in Consumer Genomics Add to Public Fear and Potential Health Care Burden

We have entered an era of direct-to-consumer (DTC) genomics. Patients have relayed many success stories of DTC genomics about finding causal mutations of genetic diseases before showing any symptoms and taking precautions. However, consumers may also take unnecessary medical actions based on false alarms of “pathogenic alleles”. The severity of this problem is not well known. Using publicly available data, we compared DTC microarray genotyping data with deep-sequencing data of 5 individuals and manually checked each inconsistently reported single nucleotide variants (SNVs). We estimated that, on average, a person would have ~5 “pathogenic” alleles reported due to wrongly reported genotypes if using a 23andMe genotyping microarray. We also found that the number of wrongly classified “pathogenic” alleles per person is at least as significant as those due to wrongly reported genotypes. We show that the scale of the false alarm problem could be large enough that the medical costs will become a burden to public health.

Utility of a high-resolution mouse single nucleotide polymorphism microarray assessed for rodent comparative genomics

In the study of genetic diversity in non-model species there is a notable lack of the low-cost, high resolution tools that are readily available for model organisms. Genotyping microarray technology for model organisms is well-developed, affordable, and potentially adaptable for cross-species hybridization. The Mouse Diversity Genotyping Array (MDGA), a single nucleotide polymorphism (SNP) genotyping tool designed for Mus musculus, was tested as a tool to survey genomic diversity of wild species for inter-order, inter-genus, and intra-genus comparisons. Application of the MDGA cross-species provides genetic distance information that reflects known taxonomic relationships reported previously between non-model species, but there is an underestimation of genetic diversity for non-Mus samples, indicated by a plateau in loci genotyped beginning 10-15 millions of years divergence from the house mouse. The number and types of samples included in datasets genotyped together must be considered in cross-species hybridization studies. The number of loci with heterozygous genotypes mapped to published genome sequences indicates potential for cross-species MDGA utility. A case study of seven deer mice yielded 159,797 loci (32% of loci queried by the MDGA) that were genotyped in these rodents. For one species, Peromyscus maniculatus, 6,075 potential polymorphic loci were identified. Cross-species utility of the MDGA provides needed genetic information for non-model species that are lacking genomic resources. Genotyping arrays are widely available, developed tools that are capable of capturing large amounts of genetic information in a single application, and represent a unique opportunity to identify genomic variation in closely related species that currently have a paucity of genomic information available. A candidate list of MDGA loci that can be utilized in cross-species hybridization studies was identified and may prove to be informative for rodent species that are known as environmental sentinels. Future studies may evaluate the utility of candidate SNP loci in populations of non-model rodents.Author SummaryThere is a need for a tool that can assay DNA sequence differences in species for which there is little or no DNA information available. One method of analyzing differences in DNA sequences in species with well-understood genomes is through a genotyping microarray, which has demonstrated utility cross-species. The Mouse Diversity Genotyping Array (MDGA) is a tool designed to examine known differences across the genome of the house mouse, Mus musculus. Given that related organisms share genetic similarity, the MDGA was tested for utility in identifying genome variation in other wild mice and rodents. Variation identified from distantly related species that were not of the same genus as the house mouse was an underestimate of the true amount of variation present in the genomes of wild species. Utility of the MDGA for wild species is best suited to mice from the same genus as the house mouse, and candidate variation identified can be tested in rodent populations in future studies. Identifying changes in genetic variation within populations of wild rodents can help researchers understand the links between specific genome changes and the ability to adapt to pressures in the environment, as well as better understand the evolution of rodents.

A universal genotyping–microarray constructed by ligating a universal fluorescence-probe with SNP-encoded flaps cleaved from multiplex invasive reactions

The universal chip and fluorescence probe enable genotyping multiple SNPs more labor-saving and cost-saving.