Genetic Sex Validation for Sample Tracking in Clinical Testing

Background Next generation DNA sequencing (NGS) has been rapidly adopted by clinical testing laboratories for detection of germline and somatic genetic variants. The complexity of sample processing in a clinical DNA sequencing laboratory creates multiple opportunities for sample identification errors, demanding stringent quality control procedures. Methods We utilized DNA genotyping via a 96-SNP PCR panel applied at sample acquisition in comparison to the final sequence, for tracking of sample identity throughout the sequencing pipeline. The 96-SNP PCR panel’s inclusion of sex SNPs also provides a mechanism for a genotype-based comparison to recorded sex at sample collection for identification. This approach was implemented in the clinical genomic testing pathways, in the multi-center Electronic Medical Records and Genomics (eMERGE) Phase III program Results We identified 110 inconsistencies from 25,015 (0.44%) clinical samples, when comparing the 96-SNP PCR panel data to the test requisition-provided sex. The 96-SNP PCR panel genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density hybridization-based genotyping arrays. Results identified clerical errors, samples from transgender participants and stem cell or bone marrow transplant patients and undetermined sample mix-ups. Conclusion The 96-SNP PCR panel provides a cost-effective, robust tool for tracking samples within DNA sequencing laboratories, while the ability to predict sex from genotyping data provides an additional quality control measure for all procedures, beginning with sample collections. While not sufficient to detect all sample mix-ups, the inclusion of genetic versus reported sex matching can give estimates of the rate of errors in sample collection systems. ### Competing Interest Statement The authors have declared no competing interest. * HGSC : Human Genome Sequencing Center LMM : Laboratory for Molecular Medicine NGS : Next generation DNA sequencing STR : short tandem repeat SNP : single nucleotide polymorphism PCR : polymerase chain reaction eMERGE : Electronic Medical Records and Genomics EMR : electronic medical record HGSC-CL : Human Genome Sequencing Center Clinical Laboratory BCM : Baylor College of Medicine CRSP : Clinical Research Sequencing Platform STA : specific target amplification LSP : locus specific primer IFC : Integrated Fluidic Circuit ASP : Allele Specific Primers ACMG : American College of Medical Genetics NHGRI : National Human Genome Research Institute IRB : institutional review board