NGS sex validation

The Sex validation column indicates whether the biological sex inferred from genomic data matches the sex information provided during case creation.

This helps identify potential sample mix-ups or metadata errors before interpretation begins.

Sex validation results:

• Pass

  Reported sex matches the estimated sex
• Fail A mismatch was detected between reported and estimated sex.
• N/A QC file not available; validation could not be performed.

Sex validation is performed by comparing the observed homozygous/heterozygous genotype ratio on the X chromosome with the expected ratios:

• <2 for females
• >2 for males

Prerequisites:

• Only high-quality SNVs from targeted regions—either kit-specific or RefSeq coding regions—are used for sex validation
• A minimum of 50 variants is required to generate a reliable result. If this threshold is not met, sex validation cannot be performed, and no result is displayed

If the sex was marked as unknown during case creation, the system will display the predicted sex instead of a validation status.

CNV calling on sex chromosomes

Emedgene uses the sex provided in the sample metadata to determine the expected copy number for sex chromosomes CNVs.

• If the sample’s sex is marked as unknown, Emedgene defaults to Female for CNV calling.
• If the predicted sex does not match the reported sex, we recommend updating it and re-analyzing the case.