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In most organisms, sex is determined by the ratio of X and Y chromosomes. However, in some organisms, such as Drosophila and C.elegans, sex is determined by the ratio of the number of X chromosomes to the number of sets of autosomes. The Y chromosome in Drosophila is active but does not determine sex. It contains genes responsible for the production of sperms in adult flies.  
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Genetic Sex Validation for Sample Tracking in Clinical Testing.

Jianhong Hu1, Viktoriya Korchina1, Hana Zouk2

  • 1Baylor College of Medicine, Human Genome Sequencing Center (HGSC).

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|October 4, 2023
PubMed
Summary
This summary is machine-generated.

A 96-SNP panel accurately tracked sample identity in a clinical network, identifying 0.44% of samples with sex discrepancies due to collection or accessioning errors, not lab swaps.

Keywords:
Clinical testingNext Generation Sequencing (NGS)SNP genotypingSex concordance

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Area of Science:

  • Genetics
  • Clinical Diagnostics
  • Bioinformatics

Background:

  • Clinical sequencing networks require robust quality control to ensure sample identity and data integrity.
  • DNA genotyping panels offer a method for verifying sample origin and detecting potential mix-ups.

Approach:

  • A 96-single nucleotide polymorphism (SNP) panel was used for quality control in a study of 25,015 clinical samples.
  • The panel's utility for tracking sample identity and predicting participant sex-by-genotype was evaluated.
  • Genetic sex predictions were cross-validated using sequencing data and high-density genotyping arrays.

Key Points:

  • SNP tracking confirmed no sample swap errors within clinical testing laboratories.
  • 110 inconsistencies (0.44%) were found between predicted sex-by-genotype and reported sex, originating from sample collection or accessioning.
  • Discrepancies were attributed to clerical errors, samples from transgender individuals, transplant patients, or unresolvable mix-ups.

Conclusions:

  • A 96-SNP genotyping panel is effective for sample identity tracking and detecting sex discrepancies in clinical sequencing.
  • The study highlights the importance of rigorous pre-analytical sample handling to minimize errors.
  • Genetic sex prediction serves as a valuable quality control measure in clinical genetics.