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Clinical experience with a single-nucleotide polymorphism-based non-invasive prenatal test for five clinically

K Martin1, S Iyengar1, A Kalyan1

  • 1Natera, Inc., San Carlos, California.

Clinical Genetics
|July 12, 2017
PubMed
Summary

Single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT) shows improved accuracy for detecting microdeletion syndromes like 22q11.2 deletion syndrome. High-depth resequencing significantly enhances the positive predictive value and reduces false positives in prenatal screening.

Keywords:
aneuploidymicrodeletionnon-invasive prenatal testingsingle-nucleotide polymorphismsubmicroscopic chromosome abnormality

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Area of Science:

  • Genetics
  • Prenatal Diagnostics
  • Molecular Biology

Background:

  • Single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT) is a valuable tool for detecting submicroscopic chromosomal abnormalities.
  • Microdeletion syndromes, such as 22q11.2 deletion syndrome and others affecting chromosomes 1p36, cri-du-chat, Prader-Willi, and Angelman, are associated with severe clinical manifestations.

Purpose of the Study:

  • To evaluate the performance of SNP-based NIPT for specific microdeletion syndromes.
  • To compare the effectiveness of an original screening protocol with a revised protocol involving high-depth resequencing for high-risk calls.
  • To estimate the prevalence of these microdeletion syndromes within a referral population.

Main Methods:

  • Retrospective analysis of 80,449 referrals for 22q11.2 deletion syndrome and 42,326 referrals for 1p36, cri-du-chat, Prader-Willi, and Angelman microdeletion syndromes.
  • Comparison of an original SNP-based NIPT protocol with a revised protocol utilizing reflexive high-depth sequencing for elevated-risk results.
  • Estimation of minimal prevalences for the studied microdeletion syndromes.

Main Results:

  • The revised protocol significantly increased the positive predictive value (PPV) for 22q11.2 deletion syndrome from 15.7% to 44.2% and for other microdeletions from 5.2% to 31.7%.
  • The false-positive rate (FPR) for 22q11.2 deletion syndrome decreased from 0.33% to 0.07%, and for other microdeletions from 0.56% to 0.07% with the revised protocol.
  • Minimal prevalences were estimated at 1 in 1255 for 22q11.2 deletion syndrome and 1 in 1464 for the combined group of other microdeletions.

Conclusions:

  • Microdeletion syndromes are relatively common in the analyzed referral population.
  • SNP-based NIPT performance, particularly its positive predictive value and false-positive rate, is substantially improved by implementing high-depth resequencing for high-risk cases.
  • The findings support the utility of enhanced SNP-based NIPT protocols for accurate prenatal detection of microdeletion syndromes.