NIPT detects variant of Turner Syndrome not detectable by FISH

Reported first case of X chromosome variant detected by NIPT confirmed by karyotyping, missed by FISH. Savitha (name changed) a 24 year old from Delhi was pregnant with her first child. She was referred for NIPT as her biochemical screening score showed high risk. The Claria NIPT results showed a low risk for trisomy 21, 18 and 13 but high risk of monosomy X (Turner Syndrome) and was advised confirmatory amniocentesis.
The Flourescence in situ hybridization (FISH) report revealed no numerical abnormality detected for any of the five chromosomes tested. On receiving the discordant report, the sample was rerun for NIPT to rule out lab errors. The results of the rerun were consistent with the first report. The karyotype report 3 weeks later showed a rare variant of Turners syndrome
This is possibly the first case of a chromosomal abnormality detected by NIPT, not detected by FISH and confirmed by Karyotyping prenatal diagnosis for chromosome X. Claria NIPT uses the single nucleotide polymorphisms (SNP) method of analysis. The high sensitivity and specificity of the SNP based technique was able to pick up the rare variant of the Turner syndrome.


  • First documented case of an NIPT test picking up a disease variant that was missed by FISH
  • Claria NIPT’s SNP based methodology is highly sensitive and specific with low false positive and negative rate
*Eswarachari V, et al. Noninvasive prenatal testing (NIPT) detects variant of Turner syndrome not detectable by fluorescent in situ hybridization. J Matern Fetal Neonatal Med. 2018 Jun 13:1-4.

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