Uncertainity of fetal fraction determination in non-invasive prenatal screening by highly polymorphic SNPs

Grendár M
Loderer D
Laucekova Z
Svecova I
Hrtankova M
Hornakova A
Nagy B
Lasabova Z
Danko J
Nagy Bálint (1956-) (molekuláris genetikus)

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Publication date

May 2019

DOI

10.1016/j.jbiotec.2019.04.020

Publisher

Elsevier BV

Abstract

Fetal fractionandthechromosomerepresentationare the two keyquantities usedinNon-Invasive PrenatalScreening(NIPS)todeterminetheaneuploidystatusofafetus.Severalmethodsforfetalfractiondeterminationhavebeenproposedintheliterature,includingaclassofthemethods,denotedsnpFF,basedonhigh-coveragetargeted sequencing of highly polymorphic Single Nucleotide Polymorphisms (SNPs). The variant of snpFF,investigatedhere,hassimilarpropertiesastheothervariantsofsnpFF.WepointoutthatthevariabilityoftheindividualinformativeSNPs-basedestimatesoffetalfractionincreaseswiththeincreaseoffetalfraction.At4%fetalfractiontheInter-QuartileRange(IQR)oftheindividualestimatesoffetalfractionisaround3%anditincreasesto6%at15%fetalfraction.snpFFcannotdetectfetalfractionbelow2.5%...