Genome-Wide Noninvasive Prenatal Diagnosis of SNPs and Indels

Tom Rabinowitz, Noam Shomron*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Noninvasive prenatal diagnosis (NIPD) is an emerging field, that enables testing for diseases in the fetus with no risk to the pregnancy, compared to invasive methods (e.g., amniocentesis). The procedure is based on the presence of fetal DNA within the mother’s plasma cell-free DNA (cfDNA). Today, NIPD is performed for chromosomal abnormalities (e.g., Down syndrome) and some large deletions/duplications. It is also available for point mutations but is limited for one mutation or up to several genes simultaneously. Genome-wide detection of fetal point mutations was presented in a few studies, and the first software tool for this task, Hoobari, has recently become available. Here we describe the necessary steps in genome-wide noninvasive fetal genotyping, including examples using the Hoobari software. We discuss the various materials, software, computational infrastructure, and samples required for this analysis. Genome-wide analysis of point mutations in the fetus is not widely studied, albeit much space for algorithmic improvements exists. Here we suggest practical solutions for challenges along the process. Our work assists bioinformaticians in accessing NIPD data analysis and can eventually be utilized for other cfDNA-related fields.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages22
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Cell-free DNA
  • Cell-free fetal DNA
  • Circulating tumor DNA
  • Fetal
  • Hoobari
  • Liquid biopsy
  • NIPD
  • Noninvasive prenatal diagnosis
  • cfDNA
  • cffDNA
  • ctDNA


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