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SELECTBIO Conferences Emerging Role of Next Generation Sequencing in Clinical Genomics


Non-Invasive Prenatal Testing (NIPT)

Jenneke Weiss, Head NGS facility and NIPT unit , VUMC

This presentation will be separated in three parts.

I) General introduction

This part of the presentation will provide you with background information on the biology underlying NIPT. It will explain what cell-free DNA is, the source of cfDNA will be discussed, and the consequence for the sensitivity and specificity of cfDNA testing. The basics of the different available technologies will be discussed briefly. Finally, a short introduction will be given on the most commonly used bioinformatics tools, based on z-score analysis.

II) Tools, pitfalls and tricks: causes of false positive and false negative results

Although NIPT analysis for the detection of Trisomy 21, 13 and 18 is rather straightforward, there are several biological factors that might cause false positive and false negative effects. Although most of them are rare, testing of large numbers of pregnant women will assure the fact that all of these causes might be encountered. The most important causes are:

-False negative results

-Low foetal fraction

-True foetal mosaics

-Twin pregnancies

-False positive results

-Confined Placental Mosaicism (CPM)

-Maternal CNVs

-Maternal malignancies

-Maternal mosaics

-Vanishing twin

Most of these causes will be discussed based on examples from daily practice. Furthermore, we will discuss how to discern between true negative/positive and false negative/positive results based on several different bioinformatics tools that were developed at VUmc Amsterdam, such as WISECONDOR and Defrag. WISECONDOR detects smaller chromosomal deletions and duplications without increasing the need for NIPT/NGS data. It is now widely used in many countries for routine diagnostic NIPT analysis, including the Netherlands, Denmark, France and South Korea. Defrag has not yet been published, but is a tool to determine foetal fraction. Defrag is based on Y-chromosome fraction. All tools are freely available for non-commercial use  ( also be used for the detection of tumour profiles in cfDNA from cancer patients.

III) The introduction of NIPT in the Netherlands.

The Netherlands are the first country where NIPT is incorporated into a governmentally supported and health care funded prenatal Down syndrome screening program. In many countries, NIPT has been introduced commercially, without governmental guidance. In the Netherlands the Population Screening Act regulates the introduction of screening programs for untreatable diseases such as Down syndrome. The Dutch NIPT consortium, consisting of all relevant stakeholders (midwifes, gynaecologists, clinical geneticists and clinical laboratory geneticists), obtained a license for a nationwide NIPT implementation study called TRIDENT-1, which started April 1st 2014. Inclusion criteria are an increased risk (>1:200) for trisomy (T) 21, 18 or 13 based on the first trimester combined test, or because of medical history. Data of the first year will be presented, including full clinical follow up of the first five months, and information on findings other than trisomy 21, 13 or 18. On April 1st 2017 we started the TRIDENT-2 study, which offers NIPT to all pregnant women. In TRIDENT-2, women have the choice to either receive information on Trisomies 21, 13 and 18 alone, or to learn about other chromosomal abnormalities as well (with the exclusion of the sex chromosomes). A brief overview of the results of the first weeks will be presented.

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