Establishing and validating noninvasive prenatal testing procedure for fetal aneuploidies in Vietnam

Abstract

Objective: Non-invasive prenatal testing (NIPT) for fetal aneuploidies has been widely adopted in developed countries. Despite the sharp decrease in the cost of massively parallel sequencing, the technical know-how and skilled personnel are still one of the major limiting factors for applying this technology to NIPT in low-income settings. Here, we present the establishment and validation of our NIPT procedure called triSure for detection of fetal aneuploidies. Methods: We established the triSure algorithm based on the difference in proportion of fetal and maternal fragments from the target chromosome to all chromosomes. Our algorithm was validated using a published data set and an in-house data set obtained from high-risk pregnant women in Vietnam who have undergone amniotic testing. Several other aneuploidy calling methods were also applied to the same data set to benchmark triSure performance. Results: The triSure algorithm showed similar accuracy to size-based method when comparing them using published data set. Using our in-house data set from 130 consecutive samples, we showed that triSure correctly identified the most samples (overall sensitivity and specificity of 0.983 and 0.986, respectively) compared to other methods tested including count-based, sized-based, RAPIDR and NIPTeR. Conclusion: We have demonstrated that our triSure NIPT procedure can be applied to pregnant women in low-income settings such as Vietnam, providing low-risk screening option to reduce the need for invasive diagnostic tests.

Genetic profiling of 2,683 Vietnamese genomes from non-invasive prenatal testing data

“…In this study, we analyzed the genomes of 2,683 pregnant Vietnamese women from their noninvasive prenatal testing data. The genomes were originally sequenced at a low depth of approximately 0.17x per sample for the purpose of fetal aneuploidy testing [14]. Here we combined the 2,683 samples to a total sequencing depth of 364x and performed variant calling and analysis for the Vietnamese population.…”

“…An alternative approach has been proposed recently to re-use the low-coverage genome sequencing data from non-invasive prenatal testing (NIPT) for large-scale population genetics studies [12,13]. NIPT is a method that sequences cell-free DNA from maternal plasma at an ultra-low depth of 0.1-0.2x to detect fetal aneuploidy [14]. By combining a sufficiently large number of NIPT samples, one could obtain a good representation of the population genetic variation.…”

“…First, the data can be re-used at no extra cost given the approval and consent of the participants. As one of 4 the most rapidly adopted genetic tests, NIPT has been successfully established and become a standard screening procedure with thousands to millions of tests performed world-wide, including many developing countries such as Vietnam [14]. Using NIPT data for population genetic studies may also reduce privacy concerns since the genetic variants can only be analyzed by aggregating a large number of samples and the results can only be interpreted at the population level.…”

Reducing false positive rate of fetal monosomy X in non‐invasive prenatal testing using a combined algorithm to detect maternal mosaic monosomy X

“…Prep Kit from New England Biolabs (Ipswich, MA, USA) and sequenced on the NextSeq platform using paired-end 2 × 75-bp Reagent Kit from Illumina (San Diego, CA, USA). The z-scores for chromosome X (z X ) and chromosome Y (z Y ) were calculated using two methods: the triSure 11 and NIPTeR 12 with reference sets consist of all female fetal samples.…”

“…Library preparation was done using NEBNext Ultra II DNA Library Prep Kit from New England Biolabs (Ipswich, MA, USA) and sequenced on the NextSeq platform using paired‐end 2 × 75‐bp Reagent Kit from Illumina (San Diego, CA, USA). The z ‐scores for chromosome X (z X ) and chromosome Y (z Y ) were calculated using two methods: the triSure and NIPTeR with reference sets consist of all female fetal samples. Our interpretation of z X is as follows: having two copies of chromosome X (XX) when −2.5 ≤ z X ≤ 2.5, single copy of chromosome X (X) when z X < −2.5 and three copies of chromosome X (XXX) when z X > 2.5.…”