Ultrasensitive detection of minor allele fractions in maternal samples based on microhaplotype analysis

Study ID Alternative Stable ID Type
EGAS00001007057 Other

Study Description

Background: Tools for quantifying and studying genetic variation in heterogeneous cell populations have a limited sensitivity. However, many biological problems require ultrasensitive genetic deconvolution of cell mixtures. The detection of fetal cells in cervical samples from pregnant women presents such a challenge. Methods: Using deep sequencing of microhaplotype loci and analysis of the error profiles in genetically pure and mixed samples, we increase the sensitivity for minor allele detection and demonstrate the potential for paternal allele detection in cervical samples from pregnant women. Results: Using artificial DNA mixtures, we show that unique alleles can be readily identified in mixtures with a ratio of 1 in 10,000 (0.01%). By applying this method on ten non-invasive cervical samples from pregnant women we could identify the presence of paternal alleles in half of the samples. Unexpectedly, we demonstrate those alleles not to be of fetal origin but of sperm. Conclusions: We developed a novel method that can deconvolute genetic mixtures to at least 0.01%, which can be ... (Show More)

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
Microhaplotype amplicon sequencing of cervical samples (n=10), parental DNA (n=20), cfDNA (n=10) and control experiments using HapMap DNA in different spike-in percentages.
Illumina NovaSeq 6000 81

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