ArticleScientific reports2018
NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data.Genome biology · 2025Article
- KF-NIPT: K-mer and fetal fraction-based estimation of chromosomal anomaly from NIPT data.BMC bioinformatics · 2025Article
- Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.BMC genomics · 2024Article
- The Impact of Chromosomal Mosaicisms on Prenatal Diagnosis and Genetic Counseling-A Narrative Review.Journal of personalized medicine · 2024Review
- GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads.Scientific reports · 2023Article
- DOCEST-fast and accurate estimator of human NGS sequencing depth and error rate.Bioinformatics advances · 2023Article
- Prenatal diagnosis of a 46,XY karyotype female fetus with an SRY-associated gonadal dysgenesis, conceived through an intracytoplasmic sperm injection: a case report.BMC pregnancy and childbirth · 2022Article
- Development and performance evaluation of an artificial intelligence algorithm using cell-free DNA fragment distance for non-invasive prenatal testing (aiD-NIPT).Frontiers in genetics · 2022Article
- Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples.PLoS computational biology · 2021Article
- Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing.Clinical epigenetics · 2020Article
- Article
- NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing.BMC bioinformatics · 2018Article
Corrections and comments
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Authors and funding
14 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts. Additionally, the filtering process used for k-mer list creation allows one to take into account the genetic variance in a specific sample, thus reducing the source of uncertainty. The processing time of one sample is less than 10 CPU-minutes on a high-end workstation. NIPTmer was validated on a cohort of 583 NIPT samples and it correctly predicted 37 non-mosaic fetal aneuploidies. NIPTmer has the potential to reduce significantly the time and complexity of NIPT post-sequencing analysis compared to mapping-based methods. For non-commercial users the software package is freely available at http://bioinfo.ut.ee/NIPTMer/ .
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