Paper Info
Title
Cost-effective and accurate method of measuring fetal fraction using SNP imputation.
Abstract
Motivation: With the discovery of cell-free fetal DNA in maternal blood, the demand for non-invasive prenatal testing (NIPT) has been increasing. To obtain reliable NIPT results, it is important to accurately estimate the fetal fraction. In this study, we propose an accurate and cost-effective method for measuring fetal fractions using single-nucleotide polymorphisms (SNPs). Results: A total of 84 samples were sequenced via semiconductor sequencing using a 0.3x sequencing coverage. SNPs were genotyped to estimate the fetal fraction. Approximately 900 000 SNPs were genotyped, and 250 000 of these SNPs matched the semiconductor sequencing results. We performed SNP imputation (1000Genome phase3 and HRC v1.1 reference panel) to increase the number of SNPs. The correlation coefficients (R-2) of the fetal fraction estimated using the ratio of non-maternal alleles when coverage was reduced to 0.01 following SNP imputation were 0.93 (HRC v1.1 reference panel) and 0.90 (1000GP3 reference panel). An R-2 of 0.72 was found at 0.01x sequencing coverage with no imputation performed. We developed an accurate method to measure fetal fraction using SNP imputation, showing cost-effectiveness by using different commercially available SNP chips and lowering the coverage. We also showed that semiconductor sequencing, which is an inexpensive option, was useful for measuring fetal fraction.
Year
DOI
Venue
2018
10.1093/bioinformatics/btx728
BIOINFORMATICS
Field
DocType
Volume
Data mining,Computer science,Imputation (statistics),SNP
Journal
34
Issue
ISSN
Citations 
7
1367-4803
0
PageRank 
References 
Authors
0.34
1
4
Name
Order
Citations
PageRank
Minjeong Kim100.34
Jai-Hoon Kim223334.07
Kangseok Kim38216.72
Sunshin Kim432.56