Noninvasive prenatal paternity testing using targeted massively parallel sequencing

Qu, Ning; Xie, Yifan; Li, Haiyan; Liang, Hao; Lin, Shaobin; Huang, Erwen; Gao, Jun; Chen, Fang; Shi, Yan‐Wei

doi:10.1111/trf.14577

Cited by 14 publications

(20 citation statements)

References 20 publications

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“…Such tests require the genotyping of only 15 to 20 STR markers to generate highly accurate results, with the industry standard for paternity probability set at 99.99% to establish unambiguous paternity. Current noninvasive prenatal paternity methods based on maternal cfDNA use only Y‐STRs or alternatively, a large number, typically thousands, of SNPs as genetic markers . SNP‐based approaches are superior because of higher compatibility with the fragmented nature of cfDNA via the use of shorter amplicon lengths, reduced false positives and false negatives, and no fetus gender limitations.…”

Section: Discussionmentioning

confidence: 99%

“…In the present study, we hypothesized that with systematic selection of SNP loci and accurate genotyping achieved through UMI‐based targeted sequencing, the number of tested SNPs could be reduced from thousands to hundreds. To this end, SNP selection was performed based on population genetics data and comprised selection criteria that would simplify calculations, reduce SNP redundancy, and increase discriminative power (Data S1).…”

Section: Discussionmentioning

confidence: 99%

“…The low fetal allele counts in the presence of high maternal allele counts translate to difficulty in reliable detection of fetal alleles and constitute a major challenge in maternal cfDNA analysis. In sequencing approaches, this issue was previously addressed by employing targeted deep sequencing wherein target enrichment was hybridization based . To our knowledge, this is the first report where target enrichment was performed by multiplex amplification with the incorporation of UMIs.…”

Section: Discussionmentioning

confidence: 99%

“…A major challenge of SNP‐based tests is the accurate genotyping of fetal SNPs in the low fetal fraction (FF; average approximately 10% at 10‐13 gestation weeks) in cfDNA extracted from maternal blood (maternal cfDNA). High‐density array chips and high‐throughput next‐generation sequencing are efficient SNP genotyping platforms, and both have shown success in this application. The use of targeted sequencing (hybridization‐based target enrichment of 5000‐8000 SNPs) and a Bayesian analysis approach successfully determined paternity in 17 clinical cases .…”

Section: Introductionmentioning

confidence: 99%

“…The use of targeted sequencing (hybridization‐based target enrichment of 5000‐8000 SNPs) and a Bayesian analysis approach successfully determined paternity in 17 clinical cases . Likewise, Qu et al sequenced 1795 SNPs for successful paternity determination in 34 parentage test cases . Target enrichment can also be amplicon‐based, which allows the important implementation of molecular barcoding through the incorporation of Unique Molecular Identifiers (UMIs).…”

Section: Introductionmentioning

confidence: 99%

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Noninvasive prenatal paternity testing by means of SNP‐based targeted sequencing

Tam¹,

Chan²,

Tsang³

et al. 2020

Prenatal Diagnosis

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Objective To develop a method for noninvasive prenatal paternity testing based on targeted sequencing of single nucleotide polymorphisms (SNPs). Method SNPs were selected based on population genetics data. Target‐SNPs in cell‐free DNA extracted from maternal blood (maternal cfDNA) were analyzed by targeted sequencing wherein target enrichment was based on multiplex amplification using QIAseq Targeted DNA Panels with Unique Molecular Identifiers. Fetal SNP genotypes were called using a novel bioinformatics algorithm, and the combined paternity indices (CPIs) and resultant paternity probabilities were calculated. Results Fetal SNP genotypes obtained from targeted sequencing of maternal cfDNA were 100% concordant with those from amniotic fluid‐derived fetal genomic DNA. From an initial panel of 356 target‐SNPs, an average of 148 were included in paternity calculations in 15 family trio cases, generating paternity probabilities of greater than 99.9999%. All paternity results were confirmed by short‐tandem‐repeat analysis. The high specificity of the methodology was validated by successful paternity discrimination between biological fathers and their siblings and by large separations between the CPIs calculated for the biological fathers and those for 60 unrelated men. Conclusion The novel method is highly effective, with substantial improvements over similar approaches in terms of reduced number of target‐SNPs, increased accuracy, and reduced costs.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Noninvasive prenatal paternity testing by means of SNP‐based targeted sequencing

Tam¹,

Chan²,

Tsang³

et al. 2020

Prenatal Diagnosis

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A microhap panel for kinship analysis through massively parallel sequencing technology

Lin

Gao

et al. 2019

Electrophoresis

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A microhap panel for kinship analysis through massively parallel sequencing technologyIt is widely recognized that microhaps are powerful markers for different forensic purposes, mainly due to their advantages of both short tandem repeats and single nucleotide polymorphisms, including multiple alleles, low mutation rate, and absence of stutter peaks. In the present study, a panel of 60 microhap loci was developed and utilized in forensic kinship analysis as a preliminary study. Genotyping of microhap was performed by massively parallel sequencing and haplotypes were directly achieved from sequence reads of 73 samples from Chinese Han population. We observed that 49 out of 60 loci have effective number of alleles greater than 3.0 and 10 out of 60 have values above 4.0, with an average value of 3.5598. The heterozygosity values were in a range from 0.5840 to 0.8546 with an average of 0.7268 and the cumulative power of exclusion value of the 60 loci is equal to 1-4.78 × 10 −18 . Moreover, we demonstrated the applicability of this method by different relationship inference problems, including identification of single parent-offspring, full-sibling, and second-degree relative. The results indicated that the assembled microhap panel provided more power for relationship inference, than commonly used short tandem repeats or single nucleotide polymorphism system.Abbreviations: Ae, effective number of alleles; LR, likelihood ratio; MH, microhap; MPS, massively parallel sequencing; PD, power of discriminative; PE, power of exclusion; PIC, polymorphism information content; ROI, region of interest; TPI, typical paternity index * These authors contributed equally to this work.Color online: See the article online to view Figs. 1-6 in color.

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Noninvasive prenatal paternity testing by maternal plasma DNA sequencing in twin pregnancies

Xie

Lin

et al. 2020

Electrophoresis

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SNPs, combined with massively parallel sequencing technology, have proven applicability in noninvasive prenatal paternity testing (NIPPT) for singleton pregnancies in our previous research, using circulating cell‐free DNA in maternal plasma. However, the feasibility of NIPPT in twin pregnancies has remained uncertain. As a pilot study, we developed a practical method to noninvasively determine the paternity of twin pregnancies by maternal plasma DNA sequencing based on a massively parallel sequencing platform. Blood samples were collected from 15 pregnant women (twin pregnancies at 9–18 weeks of gestation). Parental DNA and maternal plasma cell‐free DNA were analyzed with custom‐designed probes covering 5226 polymorphic SNP loci. A mathematical model for data interpretation was established, including the zygosity determination and paternity index calculations. Each plasma sample was independently tested against the alleged father and 90 unrelated males. As a result, the zygosity in each twin case was correctly determined, prior to paternity analysis. Further, the correct biological father was successfully identified, and the paternity of all 90 unrelated males was excluded in each case. Our study demonstrates that NIPPT can be performed for twin pregnancies. This finding may contribute to development in NIPPT and diagnosis of certain genetic diseases.

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Noninvasive prenatal paternity testing using targeted massively parallel sequencing

Cited by 14 publications

References 20 publications

Noninvasive prenatal paternity testing by means of SNP‐based targeted sequencing

Noninvasive prenatal paternity testing by means of SNP‐based targeted sequencing

A microhap panel for kinship analysis through massively parallel sequencing technology

Noninvasive prenatal paternity testing by maternal plasma DNA sequencing in twin pregnancies

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