NGSremix: a software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

Nøhr, Anne Krogh; Hanghøj, Kristian; Garcia‐Erill, Genís; Li, Zilong; Moltke, Ida; Albrechtsen, Anders

doi:10.1093/g3journal/jkab174

Cited by 16 publications

(28 citation statements)

References 31 publications

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“…Investigating methods that operate directly on genotype likelihoods was out of the scope of the current study. Recently published methods including NgsRelate ( Korneliussen and Moltke, 2015 ) and NGSremix ( Nøhr et al, 2021 ) operate directly on genotype likelihoods. Future research should assess how these methods perform when dealing with low-quality sequencing data from degraded or low-quantity sequencing data.…”

Section: Discussionmentioning

confidence: 99%

Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples

et al. 2022

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Technological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic genealogy (FGG) has facilitated the identification of distant relatives of both unidentified remains and unknown donors of crime scene DNA, invigorating the use of biological samples to resolve open cases. Forensic samples are often degraded or contain only trace amounts of DNA. In this study, the accuracy of genome-wide relatedness methods and identity by descent (IBD) segment approaches was evaluated in the presence of challenges commonly encountered with forensic data: missing data and genotyping error. Pedigree whole-genome simulations were used to estimate the genotypes of thousands of individuals with known relationships using multiple populations with different biogeographic ancestral origins. Simulations were also performed with varying error rates and types. Using these data, the performance of different methods for quantifying relatedness was benchmarked across these scenarios. When the genotyping error was low (<1%), IBD segment methods outperformed genome-wide relatedness methods for close relationships and are more accurate at distant relationship inference. However, with an increasing genotyping error (1–5%), methods that do not rely on IBD segment detection are more robust and outperform IBD segment methods. The reduced call rate had little impact on either class of methods. These results have implications for the use of dense SNP data in forensic genomics for distant kinship analysis and FGG, especially when the sample quality is low.

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Section: Discussionmentioning

confidence: 99%

Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples

et al. 2022

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“…We used NGSremix to estimate pairwise relatedness between all S. bovis, S. curassoni and admixed samples [93]. The LD pruned BED file was used as input along with admixture proportions and ancestral allele frequencies estimated by ADMIXTURE.…”

Section: Relatedness Estimationmentioning

confidence: 99%

Genomic evidence of contemporary hybridization between Schistosoma species

et al. 2022

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Hybridization between different species of parasites is increasingly being recognised as a major public and veterinary health concern at the interface of infectious diseases biology, evolution, epidemiology and ultimately control. Recent research has revealed that viable hybrids and introgressed lineages between Schistosoma spp. are prevalent across Africa and beyond, including those with zoonotic potential. However, it remains unclear whether these hybrid lineages represent recent hybridization events, suggesting hybridization is ongoing, and/or whether they represent introgressed lineages derived from ancient hybridization events. In human schistosomiasis, investigation is hampered by the inaccessibility of adult-stage worms due to their intravascular location, an issue which can be circumvented by post-mortem of livestock at abattoirs for Schistosoma spp. of known zoonotic potential. To characterise the composition of naturally-occurring schistosome hybrids, we performed whole-genome sequencing of 21 natural livestock infective schistosome isolates. To facilitate this, we also assembled a de novo chromosomal-scale draft assembly of Schistosoma curassoni. Genomic analyses identified isolates of S. bovis, S. curassoni and hybrids between the two species, all of which were early generation hybrids with multiple generations found within the same host. These results show that hybridization is an ongoing process within natural populations with the potential to further challenge elimination efforts against schistosomiasis.

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“…Recent methods (such as RAFFI [46], IBDKin [47]) use fast algorithms to search for IBD matches from phased genotypes and estimate kinship from shared IBD estimates. There are also methods that estimate kinship from next-generation sequencing data, which are especially useful from lowcoverage sequencing approaches (NGSRemix [48], LASER [49], SEEKIN [50]). While most methods can accurately estimate kinship for individuals with homogeneous ancestry, this is not a tenable assumption in admixed populations [2,51].…”

Section: Introductionmentioning

confidence: 99%

Privacy-Aware Kinship Inference in Admixed Populations using Projection on Reference Panels

Wang

Kim

et al. 2022

Preprint

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Estimation of genetic relatedness, or kinship, is used occasionally for recreational purposes and in forensic applications. While numerous methods were developed to estimate kinship, they suffer from high computational requirements and often make an untenable assumption of homogeneous population ancestry of the samples. Moreover, genetic privacy is generally overlooked in the usage of kinship estimation methods. There can be ethical concerns about finding unknown familial relationships in 3rd party databases. Similar ethical concerns may arise while estimating and reporting sensitive population-level statistics such as inbreeding coefficients for the concerns around marginalization and stigmatization. Here, we make use of existing reference panels with a projection-based approach that simplifies kinship estimation in the admixed populations. We use simulated and real datasets to demonstrate the accuracy and efficiency of kinship estimation. We present a secure federated kinship estimation framework and implement a secure kinship estimator using homomorphic encryption-based primitives for computing relatedness between samples in 2 different sites while genotype data is kept confidential.

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NGSremix: a software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

Cited by 16 publications

References 31 publications

Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples

Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples

Genomic evidence of contemporary hybridization between Schistosoma species

Privacy-Aware Kinship Inference in Admixed Populations using Projection on Reference Panels

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