scholarly journals Genotype Fingerprints Enable Fast and Private Comparison of Genetic Testing Results for Research and Direct-to-Consumer Applications

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 481
Author(s):  
Max Robinson ◽  
Gustavo Glusman
Keyword(s):  
Genetic Testing ◽  
De Novo ◽  
Personal Health ◽  
Nucleotide Polymorphism ◽  
Consumer Market ◽  
Single Nucleotide ◽  
Direct To Consumer ◽  
Background Population ◽  
Individual Marker ◽  
Related Individuals

Genetic testing has expanded out of the research laboratory into medical practice and the direct-to-consumer market. Rapid analysis of the resulting genotype data now has a significant impact. We present a method for summarizing personal genotypes as ‘genotype fingerprints’ that meets these needs. Genotype fingerprints can be derived from any single nucleotide polymorphism-based assay, and remain comparable as chip designs evolve to higher marker densities. We demonstrate that these fingerprints support distinguishing types of relationships among closely related individuals and closely related individuals from individuals from the same background population, as well as high-throughput identification of identical genotypes, individuals in known background populations, and de novo separation of subpopulations within a large cohort through extremely rapid comparisons. Although fingerprints do not preserve anonymity, they provide a useful degree of privacy by summarizing a genotype while preventing reconstruction of individual marker states. Genotype fingerprints are therefore well-suited as a format for public aggregation of genetic information to support ancestry and relatedness determination without revealing personal health risk status.

scholarly journals Genotype Fingerprints Enable Fast and Private Comparison of Genetic Testing Results for Research and Direct-to-Consumer Applications

2018 ◽  
Author(s):  
Max Robinson ◽  
Gustavo Glusman
Keyword(s):  
Genetic Testing ◽  
De Novo ◽  
Personal Health ◽  
Nucleotide Polymorphism ◽  
Consumer Market ◽  
Single Nucleotide ◽  
Direct To Consumer ◽  
Background Population ◽  
Individual Marker ◽  
Related Individuals

Genetic testing has expanded out of the research laboratory into medical practice and the direct-to-consumer market, and rapid analysis of the resulting genotype data can now have significant impact. We present a method for summarizing personal genotypes as ‘genotype fingerprints’ that meet these needs. Genotype fingerprints can be derived from any single nucleotide polymorphism (SNP)-based assay, and remain comparable as chip designs evolve to higher marker densities. We demonstrate that they support distinguishing types of relationships among closely related individuals and closely related individuals from individuals from the same background population, as well as high-throughput identification of identical genotypes, individuals in known background populations, and de novo separation of subpopulations within a large cohort through extremely rapid comparisons. While fingerprints do not preserve anonymity, they provide a useful degree of privacy by summarizing a genotype in a way that prevents reconstruction of individual marker states. Genotype fingerprints are therefore well-suited as a format for public aggregation of genetic information to support ancestry and relatedness determination without revealing personal health risk status.

scholarly journals Genotype fingerprints enable fast and private comparison of genetic testing results for research and direct-to-consumer applications

2017 ◽  
Author(s):  
Max Robinson ◽  
Gustavo Glusman
Keyword(s):  
Genetic Testing ◽  
De Novo ◽  
Consumer Market ◽  
Single Nucleotide ◽  
Relationship Type ◽  
Direct To Consumer ◽  
Background Population ◽  
Public Sharing ◽  
Individual Marker ◽  
Related Individuals

AbstractAs genetic testing expands out of the research laboratory into medical practice as well as the direct-to-consumer market, the efficiency with which the resulting genotype data can be compared between individuals is of increasing importance.We present a method for summarizing personal genotypes, yielding ’genotype fingerprints’ that can be derived from any single nucleotide polymorphism (SNP)-based assay and readily compared to estimate relatedness. The resulting fingerprints remain comparable as chip designs evolve to higher marker densities. We demonstrate that they support applications including distinguishing genotypes of closely related individuals by relationship type, distinguishing closely related individuals from individuals from the same background population, identification of individuals in known background populations, and de novo identification of subpopulations within a large cohort in a high-throughput manner.An important feature of genotype fingerprints is that, while fingerprints do not preserve anonymity, they summarize individual marker data in a way that prevents phenotype prediction. Genotype fingerprints are therefore well-suited to public sharing for ancestry determination purposes, without revealing personal health risk status.

scholarly journals Species-Specific Marker Discovery in Tilapia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mochamad Syaifudin ◽  
Michaël Bekaert ◽  
John B. Taggart ◽  
Kerry L. Bartie ◽  
Stefanie Wehner ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Restriction Site ◽  
De Novo ◽  
Snp Markers ◽  
Specific Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Species Analysis ◽  
Species Specific ◽  
Marker Discovery

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

scholarly journals Optimized Genetic Testing for Polledness in Multiple Breeds of Cattle

2019 ◽  
Vol 10 (2) ◽  
pp. 539-544 ◽  
Author(s):  
Imtiaz A. S. Randhawa ◽  
Brian M. Burns ◽  
Michael R. McGowan ◽  
Laercio R. Porto-Neto ◽  
Ben J. Hayes ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Life Prediction ◽  
Selective Breeding ◽  
Bos Indicus ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Complex Genetics ◽  
Gene Testing ◽  
Direct Gene ◽  
Gene Test

Many breeds of modern cattle are naturally horned, and for sound husbandry management reasons the calves frequently undergo procedures to physically remove the horns by disbudding or dehorning. These procedures are however a welfare concern. Selective breeding for polledness – absence of horns – has been effective in some cattle breeds but not in others (Bos indicus genotypes) due in part to the complex genetics of horn phenotype. To address this problem different approaches to genetic testing which provide accurate early-in-life prediction of horn phenotype have been evaluated, initially using microsatellites (MSAT) and more recently single nucleotide polymorphism (SNP). A direct gene test is not effective given the genetic heterogeneity and large-sized sequence variants associated with polledness in different breeds. The current study investigated 39,943 animals of multiple breeds to assess the accuracy of available poll testing assays. While the standard SNP-based test was an improvement on the earlier MSAT haplotyping method, 1999 (9.69%) out of 20,636 animals tested with this SNP-based assay did not predict a genotype, most commonly associated with the Indicus-influenced breeds. The current study has developed an optimized poll gene test that resolved the vast majority of these 1999 unresolved animals, while the predicted genotypes of those previously resolved remained unchanged. Hence the optimized poll test successfully predicted a genotype in 99.96% of samples assessed. We demonstrated that a robust set of 5 SNPs can effectively determine PC and PF alleles and eliminate the ambiguous and undetermined results of poll gene testing previously identified as an issue in cattle.

scholarly journals DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9291
Author(s):  
Jérémy Gauthier ◽  
Charlotte Mouden ◽  
Tomasz Suchan ◽  
Nadir Alvarez ◽  
Nils Arrigo ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Restriction Site ◽  
Population Genomics ◽  
De Novo ◽  
State Of The Art ◽  
Phylogenetic Reconstruction ◽  
Original Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Require Time

Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.

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