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 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 R1352Q CACNA1A Variant in a Patient with Sporadic Hemiplegic Migraine, Ataxia, Seizures and Cerebral Oedema: A Case Report

2021 ◽  
pp. 123-130
Author(s):  
Anker Stubberud ◽  
Emer O’Connor ◽  
Erling Tronvik ◽  
Henry Houlden ◽  
Manjit Matharu
Keyword(s):  
Mental Retardation ◽  
Case Report ◽  
Genetic Testing ◽  
Head Trauma ◽  
Cerebral Oedema ◽  
De Novo ◽  
Minor Head Trauma ◽  
Hemiplegic Migraine ◽  
Wide Range ◽  
History Of

Mutations in the <i>CACNA1A</i> gene show a wide range of neurological phenotypes including hemiplegic migraine, ataxia, mental retardation and epilepsy. In some cases, hemiplegic migraine attacks can be triggered by minor head trauma and culminate in encephalopathy and cerebral oedema. A 37-year-old male without a family history of complex migraine experienced hemiplegic migraine attacks from childhood. The attacks were usually triggered by minor head trauma, and on several occasions complicated with encephalopathy and cerebral oedema. Genetic testing of the proband and unaffected parents revealed a de novo heterozygous nucleotide missense mutation in exon 25 of the <i>CACNA1A</i> gene (c.4055G&#x3e;A, p.R1352Q). The R1352Q <i>CACNA1A</i> variant shares the phenotype with other described <i>CACNA1A</i> mutations and highlights the interesting association of trauma as a precipitant for hemiplegic migraine. Subjects with early-onset sporadic hemiplegic migraine triggered by minor head injury or associated with seizures, ataxia or episodes of encephalopathy should be screened for mutations. These patients should also be advised to avoid activities that may result in head trauma, and anticonvulsants should be considered as prophylactic migraine therapy.

scholarly journals Clinical impact of post-mortem genetic testing in cardiac death and cardiomyopathy

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 435-446
Author(s):  
Isabelle Marey ◽  
Véronique Fressart ◽  
Caroline Rambaud ◽  
Paul Fornes ◽  
Laurent Martin ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Cardiac Death ◽  
De Novo ◽  
Family Care ◽  
Prenatal Testing ◽  
Added Value ◽  
Molecular Testing ◽  
Post Mortem ◽  
Genetic Analyses ◽  
Conventional Autopsy

AbstractPost-mortem genetic analyses may help to elucidate the cause of cardiac death. The added value is however unclear when a cardiac disease is already suspected or affirmed. Our aim was to study the feasibility and medical impact of post-mortem genetic analyses in suspected cardiomyopathy. We studied 35 patients with cardiac death and suspected cardiomyopathy based on autopsy or clinical data. After targeted sequencing, we identified 15 causal variants in 15 patients (yield 43%) in sarcomeric (n = 8), desmosomal (n = 3), lamin A/C (n = 3) and transthyretin (n = 1) genes. The results had various impacts on families, i.e. allowed predictive genetic testing in relatives (15 families), planned early therapeutics based on the specific underlying gene (5 families), rectified the suspected cardiomyopathy subtype (2 families), assessed the genetic origin of cardiomyopathy that usually has an acquired cause (1 family), assessed the diagnosis in a patient with uncertain borderline cardiomyopathy (1 family), reassured the siblings because of a de novo mutation (2 families) and allowed prenatal testing (1 family). Our findings suggest that post-mortem molecular testing should be included in the strategy of family care after cardiac death and suspected cardiomyopathy, since genetic findings provide additional information useful for relatives, which are beyond conventional autopsy.

Experiences of individuals receiving “Not Parent Expected” (NPE) results through direct-to-consumer genetic testing

2021 ◽  
Vol 132 ◽  
pp. S289
Author(s):  
Julia Becker ◽  
Janey Youngblom ◽  
Brianne Kirkpatrick ◽  
Liane Abrams
Keyword(s):  
Genetic Testing ◽  
Direct To Consumer

scholarly journals An exploratory assessment of the applicability of direct-to-consumer genetic testing to translational research in Japan

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Masahiro Inoue ◽  
Shota Arichi ◽  
Tsuyoshi Hachiya ◽  
Anna Ohtera ◽  
Seok-Won Kim ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Translational Research ◽  
Drug Target ◽  
Target Genes ◽  
Healthy Individuals ◽  
Alcohol Sensitivity ◽  
Direct To Consumer ◽  
Disease States ◽  
Multiple Phenotypes ◽  
Related Phenotype

Abstract Objective In order to assess the applicability of a direct-to-consumer (DTC) genetic testing to translational research for obtaining new knowledge on relationships between drug target genes and diseases, we examined possibility of these data by associating SNPs and disease related phenotype information collected from healthy individuals. Results A total of 12,598 saliva samples were collected from the customers of commercial service for SNPs analysis and web survey were conducted to collect phenotype information. The collected dataset revealed similarity to the Japanese data but distinguished differences to other populations of all dataset of the 1000 Genomes Project. After confirmation of a well-known relationship between ALDH2 and alcohol-sensitivity, Phenome-Wide Association Study (PheWAS) was performed to find association between pre-selected drug target genes and all the phenotypes. Association was found between GRIN2B and multiple phenotypes related to depression, which is considered reliable based on previous reports on the biological function of GRIN2B protein and its relationship with depression. These results suggest possibility of using SNPs and phenotype information collected from healthy individuals as a translational research tool for drug discovery to find relationship between a gene and a disease if it is possible to extract individuals in pre-disease states by properly designed questionnaire.

scholarly journals Secondary Data Usage in Direct-to-Consumer Genetic Testing: To What Extent Are Customers Aware and Concerned?

2021 ◽  
pp. 1-8
Author(s):  
Janessa Mladucky ◽  
Bonnie Baty ◽  
Jeffrey Botkin ◽  
Rebecca Anderson
Keyword(s):  
Genetic Testing ◽  
Secondary Data ◽  
Structured Interviews ◽  
Customer Data ◽  
Secondary Use ◽  
Data Usage ◽  
Direct To Consumer ◽  
New Information ◽  
Opt Out ◽  
Potential Risks

Introduction: Customer data from direct-to-consumer genetic testing (DTC GT) are often used for secondary purposes beyond providing the customer with test results. Objective: The goals of this study were to determine customer knowledge of secondary uses of data, to understand their perception of risks associated with these uses, and to determine the extent of customer concerns about privacy. Methods: Twenty DTC GT customers were interviewed about their experiences. The semi-structured interviews were transcribed, coded, and analyzed for common themes. Results: Most participants were aware of some secondary uses of data. All participants felt that data usage for research was acceptable, but acceptability for non-research purposes varied across participants. The majority of participants were aware of the existence of a privacy policy, but few read the majority of the privacy statement. When previously unconsidered uses of data were discussed, some participants expressed concern over privacy protections for their data. Conclusion: When exposed to new information on secondary uses of data, customers express concerns and a desire to improve consent with transparency, more opt-out options, improved readability, and more information on future uses and potential risks from direct-to-consumer companies. Effective ways to improve readership about the secondary use, risk of use, and protection of customer data should be investigated and the findings implemented by DTC companies to protect public trust in these practices.

scholarly journals The study of sodium and potassium channel gene single-nucleotide variation significance in non-mechanical forms of epilepsy

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ozada Khamdiyeva ◽  
Zhanerke Tileules ◽  
Gulminyam Baratzhanova ◽  
Anastassiya Perfilyeva ◽  
Leyla Djansugurova
Keyword(s):  
Ion Channel ◽  
Potassium Channel ◽  
De Novo ◽  
Potassium Ion ◽  
Dravet Syndrome ◽  
De Novo Mutations ◽  
Single Nucleotide ◽  
Channel Gene ◽  
Sodium And Potassium ◽  
Potassium Channel Gene

Abstract Background Epilepsy is one of the most common and heterogeneous neurological diseases. The main clinical signs of the disease are repeated symptomatic or idiopathic epileptic seizures of both convulsive and non-convulsive nature that develop against a background of lost or preserved consciousness. The genetic component plays a large role in the etiology of idiopathic forms of epilepsy. The study of the molecular genetic basis of neurological disorders has led to a rapidly growing number of gene mutations known to be involved in hereditary ion channel dysfunction. The aim of this research was to evaluate the involvement of single-nucleotide variants that modify the function of genes (SCN1A, KCNT1, KCNTС1, and KCNQ2) encoding sodium and potassium ion channel polypeptides in the development of epilepsy. Results De novo mutations in the sodium channel gene SCN1A c.5347G>A (p. Ala1783Thr) were detected in two patients with Dravet syndrome, with a deletion in exon 26 found in one. Three de novo mutations in the potassium channel gene KCNT1 c.2800G>A (p. Ala934Thr), were observed in two patients with temporal lobe epilepsy (TLE) and one patient with residual encephalopathy. Moreover, a control cohort matched to the case cohort did not reveal any SNVs among conditionally healthy individuals, supporting the pathogenic significance of the studied SNVs. Conclusion Our results are supported by literature data showing that the sodium ion channel gene SCN1A c.5347G>A mutation may be involved in the pathogenesis of Dravet syndrome. We also note that the c.2800G>A mutation in the potassium channel gene KCNT1 can cause not only autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) but also other forms of epilepsy. To treat pathogenetic mutations that accelerate the function of sodium and potassium ion channels, we recommend ion channel blockade drug therapy.

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