Journal:

Article Title: A new and simple approach for genotyping Alzheimer's disease presenilin-1 mutant knockin mice

doi: 10.1016/j.jneumeth.2009.05.009

Figure Lengend Snippet: The specific set of primers designed for PS1 gene generated a 231 bp PCR product in three different DNA samples tested whose genotypes were determined using the classical method (+/+, +/KI, KI/KI). PCR was performed in triplicate for each sample. No PCR product was detected in the negative control lane (T−).

Article Snippet: The classical method for genotyping PS1 mice, described by Guo et al. (1999) and recommended by the Jackson Laboratories is a multistep method.

Techniques: Generated, Negative Control

Journal:

Article Title: A new and simple approach for genotyping Alzheimer's disease presenilin-1 mutant knockin mice

doi: 10.1016/j.jneumeth.2009.05.009

Figure Lengend Snippet: Photomicrograph of a polyacrylamide gel of SSCP electrophoresis. Migration was stopped when the loading dye had totally migrated outside of the gel (i.e. overnight). The lower part of the gel was cut off. Arrows indicate targeted specific bands. The upper band represents wild-type allele and the lower band the mutated allele KI of PS1

Article Snippet: The classical method for genotyping PS1 mice, described by Guo et al. (1999) and recommended by the Jackson Laboratories is a multistep method.

Techniques: Electrophoresis, Migration

Journal:

Article Title: A new and simple approach for genotyping Alzheimer's disease presenilin-1 mutant knockin mice

doi: 10.1016/j.jneumeth.2009.05.009

Figure Lengend Snippet: Efficiency of SSCP analysis for genotyping Description of the tails (samples) tested corresponding to the number of lane and the genotypes obtained by classical PCR in order to confirm the efficiency of SSCP method. In total, 33 fragments of tails were analysed from the three genotypes blind to the tester: 7 fragments from +/+ mice among which 6 were duplicated; 4 fragments from +/KI mice among which 4 were duplicated and 6 fragments from KI/KI mice among which 6 were duplicated. The efficiency of SSCP method for genotyping was clearly confirmed (100% match).

Article Snippet: The classical method for genotyping PS1 mice, described by Guo et al. (1999) and recommended by the Jackson Laboratories is a multistep method.

Techniques: Polymerase Chain Reaction

Journal: Cell

Article Title: Data sanitization to reduce private information leakage from functional genomics

doi: 10.1016/j.cell.2020.09.036

Figure Lengend Snippet: Effect of functional genomics assay type on de-anonymization. See also Figure S2 and S3. (a) The linking scores and gap as a function of sequencing coverage for individual NA12878 for different functional genomics assays. (b) Linking score per base pair for each assay was calculated by normalizing the linking score values per subsampling by the total number of nucleotides in the sample. (c) Mean genotyping frequency per sequencing coverage for different assays. (d) The linking score and gap values from two individuals for ChIA-PET and ChIP-Seq experiments, (e) ChIP-Seq experiments, and (f) repli-Seq experiments. See also Figure S2.

Article Snippet: Another genotyping method popular for its low cost and portability is the Oxford Nanopore.

Techniques: Functional Assay, Sequencing, ChIA Pet Assay, ChIP-sequencing

Journal: Cell

Article Title: Data sanitization to reduce private information leakage from functional genomics

doi: 10.1016/j.cell.2020.09.036

Figure Lengend Snippet: Impact of sequencing depth on genotyping and linking accuracy. (a) The process of pooling reads from functional genomics data to generate different attacked databases. c amount of reads were pooled and a new cohort was generated. A linkage attack was performed for each new database using genomes as perfect information. (b) Variant calling was performed for pooled reads for each individual in the database. The panel shows the distribution of precision and sensitivity of the called genotypes over all individuals at different subsampling percentages using their genomes as the ground truth. (c) Cumulative linking accuracy before and after adding the false-positive genotypes. Linking accuracy was calculated as the ratio between the total number of correctly linked individuals.

Article Snippet: Another genotyping method popular for its low cost and portability is the Oxford Nanopore.

Techniques: Sequencing, Functional Assay, Generated, Variant Assay

Journal: Principles and Applications of Molecular Diagnostics

Article Title: Molecular Microbiology

doi: 10.1016/B978-0-12-816061-9.00005-9

Figure Lengend Snippet: Features of Food and Drug Administration–Cleared High-Risk Human Papillomavirus Tests

Article Snippet: A novel HCV genotyping method using a solid phase electrochemical array was developed by GenMark Diagnostics.

Techniques: Real-time Polymerase Chain Reaction, Amplification

Journal: Prostaglandins, leukotrienes, and essential fatty acids

Article Title: Genetic variation in FADS genes is associated with maternal long-chain PUFA status but not with cognitive development of infants in a high fish-eating observational study

doi: 10.1016/j.plefa.2015.08.004

Figure Lengend Snippet: Summary statistics for the NC1 and NC2 cohorts a , b , c .

Article Snippet: As this SNP was genotyped with two different methods (NC1 with Sequenom and NC2 with Taqman) and there was a perfect match between re-runs, we considered the genotyping results correct.

Techniques:

Journal: Prostaglandins, leukotrienes, and essential fatty acids

Article Title: Genetic variation in FADS genes is associated with maternal long-chain PUFA status but not with cognitive development of infants in a high fish-eating observational study

doi: 10.1016/j.plefa.2015.08.004

Figure Lengend Snippet: Genotype distribution in NC1 and NC2 mothers a , b , c .

Article Snippet: As this SNP was genotyped with two different methods (NC1 with Sequenom and NC2 with Taqman) and there was a perfect match between re-runs, we considered the genotyping results correct.

Techniques:

Journal: Prostaglandins, leukotrienes, and essential fatty acids

Article Title: Genetic variation in FADS genes is associated with maternal long-chain PUFA status but not with cognitive development of infants in a high fish-eating observational study

doi: 10.1016/j.plefa.2015.08.004

Figure Lengend Snippet: Relative differences in PUFA concentrations (mg/ml) by FADS genotypes compared to the reference genotype in NC1 and NC2 a , b , c .

Article Snippet: As this SNP was genotyped with two different methods (NC1 with Sequenom and NC2 with Taqman) and there was a perfect match between re-runs, we considered the genotyping results correct.

Techniques:

Journal: Prostaglandins, leukotrienes, and essential fatty acids

Article Title: Genetic variation in FADS genes is associated with maternal long-chain PUFA status but not with cognitive development of infants in a high fish-eating observational study

doi: 10.1016/j.plefa.2015.08.004

Figure Lengend Snippet: Prenatal arachidonic acid (AA; to compare the two cohorts we report the relative difference compared to the mean AA in carriers of the reference genotype). Boxplots are shown for each genotype in both the NC1 and NC2 cohorts. Differences between the genotypes are significant for all four SNPs in both cohorts except rs174575 in the NC1 cohort (see and ).

Article Snippet: As this SNP was genotyped with two different methods (NC1 with Sequenom and NC2 with Taqman) and there was a perfect match between re-runs, we considered the genotyping results correct.

Techniques:

Journal: Prostaglandins, leukotrienes, and essential fatty acids

Article Title: Genetic variation in FADS genes is associated with maternal long-chain PUFA status but not with cognitive development of infants in a high fish-eating observational study

doi: 10.1016/j.plefa.2015.08.004

Figure Lengend Snippet: Prenatal Eicosapentaenoic acid (EPA; to compare the two cohorts we report the relative difference compared to the mean EPA in carriers of the reference genotype). Boxplots are shown for each genotype in both the NC1 and NC2 cohorts. Differences between the genotypes are not significant for either cohort or any SNP (see and ).

Article Snippet: As this SNP was genotyped with two different methods (NC1 with Sequenom and NC2 with Taqman) and there was a perfect match between re-runs, we considered the genotyping results correct.

Techniques:

Journal: Prostaglandins, leukotrienes, and essential fatty acids

Article Title: Genetic variation in FADS genes is associated with maternal long-chain PUFA status but not with cognitive development of infants in a high fish-eating observational study

doi: 10.1016/j.plefa.2015.08.004

Figure Lengend Snippet: Relative differences in child developmental scores by mother’s genotype compared to the reference genotype from linear regression models a , b , c .

Article Snippet: As this SNP was genotyped with two different methods (NC1 with Sequenom and NC2 with Taqman) and there was a perfect match between re-runs, we considered the genotyping results correct.

Techniques: