Journal: Nephrology Dialysis Transplantation

Article Title: Association of polymorphisms in the klotho gene with severity of non-diabetic ESRD in African Americans

doi: 10.1093/ndt/gfq214

Figure Lengend Snippet: SNP genotyping

Article Snippet: SNP genotyping was performed using the MassARRAY genotyping system (Sequenom, San Diego, CA, USA).

Techniques:

Journal: Nephrology Dialysis Transplantation

Article Title: Association of polymorphisms in the klotho gene with severity of non-diabetic ESRD in African Americans

doi: 10.1093/ndt/gfq214

Figure Lengend Snippet: SNP genotyping

Article Snippet: SNP genotyping was performed using the MassARRAY genotyping system (Sequenom, San Diego, CA, USA).

Techniques:

Journal: Nephrology Dialysis Transplantation

Article Title: Association of polymorphisms in the klotho gene with severity of non-diabetic ESRD in African Americans

doi: 10.1093/ndt/gfq214

Figure Lengend Snippet: SNP genotyping

Article Snippet: SNP genotyping was performed using the MassARRAY genotyping system (Sequenom, San Diego, CA, USA).

Techniques:

Journal: Nephrology Dialysis Transplantation

Article Title: Association of polymorphisms in the klotho gene with severity of non-diabetic ESRD in African Americans

doi: 10.1093/ndt/gfq214

Figure Lengend Snippet: SNP genotyping

Article Snippet: SNP genotyping was performed using the MassARRAY genotyping system (Sequenom, San Diego, CA, USA).

Techniques:

Journal: Nucleic Acids Research

Article Title: Using DNA pools for genotyping trios

doi: 10.1093/nar/gkl700

Figure Lengend Snippet: The error rate of the predicted genotypes using multiplexing pools in trios and the greedy algorithm for missing data estimation. The x -axis is the missing data rate and the y -axis is the resulting genotyping error rate. The pools and the corresponding confidence intervals were simulated on two datasets: The first is a dataset simulated from the coalescent model, taken from the dataset publicly available by ( 7 ). The second is chromosome 22, taken from 30 Yoruban trios collected by the HapMap consortium, ( 15 ).

Article Snippet: Allelotyping Genotyping of individual samples and allelotyping of DNA pools were both performed using the same chemistry and laboratory protocols for multiplex PCR, single-base primer extension (SBE) and generation of mass spectra (for complete details see iPLEX Application Note, Sequenom, San Diego).

Techniques: Multiplexing

Journal: Nucleic Acids Research

Article Title: Using DNA pools for genotyping trios

doi: 10.1093/nar/gkl700

Figure Lengend Snippet: The error rate of the parent–child pool genotyping versus standard genotyping as a function of increasing imprecision in allele frequency determination. All datasets are based on 200 SNPs in chromosome 22, taken from the HapMap CEU population, which includes 30 trios. For each allele frequency read (per SNP and pool), we added an error component, normally distributed with mean 0 and SD ranging from 0 to 10% (on the x -axis).

Article Snippet: Allelotyping Genotyping of individual samples and allelotyping of DNA pools were both performed using the same chemistry and laboratory protocols for multiplex PCR, single-base primer extension (SBE) and generation of mass spectra (for complete details see iPLEX Application Note, Sequenom, San Diego).

Techniques:

Journal: Nucleic Acids Research

Article Title: Using DNA pools for genotyping trios

doi: 10.1093/nar/gkl700

Figure Lengend Snippet: Allelic frequencies of pools for SNP assay ID rs1012515. The x -axes correspond to pool index, ordered by increasing known pool allelic frequency. Upper panel: the pools' allelic frequency estimate as measured by MassARRAY genotyping (raw data, open boxes) versus the Triophase-corrected estimates (closed circles). Lower panel: the pools' known allelic frequency bin (large gray circles) versus Triophase-assigned frequency bins (small dark circles). Two errors in pool frequency estimation are evident in the lower panel as lone small dark circles.

Article Snippet: Allelotyping Genotyping of individual samples and allelotyping of DNA pools were both performed using the same chemistry and laboratory protocols for multiplex PCR, single-base primer extension (SBE) and generation of mass spectra (for complete details see iPLEX Application Note, Sequenom, San Diego).

Techniques:

Journal: Nucleic Acids Research

Article Title: Using DNA pools for genotyping trios

doi: 10.1093/nar/gkl700

Figure Lengend Snippet: The increase in power resulting from the use of pairwise parent–child pools in genotyping trios. We compared the power of four different scenarios under a multiplicative disease model for a SNP with minor allele frequencies of 5 and 25%. In the first three scenarios, 500 trios are genotyped and the TDT test is performed. The first scenario assumes no genotyping errors, the second assumes that the trios were pooled using the Triophase approach and thus the errors of the child and its parents are dependent and the third one assumes that the errors for different individuals are independent, In the fourth scenario, we assume that 500 cases and 500 controls are genotyped and that a χ 2 -test is performed. Notably, the Triophase approach does not lose much power due to dependencies in the errors and for low allele frequencies, there is a considerable gain of power compared to a non-family-based case–control study.

Article Snippet: Allelotyping Genotyping of individual samples and allelotyping of DNA pools were both performed using the same chemistry and laboratory protocols for multiplex PCR, single-base primer extension (SBE) and generation of mass spectra (for complete details see iPLEX Application Note, Sequenom, San Diego).

Techniques:

Journal: Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer

Article Title: Primary Lung Adenocarcinomas in Children and Adolescents Treated for Pediatric Malignancies

doi: 10.1097/JTO.0b013e3181f69f08

Figure Lengend Snippet: Case 7. A , Right lower lobe adenocarcinoma, mixed subtype with papillary and bronchioloalveolar patterns (hematoxylin and eosin; original magnification, 40). B , Bronchioloalveolar carcinoma-like nodule in the right middle lobe not seen on preoperative CT scan (hematoxylin and eosin; original magnification, 40). C , Sequenom genotyping assay showing the presence of G 3 T mutation at position 35 in KRAS codon 12 (G12V mutation) in the mixed-type adenocarcinoma of the right lower lobe. The germline peak is indicated by an asterisk and the mutant peak by an arrow. CT, computed tomography.

Article Snippet: Molecular analysis revealed the tumor to be positive for EGFR exon 21 L858R mutation by both the PCR/restriction enzyme assay and Sequenom genotyping ( ).

Techniques: Computed Tomography, Genotyping Assay, Mutagenesis

Journal: Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer

Article Title: Primary Lung Adenocarcinomas in Children and Adolescents Treated for Pediatric Malignancies

doi: 10.1097/JTO.0b013e3181f69f08

Figure Lengend Snippet: Case 5. A , Suspicious density seen on CT scan in the right middle lobe of the lung at the time of diagnosis of osteosarcoma of the humerus. B and C , Invasive adenocarcinoma of the right middle lobe of the lung. Note the presence of invasive glands with fibrotic stroma and sharp demarcation between the tumor cells and the normal pulmonary parenchyma (hematoxylin and eosin; original magnifications, 10× and 40×). D , Immunohistochemical stain for TTF-1. This photomicrograph shows that the invasive glands are positive for TTF-1, thus confirming a pulmonary origin for this adenocarcinoma. E , Mass spectrometry-based genotyping for EGFR exon 21 L858R mutation on Sequenom platform confirming the presence of L858R mutation. The germline peak is indicated by an asterisk and the mutant peak by an arrow. CT, computed tomography; TTF, thyroid transcription factor-1.

Article Snippet: Molecular analysis revealed the tumor to be positive for EGFR exon 21 L858R mutation by both the PCR/restriction enzyme assay and Sequenom genotyping ( ).

Techniques: Computed Tomography, Immunohistochemistry, Staining, Mass Spectrometry, Mutagenesis

Journal: Skeletal Muscle

Article Title: Genetic characterization and improved genotyping of the dysferlin-deficient mouse strain Dysftm1Kcam

doi: 10.1186/s13395-015-0057-3

Figure Lengend Snippet: Novel genotyping PCR of Dysf tm1Kcam . a Schematic drawing of the targeted dysferlin locus in wild type and Dysf tm1Kcam mice, with binding sites of primers used for genotyping shown in pink . The genotyping primers previously described by Han et al. [ 12 ] are depicted in blue (#2290, #2581, #4768). b Results of a genotyping PCR using DNA from toe biopsies of homozygous mutant ( Dysf tm1Kcam/tm1Kcam ), heterozygous mutant ( Dysf tm1Kcam/+ ), and wild type mice, as well as a no template control (NTC)

Article Snippet: In an attempt to make the genotyping more efficient and more reliable, we switched to one of the genotyping protocols suggested by the supplier of the mice (Jackson Lab).

Techniques: Polymerase Chain Reaction, Mouse Assay, Binding Assay, Mutagenesis

Journal: Skeletal Muscle

Article Title: Genetic characterization and improved genotyping of the dysferlin-deficient mouse strain Dysftm1Kcam

doi: 10.1186/s13395-015-0057-3

Figure Lengend Snippet: Detection of the locus targeted for deletion in homozygous Dysf tm1Kcam mice. a Schematic drawing of the wild-type locus and the expected deletion. The arrows depict the two homologous arms used for targeted deletion. b Results of a genotyping PCR using DNA from toe biopsies of wild type, heterozygous mutant ( Dysf tm1Kcam/+ ), and homozygous mutant ( Dysf tm1Kcam/tm1Kcam ) mice, as well as a no template control (NTC). As expected, PCR to detect the targeting vector was negative for wild type mice, and positive for heterozygous and homozygous Dysf tm1Kcam mice. However, PCR to amplify the sequence encompassing exons 51–54, which had been targeted for deletion in generating the Dysf tm1Kcam line, was positive in all mice, suggesting that homologous recombination had failed to delete the targeted region

Article Snippet: In an attempt to make the genotyping more efficient and more reliable, we switched to one of the genotyping protocols suggested by the supplier of the mice (Jackson Lab).

Techniques: Mouse Assay, Polymerase Chain Reaction, Mutagenesis, Plasmid Preparation, Sequencing, Homologous Recombination