Human genomics application notes and case studies

We work with universities & laboratories on application notes & case studies in the field of human genomics.

University of Nottingham - app note

Our new application note from the University of Nottingham compares the effectiveness of two genotyping technologies, TaqMan® and KASP™, for successful design of custom genotyping assays for a novel rare deleterious missense coding variant linked to Alzheimer’s disease. The variant was identified from a next-generation sequencing study analysing gene loci previously linked with Alzheimer’s disease by GWAS.

At LGC we have optimised our KASP assay design algorithms and validation processes to ensure that we can design effective assays for all sorts of genetic variation, including rare variants. We have worked at improving our chemistry for over a decade and we are proud to see that leading academic centres find that our KASP technology can outperform other genotyping methods such as TaqMan when it comes to designing challenging assays such as the one in this example.

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The Jackson Laboratory – Mouse genomics app note

Trans-regulation of mouse meiotic recombination hotspots by Rcr1

Meiotic homologous recombination generates genetic variety amongst offspring, and ensures that the chromosomes are segregated accurately during meiosis. Recombination occurs in hotspots, and the aim of this study was to identify trans-acting factors that control hotspot positioning in mammals, specifically congenic mice, using a combination of analyses including SNP genotyping.

Use of KASP to develop speed congenics

Congenic strains of mice typically require 10 generations of backcrossing to generate, which can be a time-consuming process. The time involved in creating congenic mice can be significantly reduced through the use of marker-assisted selection (MAS), and this is termed ‘speed congenics’. Genetic markers, such as SNPs are used to identify mice from the second generation of backcrossing that contain the highest percentages of the desired genome; these mice are then used as parents for the subsequent generation. This marker-assisted selection procedure is repeated for each subsequent generation, and hence enables congenic mice to be attained after only three or four generations of backcrossing. Read here about our mouse panel which offers a set of pre-validated KASP genotyping assays that can be easily applied to the development of speed congenics.

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The Jackson Laboratory – Mouse genomics case study

The Jackson Laboratory, in a joint effort with LGC, has developed 1638 working assays for pre-validated mouse SNPs. These assays provide a powerful tool for the mapping of traits within mouse disease models and breeding populations.

In addition, The Jackson Laboratory has used LGC’s KASP genotyping to facilitate a key part of their recent research into meiotic recombination hotspots (Parvanov et al. (2009) PLoS Biol; Parvanov et al. (2010) Science).

“The advancement in genotyping technology has allowed us to design compatible assays to narrow down the genomic region and identify the gene responsible for hotspot regulation. The discovery of Prdm9 will lead to further improvements in our research to gain insight on its functions. KASP has been a valuable tool in reaching those meaningful conclusions and we are confident that it will continue to support us in better understanding of genetic factors underlying human fertility and evolution.” Dr. P. Petkov, The Jackson Laboratory.

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University of Cambridge - case study

The effect of IGF2 on developing gestational diabetes mellitus

Dr. Clive J. Petry et al., from the University of Cambridge, used our KASP™ genotyping chemistry to conduct research presented in the report “Associations between paternally transmitted fetal IGF2 variants and maternal circulating glucose concentrations in pregnancy” (Diabetes, 2011).

In the study, the team from the University of Cambridge reported for the first time an association between polymorphic variation in a paternally transmitted fetal gene and maternal glucose concentrations in pregnancy.

“We required a solution that offered rapid sample turnaround and full sample traceability, with full application and technical support. When we outsource the service to LGC it is far more efficient, the throughput is much greater, and it’s also much more cost effective than the University of Cambridge setting up the assay for one particular polymorphism.”

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