Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing

Simon, Michelle; Moresco, Eva Marie Y.; Bull, Katherine; Kumar, Saumya; Mallon, Ann Marie; Beutler, Bruce; Potter, Paul K.

doi:10.1007/s00335-015-9603-x

Cited by 28 publications

(25 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, it is still a challenge for clinicians to obtain a precise molecular diagnosis using conventional genetic methods because of the clinical and genetic heterogeneity of this disorder. Recently, targeted NGS technology is emerging as a powerful genetic tool and has been successfully used to identify causal genes in various genetic disorders (Simon et al, 2015). In the present study, we used targeted NGS of 270 neuromuscular disease-associated genes and identified two novel LAMA2 mutations in a Chinese patient with MDC1A.…”

Section: Discussionmentioning

confidence: 99%

Identification of Two Novel LAMA2 Mutations in a Chinese Patient with Congenital Muscular Dystrophy

Zhou

Tan

et al. 2018

Front. Genet.

View full text Add to dashboard Cite

Merosin-deficient CMD type 1A (MDC1A), caused by mutations of laminin subunit alpha 2 (LAMA2), is a predominant subtype of congenital muscular dystrophy (CMD). Herein, we described a Chinese patient with MDC1A who was admitted to hospital 17 days after birth because of marasmus and feeding difficulties. Mutations were identified by targeted capture and next generation sequencing (NGS) and further confirmed by Sanger sequencing. Paternity was confirmed by short tandem repeat analysis. Physical examination showed malnutrition, poor suck and appendicular hypotonia. Her serum CK levels were 2483 and 1962 U/L at 2 and 4 months of age, respectively. Brain magnetic resonance imaging performed at 1 month of age presented hyperintensity on T2-weighted images, T1-weighted images in parietal and occipital lobes, and diffusion-weighted image (DWI) as well as hypointensity on fluid attenuated inversion recovery (FLAIR) image; however, the cerebellum and corpus arenaceum were normal. At 7 months of age, delayed developmental milestones were observed, and she failed to turn her body over and raise her head up. A point mutation (c.1782+2T > G) and a frameshift duplication (c.8217dupT) in the LAMA2 gene were identified by targeted capture and NGS and further confirmed by Sanger sequencing. Moreover, genotyping with multiple short tandem repeat markers confirmed paternity to demonstrate that the point mutation is de novo. The frameshift duplication (c.8217dupT), inherited from her mother, was predicted to cause a substitution of Pro (P) to Ser (S) at the 2740th amino-acid residue and generate a prematurely truncated protein. The in silico analysis suggests that the mutation (c.1782+2T > G) may lead to aberrant splicing of LAMA2. Our case further confirms the heterogeneous clinical spectrum of MDC1A and presents two novel LAMA2 mutations to expand the mutation spectrum of MDC1A.

show abstract

Section: Discussionmentioning

confidence: 99%

Identification of Two Novel LAMA2 Mutations in a Chinese Patient with Congenital Muscular Dystrophy

Zhou

Tan

et al. 2018

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…We and others have had some success in combining forward mutagenesis, QTL mapping, and next generation sequencing to identify mutations in individual mouse genes that impact complex behavioral traits (Andrews et al 2012; Funato et al 2016; Gallego-Llamas et al 2015; Ha et al 2015; Hossain et al 2016; Kumar et al 2011; Militi et al 2016; Simon et al 2015), and while other approaches are also effective, there will likely be an important role for this screening approach in the future.…”

Section: Discussionmentioning

confidence: 99%

Whole exome sequencing reveals a functional mutation in the GAIN domain of the Bai2 receptor underlying a forward mutagenesis hyperactivity QTL

Speca

Trimmer

Peterson³

et al. 2017

Mamm Genome

View full text Add to dashboard Cite

The identification of novel genes underlying complex mouse behavioral traits remains an important step in understanding normal brain function and its dysfunction in mental health disorders. To identify dominant mutations that influence locomotor activity, we performed a mouse N-ethyl-N-nitrosourea (ENU) forward mutagenesis screen and mapped several loci as quantitative traits. Here we describe the fine mapping and positional cloning of a hyperactivity locus mapped to the medial portion of mouse chromosome four. We employed a modified recombinant progeny testing approach to fine-map the confidence interval from ≈20 Mb down to ≈5 Mb. Whole exome resequencing of all exons in this region revealed a single missense mutation in the adhesion G protein-coupled receptor Brain specific angiogenesis inhibitor 2 (Bai2). This mutation, R619W, is located in a critical extracellular domain that is a hotspot for mutations in this receptor class. We find that in two different mammalian cell lines, surface expression of Bai2 R619W is markedly reduced relative to wild-type Bai2, suggesting that R619W is a loss-of-function mutation. Our results highlight the powerful combination of ENU mutagenesis and next generation sequencing to identify specific mutations that manifest as subtle behavioral phenotypes.

show abstract

“…The process would only declare phenotypes that were heritable, and would simultaneously display the causative mutation along with information about the affected protein. This “instant positional cloning” method was a tremendous breakthrough, as it allowed the resolution of phenotype in real time (45;46). Phenotypes could be solved as quickly as they were detected.…”

Section: The Golden Age Beginsmentioning

confidence: 99%

Innate immunity and the new forward genetics

Beutler

2016

Best Practice & Research Clinical Haematology

Self Cite

View full text Add to dashboard Cite

As it is a hard-wired system for responses to microbes, innate immunity is particularly susceptible to classical genetic analysis. Mutations led the way to the discovery of many of the molecular elements of innate immune sensing and signaling pathways. In turn, the need for a faster way to find the molecular causes of mutation-induced phenotypes triggered a huge transformation in forward genetics. During the 1980s and 1990s, many heritable phenotypes were ascribed to mutations through positional cloning. In mice, this required three steps. First, a genetic mapping step was used to show that a given phenotype emanated from a circumscribed region of the genome. Second, a physical mapping step was undertaken, in which all of the region was cloned and its gene content determined. Finally, a concerted search for the mutation was performed. Such projects usually lasted for several years, but could produce breakthroughs in our understanding of biological processes. Publication of the annotated mouse genome sequence in 2002 made physical mapping unnecessary. More recently we devised a new technology for automated genetic mapping, which eliminated both genetic mapping and the search for mutations among candidate genes. The cause of phenotype can now be determined instantaneously. We have created more than 100,000 coding/splicing mutations. And by screening for defects of innate and adaptive immunity we have discovered many “new” proteins needed for innate immune function.

show abstract

Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing

Cited by 28 publications

References 75 publications

Identification of Two Novel LAMA2 Mutations in a Chinese Patient with Congenital Muscular Dystrophy

Identification of Two Novel LAMA2 Mutations in a Chinese Patient with Congenital Muscular Dystrophy

Whole exome sequencing reveals a functional mutation in the GAIN domain of the Bai2 receptor underlying a forward mutagenesis hyperactivity QTL

Innate immunity and the new forward genetics

Contact Info

Product

Resources

About