Comparison of pathogenicity prediction tools on missense variants in RYR1 and CACNA1S associated with malignant hyperthermia

BACKGROUND

Malignant hyperthermia (MH) is a pharmacogenetic disorder that has been linked to the skeletal muscle calcium release channel (RYR1) and the α1S subunit of the voltage-dependent L-type calcium channel (CACNA1S). Genomic DNA capture and next generation sequencing are becoming the preferred method to identify mutations in these genes. Bioinformatic pathogenicity prediction of identified variants may help to determine if these variants are in fact disease causing.

METHODS

Eight pathogenicity prediction programmes freely available on the web were used to determine their ability to correctly predict the impact of a missense variant on RyR1 or dihydropyridine receptor (DHPR) protein function. We tested MH-causative variants, variants that had been shown to alter calcium release in cells, and common sequence variants in RYR1 and CACNA1S.

RESULTS

None of the prediction programmes was able to identify all of the variants tested correctly as either 'damaging' (MH-causative variants, variants that had been shown to alter calcium release in cells) or as 'benign' (common sequence variants). The overall sensitivity of predictions ranged from 84% to 100% depending on the programme used, with specificity from 25% to 83%.

CONCLUSIONS

In this study we determined the sensitivity and specificity of bioinformatic pathogenicity prediction tools for RYR1 and CACNA1S. We suggest that the prediction results should be treated with caution, as none of the programmes tested predicted all the variants correctly and should only be used in combination with other available data (functional assays, segregation analysis).

Sequence capture and massively parallel sequencing to detect mutations associated with malignant hyperthermia

BACKGROUND

Malignant hyperthermia (MH) is a potentially fatal pharmacogenetic disorder in which intracellular calcium homeostasis in the skeletal muscle of susceptible individuals is disrupted upon exposure to halogenated anaesthetics. While MH is linked to the ryanodine receptor (RYR1) on chromosome 19 and the α1S subunit of the voltage-dependent L-type calcium channel (CACNA1S) on chromosome 1, mutations have been found in only 50-70% of patients, and subsequently, there is a need for a more powerful screening tool.

METHODS

Genomic DNA capture and next-generation sequencing was used to screen 32 genes involved in excitation-contraction coupling, skeletal muscle calcium homeostasis, or immune response in two MH patients. Lymphoblastoid cell lines were used to functionally characterize candidate RYR1 mutations in one family.

RESULTS

Sequence analysis revealed two putative causative mutations in RYR1 in one patient. Segregation analysis and functional analysis support a causative role of the detected variants. The amount of Ca(2+) released after stimulation with 4-chloro-m-cresol from B lymphocytes of the MH-susceptible patients in the family was significantly greater compared with that of Ca(2+) released from cells of an MH-negative family member. In the other patient, no causative mutations were identified in the 32 genes screened.

CONCLUSIONS

In this study, we successfully demonstrate the use of genomic DNA capture and next-generation sequencing for identification of putative mutations causing MH. We also suggest that whole exome sequencing may be necessary to identify MH causing mutations in patients where no mutations in RYR1 and CACNA1S have been identified thus far.

Organization and expression of the Australian sheep blowfly (Lucilia cuprina) hsp23, hsp24, hsp70 and hsp83 genes

In this study we report the isolation and characterization of a heat shock protein 70 (hsp70) gene, the hsp83 gene and two genes that encode small Hsps (Lchsp23 and Lchsp24) from the Australian sheep blowfly, Lucilia cuprina, a major agricultural pest. Phylogenetic analyses indicate that the LcHsp23 protein is the orthologue of Drosophila melanogaster Hsp23 and LcHsp24 is the orthologue of Sarcophaga crassipalpis Hsp23. Quantitative reverse-transcriptase PCR analysis showed that the basal level of Lchsp83 RNA is relatively high at all developmental stages and only moderately induced by heat shock. In contrast, Lchsp70 transcripts are present at low levels and strongly induced by heat shock at all stages. The basal levels of expression and degrees of heat induction of the Lchsp23 and Lchsp24 transcripts were more variable across the different developmental stages. Putative heat shock factor binding sites were identified in the Lchsp24, Lchsp70 and Lchsp83 gene promoters. The isolation of these hsp gene promoters will facilitate constitutive or conditional expression of a gene of interest in transgenic Lucilia.