Characterisation of a human liver cystathionine beta synthase mRNA sequence corresponding to the c.[833T>C;844_845ins68] mutation in CBS gene

A customized scaffolds approach for the detection and phasing of complex variants by next-generation sequencing

Next-generation sequencing (NGS) is widely used in genetic testing for the highly sensitive detection of single nucleotide changes and small insertions or deletions. However, detection and phasing of structural variants, especially in repetitive or homologous regions, can be problematic due to uneven read coverage or genome reference bias, resulting in false calls. To circumvent this challenge, a computational approach utilizing customized scaffolds as supplementary reference sequences for read alignment was developed, and its effectiveness demonstrated with two CBS gene variants: NM_000071.2:c.833T>C and NM_000071.2:c.[833T>C; 844_845ins68]. Variant c.833T>C is a known causative mutation for homocystinuria, but is not pathogenic when in cis with the insertion, c.844_845ins68, because of alternative splicing. Using simulated reads, the custom scaffolds method resolved all possible combinations with 100% accuracy and, based on > 60,000 clinical specimens, exceeded the performance of current approaches that only align reads to GRCh37/hg19 for the detection of c.833T>C alone or in cis with c.844_845ins68. Furthermore, analysis of two 1000 Genomes Project trios revealed that the c.[833T>C; 844_845ins68] complex variant had previously been undetected in these datasets, likely due to the alignment method used. This approach can be configured for existing workflows to detect other challenging and potentially underrepresented variants, thereby augmenting accurate variant calling in clinical NGS testing.

Short tandem repeats and methylation in the promoter region affect expression of cystathionine beta-synthase gene in the laying hen

Homocysteine can be converted to cysteine via the transsulfuration pathway where cystathionine beta-synthase (CBS) is a rate-limiting enzyme. Homocysteine is thought to play a role in bone remodelling and strength. Previous results indicated that some of the difference in bone strength of end-of-lay hens may be associated with CBS expression level. To investigate if differences in the promoter region of the CBS gene might be responsible for observed differences in gene expression between CBS alleles post mortem- and in-vitro expression studies have been undertaken. Transfection of the DF-1 avian cell line with a series of deletion fragments of the 5' promoter, or constructs containing three CBS allele sequences, with a luciferase reporter revealed that a core region of -155 to +131 bp in the CBS promoter was essential for mRNA expression. We found that a variable number of short tandem repeats (7 nucleotide motif and 6 nucleotide repeats) in the core region of the promoter affecting the transcriptional activity and a strong effect for gene expression. However, methylation of the 6 nucleotide repeats varied between allelic variants and these maybe responsible for differences in promoter activity. Our findings indicated variable short tandem repeats and the differentially methylated sites in the promoter region may be responsible for CBS expression differences in the bone of laying hens.