Diagnostic validation of a familial hypercholesterolaemia cohort provides a model for using targeted next generation DNA sequencing in the clinical setting

Summary Our aim was to assess the sensitivity and specificity of a next generation DNA sequencing (NGS) platform using a capture based DNA library preparation method. Data and experience gained from this diagnostic validation can be used to progress the applications of NGS in the wider molecular diagnostic setting. A technical cross-validation comparing the current molecular diagnostic gold standard methods of Sanger DNA sequencing and multiplex ligation-dependant probe amplification (MLPA) versus a customised capture based targeted re-sequencing method on a SOLiD 5500 sequencing platform was carried out using a cohort of 96 familial hypercholesterolaemia (FH) samples. We compared a total of 595 DNA variations (488 common single nucleotide polymorphisms, 73 missense mutations, 9 nonsense mutations, 3 splice site point mutations, 13 small indels, 2 multi-exonic duplications and 7 multi-exonic deletions) found previously in the 96 FH samples. DNA variation detection sensitivity and specificity were both 100% for the SOLiD 5500 NGS platform compared with Sanger sequencing and MLPA only when both LifeScope and Integrative Genomics Viewer softwares were utilised. The methods described here offer a high-quality strategy for the detection of a wide range of DNA mutations in diseases with a moderate number of well described causative genes. However, there are important issues related to the bioinformatic algorithms employed to detect small indels.