Genomic diagnostics in polycystic kidney disease: an assessment of real-world use of whole-genome sequencing.

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is common, with a prevalence of 1/1000 and predominantly caused by disease-causing variants in PKD1 or PKD2. Clinical diagnosis is usually by age-dependent imaging criteria, which is challenging in patients with atypical clinical features, without family history, or younger age. However, there is increasing need for definitive diagnosis of ADPKD with new treatments available.

Utility of NIST Whole-Genome Reference Materials for the Technical Validation of a Multigene Next-Generation Sequencing Test.

The sensitivity and specificity of next-generation sequencing laboratory developed tests (LDTs) are typically determined by an analyte-specific approach. Analyte-specific validations use disease-specific controls to assess an LDT's ability to detect known pathogenic variants. Alternatively, a methods-based approach can be used for LDT technical validations.

Identifying Glucokinase Monogenic Diabetes in a Multiethnic Gestational Diabetes Mellitus Cohort: New Pregnancy Screening Criteria and Utility of HbA1c.

Objective: Glucokinase monogenic diabetes (GCK-maturity-onset diabetes of the young [MODY]) should be differentiated from gestational diabetes mellitus (GDM) because management differs. New pregnancy-specific screening criteria (NSC) have been proposed to identify women who warrant GCK genetic testing. We tested NSC and HbA1c in a multiethnic GDM cohort and examined projected referrals for GCK testing.

Managing incidental findings in exome sequencing for research.

Exome sequencing for research has become available for broadly based genomic studies as well as smaller targeted investigations. New exome research projects being considered will intentionally process a large amount of common and rare DNA variation for the purpose of finding specific links between genotype and phenotype. However, the risks of uncovering a clinically relevant incidental finding are not uniform across projects but are highly dependent on the question being asked and exactly how it is intended to be answered.

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

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.

In silico analysis of the exome for gene discovery.

Here we describe a bioinformatic strategy for extracting and analyzing the list of variants revealed from an exome sequencing project to identify potential disease genes. This in silico method filters out the majority of common SNPs and extracts a list of potential candidate protein-coding and non-coding RNA (ncRNA) genes. The workflow employs Galaxy, a publically available Web-based software, to filter and sort sequence variants identified by capture-based target enrichment and sequencing from exomes including selected ncRNAs.

Computer-assisted reading of DNA sequences.

DNA sequencing is increasingly used in a range of medical activities involving DNA diagnostics and research. This is the result of improving technology and cheaper costs. Paradoxically, a greater demand for DNA sequencing has placed additional work on the laboratory because sequencing profiles must be checked visually despite the availability of informatics-based tools in interpreting DNA sequence traces.

Complex phenotypes in the haemoglobinopathies: recommendations on screening and DNA testing.

This document considers a number of scenarios involving complex haemoglobinopathies and provides 28 recommendations at both the clinical and laboratory levels on how these should be managed.