Newborns in NICU
Critically ill newborns are usually admitted to the Neonatal Intensive Care Unit (NICU) departments. Because a critically ill newborn is often affected by a genetic disorder, trials have been made to measure the effectiveness and usefulness of rapid (or ultra-rapid) genetic testing in this special set of patients. Certain studies have also included patients admitted to Pediatric Intensive Care Unit (PICU) departments.
Particularly, Whole Exome Sequencing (WES) and, more rarely, Whole Genome Sequencing (WGS), have been tested for their efficacy in confirming a diagnosis and promptly redirecting patient’s care.
Whole Exome Sequencing (WES) and its timing for the critically ill
Whole Exome Sequencing (WES) is a Next Generation Sequencing technology able to read all the 20,000 human genes in their entire coding region and exon/intron junctions. Advantages of WES are in that the methodology can analyse all human genes at once, while older methodologies such as NGS target panels and Sanger sequencing can provide the data of a limited number of genes.
In recent years, WES technology became more affordable and refined. Even if there’s no single genetic test that can see all kinds of genetic mutations yet, WES is approaching this ambitious target in its recent evolutions. So today it’s possible to detect Copy Number Variations (CNVs), mitochondrial DNA variants, and Uniparental Disomy (UPD) based on exome sequencing data. In fact, combining and comparing the data against a pool of reference WES controls, balanced in terms of capturing and coverage depth uniformity, CNVs can be detected at acceptable levels of sensitivity and, most importantly, at a much higher resolution than array-CGH.
A major limitation of WES, however, has been thus far its turn-around time. A WES analysis usually takes from 3-5 weeks, in the fastest cases, to 1-2 years, especially in a public or research settings. This is due to tens of complex laboratory procedures, from DNA extraction, to library preparation, exome capturing, sequencing, raw data production, bioinformatics and the highly operator-dependent clinical interpretation of the results.
However, ways of completing a rapid WES (13 calendar days) or even a ultra-rapid WES (3-4 calendar days) have been reached successfully, although in well specific and limited settings.
Breda Genetics and the rapid exome
At Breda Genetics, at the time we’re writing, we’ve been able to produce our fastest results for NICU patients in 17 calendar days (12 working days).
Such TAT included everything, from DNA extraction to, sequencing, bioinformatics, clinical interpretation and preliminary Medical Report.
This service has been provided through our package EXOME 60 PLUS, which includes double capturing (clinical exome sequening on 5,200 genes and whole exome sequencing on 20,000 genes plus the mitochondrial genome, for a total of 65 Mbp of human exonic content – 17 Mbp + 48 Mbp) performed with the highest priority, to give the final results in 28 days, while offering preliminary results as fast as possible.
Double capturing in EXOME 60 PLUS is done both to guarantee timely results and double safety in variant detection and confirmation.
We consider this being an excellent TAT, especially when comparing the average turn-around time of other commercial and non-commercial genetic testing labs.
Effectiveness of WES for NICU patients
The efficacy of WES in NICU and PICU patients is certain. The main problem remains surely the TAT-related operations and costs. In routine settings, a ultra-rapid TATs of 3-4 days remains very difficult to be granted under routinary conditions and acceptable technical and financial burdens. On the other side, a more normal TAT of about 2 weeks is already achieved by some labs, and this certainly is a very good compromise in terms of TAT for the critically ill.
Studies have reported a diagnostic success rate ranging from 30% up to 76% in rapid exome sequencing for NICU patients. Such rates clearly depend on the precision in selecting the patients at the beginning.
In a considerable percentage of cases, both positive (and negative!) results at exome sequencing have substantially helped in redirecting patients care towards
1. new subspecialist care
2. medical/dietary modifications
3. palliative care
Linyan Meng et al. Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management – JAMA Pediatr. 2017 Dec 4;171(12):e173438. doi: 10.1001/jamapediatrics.2017.3438. Epub 2017 Dec 4.
Sebastian Lunke et al. Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System – JAMA. 2020 Jun 23;323(24):2503-2511. doi: 10.1001/jama.2020.7671.
Ozge Ceyhan-Birsoy et al. Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project – Am J Hum Genet. 2019 Jan 3;104(1):76-93. doi: 10.1016/j.ajhg.2018.11.016.
omim.org at large
Genereviews at large (https://www.ncbi.nlm.nih.gov/books/NBK1116/?term=)