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Neonatal Diagnosis by Whole Genome Sequencing in Only Two Days

Posted Jun 19 2013 12:00am

For me, the two most important current uses of whole-genome sequencing in clinical care relate to patients with malignant neoplasms and critically ill newborn infants (see:  Neonatal Diagnosis by Whole-Genome Sequencing in 2 Days ). This latter process was detailed in a recent article an excerpt of which is provided below:

In a pilot clinical study in the U.S. researchers have applied whole-genome sequencing (WGS) to diagnose genetic diseases in critically ill newborns in under two days, rather than the 4-6 weeks turnaround time needed for genetic analysis using current methods. The approach, called STAT-Seq by its developers at Children’s Mercy Hospital in Kansas City, combines WGS sequencing of blood DNA, with a newly developed bioinformatics platform that marries the clinical symptoms of the patient with a list of possible diseases, so that analysis of the genome sequence is narrowed down to those regions harboring the mutations responsible for the candidate diseases. Taking just 50 hours to complete from sample to diagnostic result, the technology could dramatically improve the speed of diagnosing genetic disorders in neonates, potentially saving lives and reducing the numbers of unnecessary tests carried out. About 20% of infant deaths in the U.S. are caused by congenital birth defects and chromosomal abnormalities....In the case of genetic diseases, it’s imperative that a correct diagnosis is made as soon as possible so that the infant can be treated, if a suitable therapy is available. And for those neonatal genetic diseases for which there are no treatments, a fast diagnosis avoids inappropriate therapy, means parents can swiftly be given counselling, and is critical for research to develop management guidelines.

Unfortunately, diagnosing a suspected genetic disorder isn’t always possible just by looking at symptoms, and newborns might not yet exhibit the full clinical phenotype. On top of this, neonatal screens are currently only available for a handful of genetic disorders, and serial gene sequencing is too slow to be clinically useful in a neonatal intensive care unit (NICU) setting. To speed diagnosis of genetic diseases in the NICU the Children’s Mercy Hospital team have developed and trialled an approach that combines WGS carried out on Illumnina’s HiSeq 2500 system....with a new bioinformatics platform called symptom-and-sign-assisted genome analysis (SSAGA). The clinicopathological correlation tool effectively maps the clinical features of nearly 600 genetic diseases, and how they present in infants, to phenotypes and genes known to cause the same types of symptoms. Effectively, the clinician inputs the patient’s symptoms according to specified terminology, and the software identifies a set of possible diseases.

 All of this strikes me as a sophisticated initiative to rapidly apply state-of-the art genomic science to the rapid diagnosis of critically ill newborns using WGS. However and for editorial balance, here's a more negative perspective about this new diagnostic approach to newborns (see: Genome Sequencing For Babies Brings Knowledge And Conflicts ):

"In theory it sounds absolutely fantastic," says sociologist  Stefan Timmermans , who studies newborn screening at UCLA. "The reality is that there's a lot of uncertainty about each of the data points you receive. So if people start making health decisions or life-or-death decisions based on information that is so tenuous at this point, I think this could indeed be a nightmare scenario. "A nightmare, because parents could easily become overwhelmed with confusing or ambiguous information about the health of their baby during one of the most sensitive times in their lives." There's plenty of evidence that parents already often overreact to the relatively small amount of data that they're getting from little spots of blood collected at birth. 

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