Medicine is a living thing: it grows, expands, and evolves. Along the way, needs are identified and needs are met, whether it be deficiencies in diagnostic procedures or the lack of curative drugs for certain diseases.

Needs identified and needs met: this sums up how advancements in the diagnosis of the genetics underlying cholestatic diseases in infants, of which Alagille syndrome is one, are made. The need was for better, more precise diagnostic tools, aside from biochemical testing and diagnostic algorithms; the answer was next-generation sequencing. 

In this article, we will study the genetics of inherited cholestatic disorders in infants, and discuss how next-generation sequencing can speed up diagnosis, in addition to making it more accurate. 

Continue Reading

Cholestasis and Genetic Diseases

Cholestasis is defined as a reduction in bile flow due to the impairment of hepatocyte secretion or obstruction in the bile flow through the hepatic bile ducts. Feldman and Sokol, in their study on the diagnostics and treatment of neonatal cholestasis, provide a definition of cholestasis that is specific to infants: “Cholestasis in infancy is defined as serum conjugated/direct bilirubin level >1 mg/dL and >20% of the total bilirubin,” they wrote. 

Jeyaraj et al, in their study on the genetics of inherited cholestatic disorders in neonates, wrote, “In neonates and infants, cholestasis can occur due to a wide range of conditions which may have similar or overlapping presentations. This can make diagnosis based on clinical, biochemical, radiological and histological features challenging.”

The most obvious sign of cholestasis in some infants is jaundice. The current approach most commonly taken in evaluating an infant with cholestasis is to exclude biliary atresia (the most common cause of cholestasis in infants), as well as alpha-1 antitrypsin deficiency (AATD) in certain populations. An initial liver biochemistry test should be ordered. If the gamma-glutamyl transferase (GGT) levels are significantly elevated (>150-200 U/L), then a number of diseases can be suspected, including biliary atresia, mechanical bile duct obstruction, cystic fibrosis, and AATD. 

“It is estimated that 25–50% of cases of cholestasis occur due to identifiable genetic mutations,” Jeyaraj et al wrote. “These mutations involve a wide variety of genes which have either a direct or indirect effect on the synthesis, transport and flow of bile. Among the more commonly implicated genetic and metabolic diseases are AATD and Alagille syndrome.” 

Read more about AATD etiology 

Jeyaraj et al provided us with a list of genetic disorders that can cause cholestasis in neonates and infants. We will summarize a few of them below: 

  • Alagille syndrome can cause biliary tract abnormalities. 
  • Bile acid synthesis defects (such as cerebrotendinous xanthomatosis) can cause defects in the synthesis of components of bile. 
  • Progressive familial intrahepatic cholestasis types 1-6 can cause defects in the export of components of bile or in tight junction formation. 

Since we know that a number of genetic diseases, such as the ones listed above, can cause cholestasis, genetic testing becomes highly desirable.

New Diagnostic Possibilities 

“New gene sequencing technologies [such as next-generation sequencing] have allowed for rapid testing of large numbers of genes, including an individual’s entire genome, within days to weeks, thus challenging our prior use of genotyping late in the traditional paradigm for evaluation of cholestasis,” Feldman and Sokol wrote. “Next-generation sequencing (NGS) also allows for the possibility of discovering new genetic causes of neonatal cholestasis.” 

Indeed, NGS opens up new diagnostic possibilities by its ability to perform a rapid and high-throughput identification of variants from targeted gene panels. Today, it plays a vital role in the work-up of neonatal cholestasis. In breaking down the contribution that NGS has made to patients with cholestatic diseases, Jeyaraj et al wrote, “It has also allowed for a molecular diagnosis to be obtained in patients with liver disease of an otherwise uncertain cause; the ability to obtain a diagnosis in these cases can ensure that appropriate therapies are instituted while therapies which do not offer benefit are avoided.” 

Read more about Alagille syndrome diagnosis 

Feldman and Sokol cited a few studies that validated the role of NGS in diagnosing cholestatic diseases. For example, in one study, researchers used a multigene panel to sequence 61 cholestasis-related genes in a total of 141 patients and made a potential diagnosis in 22% of them. An American study “using a 66 gene panel in 716 children with cholestasis or liver disease of unknown etiology reported a positive or likely positive molecular diagnosis in 11.7% and a single pathogenic or likely pathogenic variant in another 12.7%,” wrote Feldman and Sokol. 

The message is simple: NGS has a rapid turnaround time, is cost-effective, and provides a genetic diagnosis of infants with cholestatic disease. This renders the previous diagnostic algorithm (in which NGS was not featured) obsolete. 

Of course, NGS is not without its challenges (for example, patients living in less developed parts of the globe may not have access to it). However, the rise of NGS in the diagnostic protocol of infants with cholestatic disease indicates that medicine is able to identify needs and meet them, something that should bring us cheer. 


Jeyaraj R, Bounford KM, Ruth N, et al. The genetics of inherited cholestatic disorders in neonates and infants: Evolving challenges. Genes (Basel). 2021;12(11):1837. doi: 10.3390/genes12111837

Feldman AG, Sokol RJ. Recent developments in diagnostics and treatment of neonatal cholestasis. Semin Pediatr Surg. 2020;29(4):150945. doi: 10.1016/j.sempedsurg.2020.150945