Combining Panel-Based Next-Generation Sequencing and Exome Sequencing for Genetic Liver Diseases.

OBJECTIVES: To determine how advanced genetic analysis methods may help in clinical diagnosis. STUDY DESIGN: We report a combined genetic diagnosis approach for patients with clinical suspicion of genetic liver diseases in a tertiary referral center, using tools either tier 1: Sanger sequencing on SLC2SA13, ATP8B1, ABCB11, ABCB4, and JAG1 genes, tier 2: panel-based next generation sequencing (NGS), or tier 3: whole-exome sequencing (WES) analysis. RESULTS: In a total of 374 patients undergoing genetic analysis, 175 patients received tier 1 Sanger sequencing based on phenotypic suspicion, and pathogenic variants were identified in 38 patients (21.7%). Tier 2 included 216 patients (39 of tier 1-negative patients) who received panel-based NGS, and pathogenic variants were identified in 60 (27.8%). In tier 3, 41 patients received WES analysis, and 20 (48.8%) obtained genetic diagnosis. Pathogenic variants were detected in 6 of 19 (31.6%) who tested negative in tier 2, and a greater detection rate in 14 of 22 (63.6%) patients with deteriorating/multiorgan disease receiving one-step WES (P = .041). The overall disease spectrum is comprised of 35 genetic defects; 90% of genes belong to the functional categories of small molecule metabolism, ciliopathy, bile duct development, and membrane transport. Only 13 (37%) genetic diseases were detected in more than 2 families. A hypothetical approach using a small panel-based NGS can serve as the first tier with diagnostic yield of 27.8% (98/352). CONCLUSIONS: NGS based genetic test using a combined panel-WES approach is efficient for the diagnosis of the highly diverse genetic liver diseases.

Progressive familial intrahepatic cholestasis type 3: Report of four clinical cases, novel ABCB4 variants and long-term follow-up.

INTRODUCTION AND OBJECTIVES: Progressive familial intrahepatic cholestasis type 3 (PFIC-3) is a rare autosomal recessive cholestatic liver disorder caused by mutations in the ABCB4 gene. The aim of this study was to present the phenotypic and genotypic spectrum of 4 Polish PFIC-3 patients diagnosed in a one-referral centre. MATERIALS AND METHODS: The study included 4 patients with cholestasis and pathogenic variants in the ABCB4 gene identified by next-generation sequencing (NGS) of a targeted-gene panel or whole exome sequencing (WES). Clinical, laboratory, histological, and molecular data were collected. RESULTS: Four patients (three males) were identified. The age at first noted clinical signs and symptoms was 6, 2.5, 14, and 2 years respectively; the mean age was 6 years. Those signs and symptoms include pruritus (2 out of 4 patients) and hepatomegaly with splenomegaly (4 out of 4 patients). The age at the time of referral to our centre was 9, 3, 15, and 2.5 years respectively, while the mean age was 7 years. Chronic cholestatic liver disease of unknown aetiology was established in all of them. The NGS analysis was performed in all patients at the last follow-up visit. Three novel variants including c.902T>A, p.Met301Lys, c.3279+1G>A, p.?, and c.3524T>A, p.Leu1175His were identified. The time from the first consultation to the final diagnosis was 14, 9, 3, and 1 year respectively; the mean was 6.8 years. A detailed follow-up was presented. CONCLUSIONS: The clinical phenotype of PFIC-3 could be variable. The clinical and biochemical diagnosis of PFIC-3 is difficult, thus the NGS study is very useful in making a proper diagnosis.

Ileal exclusion for pruritus treatment in children with progressive familial intrahepatic cholestasis and other cholestatic diseases.

BACKGROUND: Pruritus is a major health-related quality-of-life burden in progressive familial intrahepatic cholestasis (PFIC) and other childhood cholestatic liver diseases. Several nontransplant surgical techniques were developed in an attempt to ameliorate symptoms and slow disease progression. Very few case-series have been published on a particular intervention, ileal exclusion (IE), which has been considered to be inferior to the other approaches. METHODS: We conducted a single-center retrospective chart-review case-series of patients submitted to IE as the first-line surgical treatment at our institution from 1995 to 2018. The primary goal was pruritus relief, followed by survival with the native liver and improvement in biochemical parameters. RESULTS: Eleven patients were submitted to IE, with a mean follow-up of 60 months. Complete resolution or significant reduction of pruritus was obtained in 72.7% (n = 8) of patients. One patient (9.1%) had a major postoperative complication that required surgery. No other morbidities were reported. Two cases progressed to end-stage liver disease (ESLD) within the short-term and one year after surgery. CONCLUSIONS: This case series study shows that IE provided excellent results in pruritus control and permitted survival with the native liver. We believe IE is a safe procedure, with few associated morbidities, and should be considered more often as primary surgical treatment for PFIC and other cholestasis. LEVEL OF EVIDENCE: IV.

Panel-Based Next-Generation Sequencing for the Diagnosis of Cholestatic Genetic Liver Diseases: Clinical Utility and Challenges.

OBJECTIVE: To test the application of a target enrichment next-generation sequencing (NGS) jaundice panel in genetic diagnosis of pediatric liver diseases. STUDY DESIGN: We developed a capture-based target enrichment NGS jaundice panel containing 42 known disease-causing genes associated with jaundice or cholestasis and 10 pathway-related genes. During 2015-2017, 102 pediatric patients with various forms of cholestasis or idiopathic liver diseases were tested, including patients with initial diagnosis of cholestasis in infancy, progressive familial intrahepatic cholestasis, syndromic cholestasis, Wilson disease, and others. RESULTS: Of the 102 patients, 137 mutations/variants in 44 different genes were identified in 84 patients. The genetic disease diagnosis rate was 33 of 102 (32.4%). A total of 79 of 102 (77.5%) of patients had at least 1 heterozygous genetic variation. Those with progressive intrahepatic cholestasis or syndromic cholestasis in infancy had a diagnostic rate of 62.5%. Disease-causing mutations, including ATP8B1, ABCB11, ABCB4, ABCC2, TJP2, NR1H4 (FXR), JAG1, AKR1D1, CYP7B1, PKHD1, ATP7B, and SLC25A13, were identified. Nine patients had unpredicted genetic diagnosis with atypical phenotype or novel mutations in the investigational genes. We propose an NGS diagnosis classification categorizing patients into high (n = 24), moderate (n = 9), or weak (n = 25) levels of genotype-phenotype correlations to facilitate patient management. CONCLUSIONS: This panel enabled high-throughput detection of genetic variants and disease diagnosis in patients with a long list of candidate causative genes. A NGS report with diagnosis classification may aid clinicians in data interpretation and patient management.

A Rare BSEP Mutation Associated with a Mild Form of Progressive Familial Intrahepatic Cholestasis Type 2

ABSTRACT Progressive Familial Intrahepatic Cholestasis type 2 (PFIC2) is a rare cholestatic disorder diagnosed in infancy or childhood that can lead to severe hepatic fibrosis and liver failure. Mutations in the ABCB11 gene result in a deficiency of the bile salt export protein (BSEP) and accumulation of bile inside the hepatocytes. Hepatocellular carcinoma is another condition associated with severe forms of deletion mutations in the ABCB11 gene. Treatment options including ursodeoxycholic acid biliary diversion have mixed outcomes and some patients require liver transplantation. Here, we describe two siblings with an extremely mild form of PFIC2 inherited from heterozygous parents. The elder sibling had acute liver failure at the age of six months and both siblings had pruritus, cholestasis, coagulopathy and fat-soluble-vitamin deficiencies in infancy but have been asymptomatic past infancy. Genetic testing of the siblings revealed that each were compound heterozygotes for two missense mutations of the ABCB11 gene: p.C68Y and p.R832H. Medical treatment typical for PFIC2 has not been necessary for either patient. This is the first report of these variants following a mild course in two affected patients.(AU)

Colestasis intrahepática benigna recurrente, un reto diagnóstico / Recurrent Benign Intrahepatic Cholestasis is a Diagnostic Challenge

La colestasis hepática incluye una gran variedad de desórdenes que pueden comprometer la vía intra o extrahepática, requiriendo para su diagnóstico una asociación de hallazgos clínicos, bioquímicos, imagenológicos y en algunos casos, patológicos. Se describe el caso de un paciente que presenta episodios intermitentes y autoresolutivos de ictericia recurrente asociados con dolor abdominal y prurito intenso, en quien se encuentra durante los episodios de agudización un patrón colestásico intrahepático que se resuelve completamente durante los episodios de remisión.

Hepatic cholestasis includes a large variety of disorders which can compromise the intrahepatic and extrahepatic pathways. Diagnosis requires a combination of clinical, biochemical, imaging, and sometimes pathological, findings. We describe the case of a patient with intermittent episodes of jaundice which resolved by themselves but which were and decisive associated with abdominal pain and severe itching. These episodes occurred during exacerbation of the intrahepatic cholestatic pattern but completely resolved during episodes of remission.

Colestasias familiares: una causa común de hiperbilirrubinemia conjugada / Familial cholestasis: a comon cause of conjugated hyperbilurubinemia

Cholestasis is defined as a disorder affecting the production of bile resulting in the retention of its components in the liver and blood. In children, this disorder is almost always due to genetic alterations. Functionally, cholestasis may be the result of hepatic failure to secrete bile due to decrease in transport, synthesis or biliary obstruction. Extrahepatic cholestasis may be caused by biliary atresia and other obstructions of the bile ducts. Intrahepatic cholestasis may be the result of several disorders including progressive familial intrahepatic cholestasis (PFIC) types 1, 2 and 3, an autosomal recessive disease due to mutations in the genes ATP8B1, ABCBll and ABCB4 respectively. Pathophysiology and clinical presentation of this disease are now well understood. Clinically, these patients may present with jaundice, itching, anorexia, and generally unwell. Laboratory tests may disclose conjugated bilirubin over lmg/dl or larger than 20 percent of total bilirubin. Ursodeoxycholic acid, cholestiramine and biliary diversion may help in some of these conditions. Ongoing research into the mechanisms of genetic cholestasis could be key to therapy.

La Colestasia corresponde a un trastorno en la formación y excreción de la bilis que provoca retención de sus componentes y daño en hígado y sangre. La colestasia en el niño casi siempre se debe a una alteración hepática secundaria a causas ahora mayormente conocidas a nivel molecular. Desde el punto de vista funcional la colestasia resulta de una insuficiencia secretora del hígado debido a una disminución del flujo biliar por falla en los procesos de transporte o síntesis o a una obstrucción de la vía biliar. La colestasia extrahepática incluye la atresia de vías biliares y otras obstrucciones de la vía biliar. La colestasia intrahepática incluye las colestasias progresivas familiares PFIC 1, 2 y 3 causadas por fallas en los genes ATP8B1, ABCBll y ABCB4 respectivamente. Clínicamente pueden presentarse con ictericia, prurito, anorexia y compromiso del estado general. Desde el punto de vista del laboratorio las enfermedades colestásicas se caracterizan por hiperbilirrubinemia conjugada mayor a 1 mg/dl o mayor a 20 por ciento de bilirrubina total.