Assisting the analysis of insertions and deletions using regional allele frequencies.

Accurate estimation of population allele frequency (AF) is crucial for gene discovery and genetic diagnostics. However, determining AF for frameshift-inducing small insertions and deletions (indels) faces challenges due to discrepancies in mapping and variant calling methods. Here, we propose an innovative approach to assess indel AF. We developed CRAFTS-indels (Calculating Regional Allele Frequency Targeting Small indels), an algorithm that combines AF of distinct indels within a given region and provides "regional AF" (rAF). We tested and validated CRAFTS-indels using three independent datasets: gnomAD v2 (n=125,748 samples), an internal dataset (IGM; n=39,367), and the UK BioBank (UKBB; n=469,835). By comparing rAF against standard AF, we identified rare indels with rAF exceeding standard AF (sAF≤10-4 and rAF>10-4) as "rAF-hi" indels. Notably, a high percentage of rare indels were "rAF-hi", with a higher proportion in gnomAD v2 (11-20%) and IGM (11-22%) compared to the UKBB (5-9% depending on the CRAFTS-indels' parameters). Analysis of the overlap of regions based on their rAF with low complexity regions and with ClinVar classification supported the pertinence of rAF. Using the internal dataset, we illustrated the utility of CRAFTS-indel in the analysis of de novo variants and the potential negative impact of rAF-hi indels in gene discovery. In summary, annotation of indels with cohort specific rAF can be used to handle some of the limitations of current annotation pipelines and facilitate detection of novel gene disease associations. CRAFTS-indels offers a user-friendly approach to providing rAF annotation. It can be integrated into public databases such as gnomAD, UKBB and used by ClinVar to revise indel classifications.

Effects of partial internal biliary diversion on long-term outcomes in patients with progressive familial intrahepatic cholestasis: experience in 44 patients.

PURPOSE: Progressive familial intrahepatic cholestasis (PFIC) is a hereditary disease characterized by cholestasis, which may cause jaundice, severe pruritus, and cirrhosis in the later stages. By the invention of biliary diversion methods, these patients were prevented from undergoing liver transplant. Using biliary diversion techniques, the entero-hepatic cycle was interrupted. This lowers the bile acid pool and resolves the pruritus. Herein, we report 44 cases of PFIC who underwent partial internal biliary diversion (PIBD) and long-term follow-up of these children. This comprises the largest case series of PIBD. METHODS: All patients were diagnosed by liver biopsy as PFIC before the operation. All underwent cholecysto colic bypass by jejunal interposition due to severe pruritus unresponsive to medication. Laboratory blood tests, sonography, and physical exam were done before and after the operation once every 3 months. Besides, a questionnaire was designed to ask the patients about the symptoms after the operation, and a pruritus score was measured using the 5D-itch scale. RESULTS: 44 children (25 boys, 19 girls), between 1.75 and 27.5 years (at the time of this study) were followed for a median period of 54 months. Age at operation ranged from 2 months to 18 years, with a median of 29 months. Of these children, 14 were lost to follow up. Results showed a significant decrease in pruritus and sleep disturbance after the surgery (p < 0.001). Also, jaundice decreased from 82.1 before to 7.1% following the surgery. 50% of the patients became medication-free at follow-up. CONCLUSION: PIBD is a safe procedure which helps non-cirrhotic children preserve their liver function. Therefore, PIBD prevents them from undergoing liver transplant. Effective results were achieved in terms of severe pruritus and jaundice, and children were able to regain their sleep patterns. It also avoided external stoma, which is more convenient from the patient's point of view.